[{"status":"public","publication":"Nature Communications","ddc":["580"],"month":"11","date_published":"2022-11-15T00:00:00Z","date_updated":"2025-07-08T09:01:02Z","has_accepted_license":"1","department":[{"_id":"JiFr"}],"type":"journal_article","acknowledgement":"We thank A. Cheung,W. Lukowitz, V.Walbot, D.Weijers, and R. Yadegari for critically reading the manuscript; E. Xiong and G. Zhang for preparing some experiments, T. Schuck, J. Gonnering, and P. Engevold for plant care, the Arabidopsis Biological Resource Center (ABRC) for ARF10,ARF16, ARF17, EMS1,MIR160a BAC clones and cDNAs, the SALK_090804 seed, T. Nakagawa for pGBW vectors, Y. Zhao for the YUC1 cDNA, Q. Chen for the pHEE401E vector, R. Yadegari for pAT5G01860::n1GFP, pAT5G45980:n1GFP, pAT5G50490::n1GFP, pAT5G56200:n1GFP vectors, and D.Weijers for the pGreenII KAN SV40-3×GFP and R2D2 vectors, W. Yang for the splmutant, Y. Qin for the pKNU::KNU-VENUS vector and seed, G. Tang for the STTM160/160-48 vector, and L. Colombo for pPIN1::PIN1-GFP spl and pin1-5 seeds. This work was supported by the US National Science Foundation (NSF)-Israel Binational Science Foundation (BSF) research grant to D.Z. (IOS-1322796) and T.A. (2012756). D.Z. also\r\ngratefully acknowledges supports of the Shaw Scientist Award from the Greater Milwaukee Foundation, USDA National Institute of Food and Agriculture (NIFA, 2022-67013-36294), the UWM Discovery and Innovation Grant, the Bradley Catalyst Award from the UWM Research\r\nFoundation, and WiSys and UW System Applied Research Funding Programs.","article_type":"original","file_date_updated":"2023-01-23T11:17:33Z","language":[{"iso":"eng"}],"day":"15","date_created":"2023-01-12T12:02:41Z","author":[{"last_name":"Huang","first_name":"Jian","full_name":"Huang, Jian"},{"first_name":"Lei","last_name":"Zhao","full_name":"Zhao, Lei"},{"full_name":"Malik, Shikha","first_name":"Shikha","last_name":"Malik"},{"last_name":"Gentile","first_name":"Benjamin R.","full_name":"Gentile, Benjamin R."},{"full_name":"Xiong, Va","last_name":"Xiong","first_name":"Va"},{"full_name":"Arazi, Tzahi","last_name":"Arazi","first_name":"Tzahi"},{"last_name":"Owen","first_name":"Heather A.","full_name":"Owen, Heather A."},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Zhao","first_name":"Dazhong","full_name":"Zhao, Dazhong"}],"isi":1,"article_processing_charge":"No","file":[{"checksum":"233922a7b9507d9d48591e6799e4526e","creator":"dernst","date_updated":"2023-01-23T11:17:33Z","file_id":"12346","file_size":3375249,"content_type":"application/pdf","access_level":"open_access","date_created":"2023-01-23T11:17:33Z","relation":"main_file","success":1,"file_name":"2022_NatureCommunications_Huang.pdf"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41467-022-34723-6","volume":13,"citation":{"short":"J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen, J. Friml, D. Zhao, Nature Communications 13 (2022).","ista":"Huang J, Zhao L, Malik S, Gentile BR, Xiong V, Arazi T, Owen HA, Friml J, Zhao D. 2022. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 13, 6960.","ieee":"J. Huang <i>et al.</i>, “Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","mla":"Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>, vol. 13, 6960, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>.","apa":"Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao, D. (2022). Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>","ama":"Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>","chicago":"Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>."},"quality_controlled":"1","pmid":1,"oa":1,"intvolume":"        13","title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","publication_status":"published","_id":"12130","oa_version":"Published Version","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"abstract":[{"text":"Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants.","lang":"eng"}],"year":"2022","publication_identifier":{"eissn":["2041-1723"]},"external_id":{"isi":["000884426700001"],"pmid":["36379956"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","article_number":"6960"},{"type":"journal_article","has_accepted_license":"1","department":[{"_id":"StFr"}],"date_updated":"2024-10-09T21:03:47Z","month":"10","date_published":"2022-10-24T00:00:00Z","ddc":["540"],"publication":"Nature Communications","status":"public","author":[{"full_name":"Prehal, Christian","last_name":"Prehal","first_name":"Christian"},{"last_name":"von Mentlen","first_name":"Jean-Marc","full_name":"von Mentlen, Jean-Marc"},{"first_name":"Sara","last_name":"Drvarič Talian","full_name":"Drvarič Talian, Sara"},{"first_name":"Alen","last_name":"Vizintin","full_name":"Vizintin, Alen"},{"first_name":"Robert","last_name":"Dominko","full_name":"Dominko, Robert"},{"first_name":"Heinz","last_name":"Amenitsch","full_name":"Amenitsch, Heinz"},{"full_name":"Porcar, Lionel","last_name":"Porcar","first_name":"Lionel"},{"last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"},{"full_name":"Wood, Vanessa","first_name":"Vanessa","last_name":"Wood"}],"language":[{"iso":"eng"}],"date_created":"2023-01-16T09:45:09Z","day":"24","file_date_updated":"2023-01-27T07:19:11Z","corr_author":"1","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant NanoEvolution, grant agreement No 894042. The authors acknowledge the CERIC-ERIC Consortium for the access to the Austrian SAXS beamline and TU Graz for support through the Lead Project LP-03.\r\nLikewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. In addition, the authors acknowledge access to the D-22SANS beamline at the ILL neutron source. Electron microscopy measurements were performed at the Scientific Scenter for Optical and Electron Microscopy (ScopeM) of the Swiss Federal Institute of Technology. C.P. and J.M.M. thank A. Senol for her support with the SANS\r\nbeamtime preparation. S.D.T, A.V. and R.D. acknowledge the financial support by the Slovenian Research Agency (ARRS) research core funding P2-0393 and P2-0423. Furthermore, A.V. acknowledge the funding from the Slovenian Research Agency, research project Z2−1863.\r\nS.A.F. is indebted to IST Austria for support. ","article_type":"original","scopus_import":"1","file":[{"success":1,"file_name":"2022_NatureCommunications_Prehal.pdf","relation":"main_file","access_level":"open_access","date_created":"2023-01-27T07:19:11Z","file_id":"12411","file_size":4216931,"content_type":"application/pdf","checksum":"5034336dbf0f860030ef745c08df9e0e","creator":"dernst","date_updated":"2023-01-27T07:19:11Z"}],"article_processing_charge":"No","isi":1,"citation":{"chicago":"Prehal, Christian, Jean-Marc von Mentlen, Sara Drvarič Talian, Alen Vizintin, Robert Dominko, Heinz Amenitsch, Lionel Porcar, Stefan Alexander Freunberger, and Vanessa Wood. “On the Nanoscale Structural Evolution of Solid Discharge Products in Lithium-Sulfur Batteries Using Operando Scattering.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-33931-4\">https://doi.org/10.1038/s41467-022-33931-4</a>.","mla":"Prehal, Christian, et al. “On the Nanoscale Structural Evolution of Solid Discharge Products in Lithium-Sulfur Batteries Using Operando Scattering.” <i>Nature Communications</i>, vol. 13, 6326, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-33931-4\">10.1038/s41467-022-33931-4</a>.","apa":"Prehal, C., von Mentlen, J.-M., Drvarič Talian, S., Vizintin, A., Dominko, R., Amenitsch, H., … Wood, V. (2022). On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-33931-4\">https://doi.org/10.1038/s41467-022-33931-4</a>","ama":"Prehal C, von Mentlen J-M, Drvarič Talian S, et al. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-33931-4\">10.1038/s41467-022-33931-4</a>","ieee":"C. Prehal <i>et al.</i>, “On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ista":"Prehal C, von Mentlen J-M, Drvarič Talian S, Vizintin A, Dominko R, Amenitsch H, Porcar L, Freunberger SA, Wood V. 2022. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. Nature Communications. 13, 6326.","short":"C. Prehal, J.-M. von Mentlen, S. Drvarič Talian, A. Vizintin, R. Dominko, H. Amenitsch, L. Porcar, S.A. Freunberger, V. Wood, Nature Communications 13 (2022)."},"quality_controlled":"1","volume":13,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-022-33931-4","oa_version":"Published Version","publication_status":"published","_id":"12208","title":"On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering","intvolume":"        13","oa":1,"pmid":1,"year":"2022","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"abstract":[{"lang":"eng","text":"The inadequate understanding of the mechanisms that reversibly convert molecular sulfur (S) into lithium sulfide (Li<jats:sub>2</jats:sub>S) via soluble polysulfides (PSs) formation impedes the development of high-performance lithium-sulfur (Li-S) batteries with non-aqueous electrolyte solutions. Here, we use operando small and wide angle X-ray scattering and operando small angle neutron scattering (SANS) measurements to track the nucleation, growth and dissolution of solid deposits from atomic to sub-micron scales during real-time Li-S cell operation. In particular, stochastic modelling based on the SANS data allows quantifying the nanoscale phase evolution during battery cycling. We show that next to nano-crystalline Li<jats:sub>2</jats:sub>S the deposit comprises solid short-chain PSs particles. The analysis of the experimental data suggests that initially, Li<jats:sub>2</jats:sub>S<jats:sub>2</jats:sub> precipitates from the solution and then is partially converted via solid-state electroreduction to Li<jats:sub>2</jats:sub>S. We further demonstrate that mass transport, rather than electron transport through a thin passivating film, limits the discharge capacity and rate performance in Li-S cells."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["36280671"],"isi":["000871563700006"]},"publication_identifier":{"issn":["2041-1723"]},"article_number":"6326","publisher":"Springer Nature"},{"year":"2022","abstract":[{"text":"Embryo development requires biochemical signalling to generate patterns of cell fates and active mechanical forces to drive tissue shape changes. However, how these processes are coordinated, and how tissue patterning is preserved despite the cellular flows occurring during morphogenesis, remains poorly understood. Gastrulation is a crucial embryonic stage that involves both patterning and internalization of the mesendoderm germ layer tissue. Here we show that, in zebrafish embryos, a gradient in Nodal signalling orchestrates pattern-preserving internalization movements by triggering a motility-driven unjamming transition. In addition to its role as a morphogen determining embryo patterning, graded Nodal signalling mechanically subdivides the mesendoderm into a small fraction of highly protrusive leader cells, able to autonomously internalize via local unjamming, and less protrusive followers, which need to be pulled inwards by the leaders. The Nodal gradient further enforces a code of preferential adhesion coupling leaders to their immediate followers, resulting in a collective and ordered mode of internalization that preserves mesendoderm patterning. Integrating this dual mechanical role of Nodal signalling into minimal active particle simulations quantitatively predicts both physiological and experimentally perturbed internalization movements. This provides a quantitative framework for how a morphogen-encoded unjamming transition can bidirectionally couple tissue mechanics with patterning during complex three-dimensional morphogenesis.","lang":"eng"}],"keyword":["General Physics and Astronomy"],"intvolume":"        18","ec_funded":1,"oa":1,"oa_version":"Published Version","publication_status":"published","_id":"12209","title":"Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming","publisher":"Springer Nature","external_id":{"isi":["000871319900002"]},"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"project":[{"grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017"},{"call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank K. Sampath, A. Pauli and Y. Bellaїche for feedback on the manuscript. We also thank the members of the Heisenberg group, in particular A. Schauer and F. Nur Arslan, for help, technical advice and discussions, and the Bioimaging and Life Science facilities at IST\r\nAustria for continuous support. We thank C. Flandoli for the artwork in the figures. This work was supported by postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P. and the European Union (European Research Council starting grant 851288 to É.H. and European Research Council advanced grant 742573 to C.-P.H.).","article_type":"original","corr_author":"1","author":[{"full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","last_name":"Nunes Pinheiro","first_name":"Diana C"},{"full_name":"Kardos, Roland","last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"language":[{"iso":"eng"}],"date_created":"2023-01-16T09:45:19Z","day":"01","file_date_updated":"2023-01-27T07:32:01Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"12","date_published":"2022-12-01T00:00:00Z","ddc":["570"],"publication":"Nature Physics","status":"public","page":"1482-1493","type":"journal_article","issue":"12","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"has_accepted_license":"1","date_updated":"2025-04-14T07:46:59Z","doi":"10.1038/s41567-022-01787-6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"D. C. Nunes Pinheiro, R. Kardos, E. B. Hannezo, and C.-P. J. Heisenberg, “Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming,” <i>Nature Physics</i>, vol. 18, no. 12. Springer Nature, pp. 1482–1493, 2022.","short":"D.C. Nunes Pinheiro, R. Kardos, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 18 (2022) 1482–1493.","ista":"Nunes Pinheiro DC, Kardos R, Hannezo EB, Heisenberg C-PJ. 2022. Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. Nature Physics. 18(12), 1482–1493.","chicago":"Nunes Pinheiro, Diana C, Roland Kardos, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Morphogen Gradient Orchestrates Pattern-Preserving Tissue Morphogenesis via Motility-Driven Unjamming.” <i>Nature Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41567-022-01787-6\">https://doi.org/10.1038/s41567-022-01787-6</a>.","apa":"Nunes Pinheiro, D. C., Kardos, R., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2022). Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-022-01787-6\">https://doi.org/10.1038/s41567-022-01787-6</a>","ama":"Nunes Pinheiro DC, Kardos R, Hannezo EB, Heisenberg C-PJ. Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming. <i>Nature Physics</i>. 2022;18(12):1482-1493. doi:<a href=\"https://doi.org/10.1038/s41567-022-01787-6\">10.1038/s41567-022-01787-6</a>","mla":"Nunes Pinheiro, Diana C., et al. “Morphogen Gradient Orchestrates Pattern-Preserving Tissue Morphogenesis via Motility-Driven Unjamming.” <i>Nature Physics</i>, vol. 18, no. 12, Springer Nature, 2022, pp. 1482–93, doi:<a href=\"https://doi.org/10.1038/s41567-022-01787-6\">10.1038/s41567-022-01787-6</a>."},"quality_controlled":"1","volume":18,"file":[{"access_level":"open_access","date_created":"2023-01-27T07:32:01Z","relation":"main_file","file_name":"2022_NaturePhysics_Pinheiro.pdf","success":1,"checksum":"c86a8e8d80d1bfc46d56a01e88a2526a","creator":"dernst","date_updated":"2023-01-27T07:32:01Z","file_id":"12412","content_type":"application/pdf","file_size":36703569}],"article_processing_charge":"No","isi":1,"scopus_import":"1"},{"scopus_import":"1","file":[{"content_type":"application/pdf","file_size":22645149,"file_id":"12416","date_updated":"2023-01-27T08:14:48Z","checksum":"295261b5172274fd5b8f85a6a6058828","creator":"dernst","file_name":"2022_NatureCommunications_Randriamanantsoa.pdf","success":1,"date_created":"2023-01-27T08:14:48Z","access_level":"open_access","relation":"main_file"}],"article_processing_charge":"No","isi":1,"citation":{"ista":"Randriamanantsoa S, Papargyriou A, Maurer HC, Peschke K, Schuster M, Zecchin G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch AR. 2022. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. Nature Communications. 13, 5219.","short":"S. Randriamanantsoa, A. Papargyriou, H.C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo, M. Reichert, A.R. Bausch, Nature Communications 13 (2022).","ieee":"S. Randriamanantsoa <i>et al.</i>, “Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ama":"Randriamanantsoa S, Papargyriou A, Maurer HC, et al. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32806-y\">10.1038/s41467-022-32806-y</a>","apa":"Randriamanantsoa, S., Papargyriou, A., Maurer, H. C., Peschke, K., Schuster, M., Zecchin, G., … Bausch, A. R. (2022). Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32806-y\">https://doi.org/10.1038/s41467-022-32806-y</a>","mla":"Randriamanantsoa, S., et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” <i>Nature Communications</i>, vol. 13, 5219, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32806-y\">10.1038/s41467-022-32806-y</a>.","chicago":"Randriamanantsoa, S., A. Papargyriou, H. C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32806-y\">https://doi.org/10.1038/s41467-022-32806-y</a>."},"quality_controlled":"1","volume":13,"doi":"10.1038/s41467-022-32806-y","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","has_accepted_license":"1","department":[{"_id":"EdHa"}],"date_updated":"2025-06-11T13:53:55Z","date_published":"2022-09-05T00:00:00Z","month":"09","ddc":["570"],"publication":"Nature Communications","status":"public","author":[{"full_name":"Randriamanantsoa, S.","first_name":"S.","last_name":"Randriamanantsoa"},{"full_name":"Papargyriou, A.","last_name":"Papargyriou","first_name":"A."},{"full_name":"Maurer, H. C.","first_name":"H. C.","last_name":"Maurer"},{"last_name":"Peschke","first_name":"K.","full_name":"Peschke, K."},{"last_name":"Schuster","first_name":"M.","full_name":"Schuster, M."},{"full_name":"Zecchin, G.","first_name":"G.","last_name":"Zecchin"},{"full_name":"Steiger, K.","first_name":"K.","last_name":"Steiger"},{"first_name":"R.","last_name":"Öllinger","full_name":"Öllinger, R."},{"full_name":"Saur, D.","last_name":"Saur","first_name":"D."},{"full_name":"Scheel, C.","first_name":"C.","last_name":"Scheel"},{"first_name":"R.","last_name":"Rad","full_name":"Rad, R."},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"M.","last_name":"Reichert","full_name":"Reichert, M."},{"full_name":"Bausch, A. R.","last_name":"Bausch","first_name":"A. R."}],"day":"05","date_created":"2023-01-16T09:46:53Z","language":[{"iso":"eng"}],"file_date_updated":"2023-01-27T08:14:48Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"13068"}]},"acknowledgement":"A.R.B. acknowledges the financial support of the European Research Council (ERC) through the funding of the grant Principles of Integrin Mechanics and Adhesion (PoINT) and the German Research Foundation (DFG, SFB 1032, project ID 201269156). E.H. was supported by the European Union (European Research Council Starting Grant 851288). D.S., M.R., and R.R. acknowledge the support by the German Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project S01, project ID 329628492). C.S. and M.R. acknowledge the support by the German Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project 12, project ID 329628492). M.R. was supported by the German Research Foundation (DFG RE 3723/4-1). A.P. and M.R. were supported by the German Cancer Aid (Max-Eder Program 111273 and 70114328).\r\nOpen Access funding enabled and organized by Projekt DEAL.","article_type":"original","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000850348400025"],"pmid":["36064947"]},"publication_identifier":{"issn":["2041-1723"]},"article_number":"5219","publisher":"Springer Nature","oa_version":"Published Version","publication_status":"published","_id":"12217","title":"Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids","intvolume":"        13","ec_funded":1,"oa":1,"pmid":1,"year":"2022","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"abstract":[{"lang":"eng","text":"The development dynamics and self-organization of glandular branched epithelia is of utmost importance for our understanding of diverse processes ranging from normal tissue growth to the growth of cancerous tissues. Using single primary murine pancreatic ductal adenocarcinoma (PDAC) cells embedded in a collagen matrix and adapted media supplementation, we generate organoids that self-organize into highly branched structures displaying a seamless lumen connecting terminal end buds, replicating in vivo PDAC architecture. We identify distinct morphogenesis phases, each characterized by a unique pattern of cell invasion, matrix deformation, protein expression, and respective molecular dependencies. We propose a minimal theoretical model of a branching and proliferating tissue, capturing the dynamics of the first phases. Observing the interaction of morphogenesis, mechanical environment and gene expression in vitro sets a benchmark for the understanding of self-organization processes governing complex organoid structure formation processes and branching morphogenesis."}]},{"quality_controlled":"1","citation":{"mla":"Choueiri, George H., et al. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 32, no. 9, 093138, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0102904\">10.1063/5.0102904</a>.","apa":"Choueiri, G. H., Suri, B., Merrin, J., Serbyn, M., Hof, B., &#38; Budanur, N. B. (2022). Crises and chaotic scattering in hydrodynamic pilot-wave experiments. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0102904\">https://doi.org/10.1063/5.0102904</a>","ama":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. 2022;32(9). doi:<a href=\"https://doi.org/10.1063/5.0102904\">10.1063/5.0102904</a>","chicago":"Choueiri, George H, Balachandra Suri, Jack Merrin, Maksym Serbyn, Björn Hof, and Nazmi B Budanur. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0102904\">https://doi.org/10.1063/5.0102904</a>.","short":"G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos: An Interdisciplinary Journal of Nonlinear Science 32 (2022).","ista":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. 2022. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. 32(9), 093138.","ieee":"G. H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, and N. B. Budanur, “Crises and chaotic scattering in hydrodynamic pilot-wave experiments,” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 32, no. 9. AIP Publishing, 2022."},"volume":32,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1063/5.0102904","scopus_import":"1","file":[{"checksum":"17881eff8b21969359a2dd64620120ba","creator":"dernst","date_updated":"2023-01-30T09:41:12Z","file_id":"12445","file_size":3209644,"content_type":"application/pdf","access_level":"open_access","date_created":"2023-01-30T09:41:12Z","relation":"main_file","success":1,"file_name":"2022_Chaos_Choueiri.pdf"}],"article_processing_charge":"No","isi":1,"author":[{"first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri","full_name":"Choueiri, George H"},{"first_name":"Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","last_name":"Suri","full_name":"Suri, Balachandra"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"},{"last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"}],"day":"26","date_created":"2023-01-16T09:58:16Z","language":[{"iso":"eng"}],"file_date_updated":"2023-01-30T09:41:12Z","article_type":"original","acknowledgement":"This work was partially funded by the Institute of Science and Technology Austria Interdisciplinary Project Committee Grant “Pilot-Wave Hydrodynamics: Chaos and Quantum Analogies.”","type":"journal_article","issue":"9","department":[{"_id":"MaSe"},{"_id":"BjHo"},{"_id":"NanoFab"}],"has_accepted_license":"1","date_updated":"2025-06-11T13:41:34Z","date_published":"2022-09-26T00:00:00Z","ddc":["530"],"month":"09","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","status":"public","article_number":"093138","publisher":"AIP Publishing","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["2206.01531"],"pmid":["36182399"],"isi":["000861009600005"]},"publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"arxiv":1,"year":"2022","abstract":[{"text":"Theoretical foundations of chaos have been predominantly laid out for finite-dimensional dynamical systems, such as the three-body problem in classical mechanics and the Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena, e.g., weather, arise in systems with many (formally infinite) degrees of freedom, which limits direct quantitative analysis of such systems using chaos theory. In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer a bridge between low- and high-dimensional chaotic phenomena by allowing for a systematic study of how the former connects to the latter. Specifically, we present experimental results, which show the formation of low-dimensional chaotic attractors upon destabilization of regular dynamics and a final transition to high-dimensional chaos via the merging of distinct chaotic regions through a crisis bifurcation. Moreover, we show that the post-crisis dynamics of the system can be rationalized as consecutive scatterings from the nonattracting chaotic sets with lifetimes following exponential distributions. ","lang":"eng"}],"keyword":["Applied Mathematics","General Physics and Astronomy","Mathematical Physics","Statistical and Nonlinear Physics"],"oa_version":"Published Version","_id":"12259","publication_status":"published","title":"Crises and chaotic scattering in hydrodynamic pilot-wave experiments","intvolume":"        32","oa":1,"pmid":1},{"year":"2022","keyword":["General Physics and Astronomy"],"abstract":[{"text":"Cell migration in confining physiological environments relies on the concerted dynamics of several cellular components, including protrusions, adhesions with the environment, and the cell nucleus. However, it remains poorly understood how the dynamic interplay of these components and the cell polarity determine the emergent migration behavior at the cellular scale. Here, we combine data-driven inference with a mechanistic bottom-up approach to develop a model for protrusion and polarity dynamics in confined cell migration, revealing how the cellular dynamics adapt to confining geometries. Specifically, we use experimental data of joint protrusion-nucleus migration trajectories of cells on confining micropatterns to systematically determine a mechanistic model linking the stochastic dynamics of cell polarity, protrusions, and nucleus. This model indicates that the cellular dynamics adapt to confining constrictions through a switch in the polarity dynamics from a negative to a positive self-reinforcing feedback loop. Our model further reveals how this feedback loop leads to stereotypical cycles of protrusion-nucleus dynamics that drive the migration of the cell through constrictions. These cycles are disrupted upon perturbation of cytoskeletal components, indicating that the positive feedback is controlled by cellular migration mechanisms. Our data-driven theoretical approach therefore identifies polarity feedback adaptation as a key mechanism in confined cell migration.","lang":"eng"}],"arxiv":1,"intvolume":"        12","oa":1,"_id":"12277","publication_status":"published","title":"Geometry adaptation of protrusion and polarity dynamics in confined cell migration","oa_version":"Published Version","publisher":"American Physical Society","article_number":"031041","publication_identifier":{"issn":["2160-3308"]},"external_id":{"isi":["000861534700001"],"arxiv":["2106.01014"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank Grzegorz Gradziuk, StevenRiedijk, Janni Harju, and M. R. Schnucki for helpful discussions, and Andriy Goychuk for advice on the image segmentation. This project\r\nwas funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Project No. 201269156—SFB 1032 (Projects B01 and B12). D. B. B. is supported by the NOMIS Foundation and in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM), as well as by the Joachim Herz Stiftung.","article_type":"original","language":[{"iso":"eng"}],"date_created":"2023-01-16T10:02:06Z","day":"20","file_date_updated":"2023-01-30T11:07:27Z","author":[{"first_name":"David","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","full_name":"Brückner, David"},{"first_name":"Matthew","last_name":"Schmitt","full_name":"Schmitt, Matthew"},{"last_name":"Fink","first_name":"Alexandra","full_name":"Fink, Alexandra"},{"full_name":"Ladurner, Georg","last_name":"Ladurner","first_name":"Georg"},{"full_name":"Flommersfeld, Johannes","first_name":"Johannes","last_name":"Flommersfeld"},{"first_name":"Nicolas","last_name":"Arlt","full_name":"Arlt, Nicolas"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Rädler","first_name":"Joachim O.","full_name":"Rädler, Joachim O."},{"first_name":"Chase P.","last_name":"Broedersz","full_name":"Broedersz, Chase P."}],"status":"public","month":"09","ddc":["530","570"],"date_published":"2022-09-20T00:00:00Z","publication":"Physical Review X","date_updated":"2023-08-04T10:25:49Z","type":"journal_article","issue":"3","department":[{"_id":"EdHa"}],"has_accepted_license":"1","doi":"10.1103/physrevx.12.031041","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"D. Brückner <i>et al.</i>, “Geometry adaptation of protrusion and polarity dynamics in confined cell migration,” <i>Physical Review X</i>, vol. 12, no. 3. American Physical Society, 2022.","ista":"Brückner D, Schmitt M, Fink A, Ladurner G, Flommersfeld J, Arlt N, Hannezo EB, Rädler JO, Broedersz CP. 2022. Geometry adaptation of protrusion and polarity dynamics in confined cell migration. Physical Review X. 12(3), 031041.","short":"D. Brückner, M. Schmitt, A. Fink, G. Ladurner, J. Flommersfeld, N. Arlt, E.B. Hannezo, J.O. Rädler, C.P. Broedersz, Physical Review X 12 (2022).","chicago":"Brückner, David, Matthew Schmitt, Alexandra Fink, Georg Ladurner, Johannes Flommersfeld, Nicolas Arlt, Edouard B Hannezo, Joachim O. Rädler, and Chase P. Broedersz. “Geometry Adaptation of Protrusion and Polarity Dynamics in Confined Cell Migration.” <i>Physical Review X</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevx.12.031041\">https://doi.org/10.1103/physrevx.12.031041</a>.","ama":"Brückner D, Schmitt M, Fink A, et al. Geometry adaptation of protrusion and polarity dynamics in confined cell migration. <i>Physical Review X</i>. 2022;12(3). doi:<a href=\"https://doi.org/10.1103/physrevx.12.031041\">10.1103/physrevx.12.031041</a>","apa":"Brückner, D., Schmitt, M., Fink, A., Ladurner, G., Flommersfeld, J., Arlt, N., … Broedersz, C. P. (2022). Geometry adaptation of protrusion and polarity dynamics in confined cell migration. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevx.12.031041\">https://doi.org/10.1103/physrevx.12.031041</a>","mla":"Brückner, David, et al. “Geometry Adaptation of Protrusion and Polarity Dynamics in Confined Cell Migration.” <i>Physical Review X</i>, vol. 12, no. 3, 031041, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevx.12.031041\">10.1103/physrevx.12.031041</a>."},"quality_controlled":"1","volume":12,"isi":1,"file":[{"date_created":"2023-01-30T11:07:27Z","access_level":"open_access","relation":"main_file","success":1,"file_name":"2022_PhysicalReviewX_Brueckner.pdf","checksum":"40a8fbc3663bf07b37cb80020974d40d","creator":"dernst","date_updated":"2023-01-30T11:07:27Z","file_id":"12458","content_type":"application/pdf","file_size":4686804}],"article_processing_charge":"No","scopus_import":"1"},{"publisher":"Royal Society of Chemistry","external_id":{"pmid":["36254856"]},"publication_identifier":{"issn":["1463-9076","1463-9084"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/D2CP03921D"}],"year":"2022","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"abstract":[{"text":"In this work, a feed-forward artificial neural network (FF-ANN) design capable of locating eigensolutions to Schrödinger's equation via self-supervised learning is outlined. Based on the input potential determining the nature of the quantum problem, the presented FF-ANN strategy identifies valid solutions solely by minimizing Schrödinger's equation encoded in a suitably designed global loss function. In addition to benchmark calculations of prototype systems with known analytical solutions, the outlined methodology was also applied to experimentally accessible quantum systems, such as the vibrational states of molecular hydrogen H2 and its isotopologues HD and D2 as well as the torsional tunnel splitting in the phenol molecule. It is shown that in conjunction with the use of SIREN activation functions a high accuracy in the energy eigenvalues and wavefunctions is achieved without the requirement to adjust the implementation to the vastly different range of input potentials, thereby even considering problems under periodic boundary conditions.","lang":"eng"}],"oa_version":"Published Version","publication_status":"published","_id":"12938","title":"From vibrational spectroscopy and quantum tunnelling to periodic band structures – a self-supervised, all-purpose neural network approach to general quantum problems","intvolume":"        24","oa":1,"pmid":1,"citation":{"ista":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2022. From vibrational spectroscopy and quantum tunnelling to periodic band structures – a self-supervised, all-purpose neural network approach to general quantum problems. Physical Chemistry Chemical Physics. 24(41), 25191–25202.","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Physical Chemistry Chemical Physics 24 (2022) 25191–25202.","ieee":"J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “From vibrational spectroscopy and quantum tunnelling to periodic band structures – a self-supervised, all-purpose neural network approach to general quantum problems,” <i>Physical Chemistry Chemical Physics</i>, vol. 24, no. 41. Royal Society of Chemistry, pp. 25191–25202, 2022.","mla":"Gamper, Jakob, et al. “From Vibrational Spectroscopy and Quantum Tunnelling to Periodic Band Structures – a Self-Supervised, All-Purpose Neural Network Approach to General Quantum Problems.” <i>Physical Chemistry Chemical Physics</i>, vol. 24, no. 41, Royal Society of Chemistry, 2022, pp. 25191–202, doi:<a href=\"https://doi.org/10.1039/d2cp03921d\">10.1039/d2cp03921d</a>.","ama":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. From vibrational spectroscopy and quantum tunnelling to periodic band structures – a self-supervised, all-purpose neural network approach to general quantum problems. <i>Physical Chemistry Chemical Physics</i>. 2022;24(41):25191-25202. doi:<a href=\"https://doi.org/10.1039/d2cp03921d\">10.1039/d2cp03921d</a>","apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., &#38; Hofer, T. S. (2022). From vibrational spectroscopy and quantum tunnelling to periodic band structures – a self-supervised, all-purpose neural network approach to general quantum problems. <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d2cp03921d\">https://doi.org/10.1039/d2cp03921d</a>","chicago":"Gamper, Jakob, Florian Kluibenschedl, Alexander K. H. Weiss, and Thomas S. Hofer. “From Vibrational Spectroscopy and Quantum Tunnelling to Periodic Band Structures – a Self-Supervised, All-Purpose Neural Network Approach to General Quantum Problems.” <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry, 2022. <a href=\"https://doi.org/10.1039/d2cp03921d\">https://doi.org/10.1039/d2cp03921d</a>."},"quality_controlled":"1","volume":24,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1039/d2cp03921d","scopus_import":"1","article_processing_charge":"No","author":[{"last_name":"Gamper","first_name":"Jakob","full_name":"Gamper, Jakob"},{"last_name":"Kluibenschedl","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","first_name":"Florian","full_name":"Kluibenschedl, Florian"},{"full_name":"Weiss, Alexander K. H.","last_name":"Weiss","first_name":"Alexander K. H."},{"full_name":"Hofer, Thomas S.","last_name":"Hofer","first_name":"Thomas S."}],"day":"04","language":[{"iso":"eng"}],"date_created":"2023-05-10T14:48:46Z","article_type":"original","type":"journal_article","issue":"41","date_updated":"2023-05-15T07:54:08Z","month":"10","date_published":"2022-10-04T00:00:00Z","publication":"Physical Chemistry Chemical Physics","status":"public","page":"25191-25202"},{"main_file_link":[{"url":"https://doi.org/10.1103/PhysRevX.12.011013","open_access":"1"}],"keyword":["General Physics and Astronomy"],"abstract":[{"lang":"eng","text":"Ultrafast lasers are an increasingly important tool to control and stabilize emergent phases in quantum materials. Among a variety of possible excitation protocols, a particularly intriguing route is the direct light engineering of microscopic electronic parameters, such as the electron hopping and the local Coulomb repulsion (Hubbard \r\nU). In this work, we use time-resolved x-ray absorption spectroscopy to demonstrate the light-induced renormalization of the Hubbard U in a cuprate superconductor, La1.905Ba0.095CuO4. We show that intense femtosecond laser pulses induce a substantial redshift of the upper Hubbard band while leaving the Zhang-Rice singlet energy unaffected. By comparing the experimental data to time-dependent spectra of single- and three-band Hubbard models, we assign this effect to an approximately 140-meV reduction of the on-site Coulomb repulsion on the copper sites. Our demonstration of a dynamical Hubbard U renormalization in a copper oxide paves the way to a novel strategy for the manipulation of superconductivity and magnetism as well as to the realization of other long-range-ordered phases in light-driven quantum materials."}],"year":"2022","arxiv":1,"oa":1,"intvolume":"        12","oa_version":"Published Version","title":"Ultrafast renormalization of the on-site Coulomb repulsion in a cuprate superconductor","publication_status":"published","_id":"13994","publisher":"American Physical Society","article_number":"011013","external_id":{"arxiv":["2109.13229"]},"publication_identifier":{"eissn":["2160-3308"]},"article_type":"original","author":[{"full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova"},{"last_name":"Jang","first_name":"Hoyoung","full_name":"Jang, Hoyoung"},{"last_name":"Husain","first_name":"Ali A.","full_name":"Husain, Ali A."},{"full_name":"Lee, Sangjun","last_name":"Lee","first_name":"Sangjun"},{"full_name":"TenHuisen, Sophia F. R.","first_name":"Sophia F. R.","last_name":"TenHuisen"},{"last_name":"Zhou","first_name":"Preston","full_name":"Zhou, Preston"},{"first_name":"Sunwook","last_name":"Park","full_name":"Park, Sunwook"},{"full_name":"Kim, Hoon","first_name":"Hoon","last_name":"Kim"},{"full_name":"Kim, Jin-Kwang","last_name":"Kim","first_name":"Jin-Kwang"},{"first_name":"Hyeong-Do","last_name":"Kim","full_name":"Kim, Hyeong-Do"},{"full_name":"Kim, Minseok","last_name":"Kim","first_name":"Minseok"},{"full_name":"Park, Sang-Youn","last_name":"Park","first_name":"Sang-Youn"},{"full_name":"Abbamonte, Peter","first_name":"Peter","last_name":"Abbamonte"},{"last_name":"Kim","first_name":"B. J.","full_name":"Kim, B. J."},{"last_name":"Gu","first_name":"G. D.","full_name":"Gu, G. D."},{"first_name":"Yao","last_name":"Wang","full_name":"Wang, Yao"},{"first_name":"Matteo","last_name":"Mitrano","full_name":"Mitrano, Matteo"}],"date_created":"2023-08-09T13:08:26Z","language":[{"iso":"eng"}],"day":"20","publication":"Physical Review X","date_published":"2022-01-20T00:00:00Z","month":"01","status":"public","issue":"1","type":"journal_article","date_updated":"2024-10-14T12:23:26Z","extern":"1","doi":"10.1103/physrevx.12.011013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":12,"quality_controlled":"1","citation":{"mla":"Baykusheva, Denitsa Rangelova, et al. “Ultrafast Renormalization of the On-Site Coulomb Repulsion in a Cuprate Superconductor.” <i>Physical Review X</i>, vol. 12, no. 1, 011013, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevx.12.011013\">10.1103/physrevx.12.011013</a>.","ama":"Baykusheva DR, Jang H, Husain AA, et al. Ultrafast renormalization of the on-site Coulomb repulsion in a cuprate superconductor. <i>Physical Review X</i>. 2022;12(1). doi:<a href=\"https://doi.org/10.1103/physrevx.12.011013\">10.1103/physrevx.12.011013</a>","apa":"Baykusheva, D. R., Jang, H., Husain, A. A., Lee, S., TenHuisen, S. F. R., Zhou, P., … Mitrano, M. (2022). Ultrafast renormalization of the on-site Coulomb repulsion in a cuprate superconductor. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevx.12.011013\">https://doi.org/10.1103/physrevx.12.011013</a>","chicago":"Baykusheva, Denitsa Rangelova, Hoyoung Jang, Ali A. Husain, Sangjun Lee, Sophia F. R. TenHuisen, Preston Zhou, Sunwook Park, et al. “Ultrafast Renormalization of the On-Site Coulomb Repulsion in a Cuprate Superconductor.” <i>Physical Review X</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevx.12.011013\">https://doi.org/10.1103/physrevx.12.011013</a>.","short":"D.R. Baykusheva, H. Jang, A.A. Husain, S. Lee, S.F.R. TenHuisen, P. Zhou, S. Park, H. Kim, J.-K. Kim, H.-D. Kim, M. Kim, S.-Y. Park, P. Abbamonte, B.J. Kim, G.D. Gu, Y. Wang, M. Mitrano, Physical Review X 12 (2022).","ista":"Baykusheva DR, Jang H, Husain AA, Lee S, TenHuisen SFR, Zhou P, Park S, Kim H, Kim J-K, Kim H-D, Kim M, Park S-Y, Abbamonte P, Kim BJ, Gu GD, Wang Y, Mitrano M. 2022. Ultrafast renormalization of the on-site Coulomb repulsion in a cuprate superconductor. Physical Review X. 12(1), 011013.","ieee":"D. R. Baykusheva <i>et al.</i>, “Ultrafast renormalization of the on-site Coulomb repulsion in a cuprate superconductor,” <i>Physical Review X</i>, vol. 12, no. 1. American Physical Society, 2022."},"article_processing_charge":"No","scopus_import":"1"},{"article_processing_charge":"Yes","scopus_import":"1","extern":"1","doi":"10.1038/s41467-022-30673-1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":13,"quality_controlled":"1","citation":{"chicago":"Bravo, Jack Peter Kelly, Cristian Aparicio-Maldonado, Franklin L. Nobrega, Stan J. J. Brouns, and David W. Taylor. “Structural Basis for Broad Anti-Phage Immunity by DISARM.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30673-1\">https://doi.org/10.1038/s41467-022-30673-1</a>.","mla":"Bravo, Jack Peter Kelly, et al. “Structural Basis for Broad Anti-Phage Immunity by DISARM.” <i>Nature Communications</i>, vol. 13, 2987, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30673-1\">10.1038/s41467-022-30673-1</a>.","apa":"Bravo, J. P. K., Aparicio-Maldonado, C., Nobrega, F. L., Brouns, S. J. J., &#38; Taylor, D. W. (2022). Structural basis for broad anti-phage immunity by DISARM. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30673-1\">https://doi.org/10.1038/s41467-022-30673-1</a>","ama":"Bravo JPK, Aparicio-Maldonado C, Nobrega FL, Brouns SJJ, Taylor DW. Structural basis for broad anti-phage immunity by DISARM. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30673-1\">10.1038/s41467-022-30673-1</a>","ieee":"J. P. K. Bravo, C. Aparicio-Maldonado, F. L. Nobrega, S. J. J. Brouns, and D. W. Taylor, “Structural basis for broad anti-phage immunity by DISARM,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ista":"Bravo JPK, Aparicio-Maldonado C, Nobrega FL, Brouns SJJ, Taylor DW. 2022. Structural basis for broad anti-phage immunity by DISARM. Nature Communications. 13, 2987.","short":"J.P.K. Bravo, C. Aparicio-Maldonado, F.L. Nobrega, S.J.J. Brouns, D.W. Taylor, Nature Communications 13 (2022)."},"publication":"Nature Communications","month":"05","date_published":"2022-05-27T00:00:00Z","status":"public","type":"journal_article","date_updated":"2024-06-04T06:16:38Z","article_type":"original","author":[{"first_name":"Jack Peter Kelly","last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly"},{"full_name":"Aparicio-Maldonado, Cristian","last_name":"Aparicio-Maldonado","first_name":"Cristian"},{"full_name":"Nobrega, Franklin L.","last_name":"Nobrega","first_name":"Franklin L."},{"first_name":"Stan J. J.","last_name":"Brouns","full_name":"Brouns, Stan J. J."},{"full_name":"Taylor, David W.","last_name":"Taylor","first_name":"David W."}],"date_created":"2024-03-20T10:41:59Z","language":[{"iso":"eng"}],"day":"27","external_id":{"pmid":["35624106"]},"publication_identifier":{"issn":["2041-1723"]},"publisher":"Springer Nature","article_number":"2987","oa":1,"intvolume":"        13","pmid":1,"oa_version":"Published Version","title":"Structural basis for broad anti-phage immunity by DISARM","_id":"15133","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1038/s41467-022-30673-1","open_access":"1"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"abstract":[{"lang":"eng","text":"In the evolutionary arms race against phage, bacteria have assembled a diverse arsenal of antiviral immune strategies. While the recently discovered DISARM (Defense Island System Associated with Restriction-Modification) systems can provide protection against a wide range of phage, the molecular mechanisms that underpin broad antiviral targeting but avoiding autoimmunity remain enigmatic. Here, we report cryo-EM structures of the core DISARM complex, DrmAB, both alone and in complex with an unmethylated phage DNA mimetic. These structures reveal that DrmAB core complex is autoinhibited by a trigger loop (TL) within DrmA and binding to DNA substrates containing a 5′ overhang dislodges the TL, initiating a long-range structural rearrangement for DrmAB activation. Together with structure-guided in vivo studies, our work provides insights into the mechanism of phage DNA recognition and specific activation of this widespread antiviral defense system."}],"year":"2022"},{"oa_version":"Published Version","title":"Structural rearrangements allow nucleic acid discrimination by type I-D Cascade","publication_status":"published","_id":"15134","oa":1,"intvolume":"        13","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-022-30402-8"}],"abstract":[{"lang":"eng","text":"CRISPR-Cas systems are adaptive immune systems that protect prokaryotes from foreign nucleic acids, such as bacteriophages. Two of the most prevalent CRISPR-Cas systems include type I and type III. Interestingly, the type I-D interference proteins contain characteristic features of both type I and type III systems. Here, we present the structures of type I-D Cascade bound to both a double-stranded (ds)DNA and a single-stranded (ss)RNA target at 2.9 and 3.1 Å, respectively. We show that type I-D Cascade is capable of specifically binding ssRNA and reveal how PAM recognition of dsDNA targets initiates long-range structural rearrangements that likely primes Cas10d for Cas3′ binding and subsequent non-target strand DNA cleavage. These structures allow us to model how binding of the anti-CRISPR protein AcrID1 likely blocks target dsDNA binding via competitive inhibition of the DNA substrate engagement with the Cas10d active site. This work elucidates the unique mechanisms used by type I-D Cascade for discrimination of single-stranded and double stranded targets. Thus, our data supports a model for the hybrid nature of this complex with features of type III and type I systems."}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"year":"2022","external_id":{"pmid":["35595728"]},"publication_identifier":{"issn":["2041-1723"]},"article_number":"2829","publisher":"Springer Nature","type":"journal_article","date_updated":"2024-06-04T06:14:28Z","publication":"Nature Communications","month":"05","date_published":"2022-05-20T00:00:00Z","status":"public","author":[{"full_name":"Schwartz, Evan A.","last_name":"Schwartz","first_name":"Evan A."},{"full_name":"McBride, Tess M.","last_name":"McBride","first_name":"Tess M."},{"orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly","first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo"},{"last_name":"Wrapp","first_name":"Daniel","full_name":"Wrapp, Daniel"},{"first_name":"Peter C.","last_name":"Fineran","full_name":"Fineran, Peter C."},{"full_name":"Fagerlund, Robert D.","first_name":"Robert D.","last_name":"Fagerlund"},{"full_name":"Taylor, David W.","first_name":"David W.","last_name":"Taylor"}],"date_created":"2024-03-20T10:42:05Z","day":"20","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","article_processing_charge":"Yes","volume":13,"citation":{"chicago":"Schwartz, Evan A., Tess M. McBride, Jack Peter Kelly Bravo, Daniel Wrapp, Peter C. Fineran, Robert D. Fagerlund, and David W. Taylor. “Structural Rearrangements Allow Nucleic Acid Discrimination by Type I-D Cascade.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30402-8\">https://doi.org/10.1038/s41467-022-30402-8</a>.","ama":"Schwartz EA, McBride TM, Bravo JPK, et al. Structural rearrangements allow nucleic acid discrimination by type I-D Cascade. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30402-8\">10.1038/s41467-022-30402-8</a>","apa":"Schwartz, E. A., McBride, T. M., Bravo, J. P. K., Wrapp, D., Fineran, P. C., Fagerlund, R. D., &#38; Taylor, D. W. (2022). Structural rearrangements allow nucleic acid discrimination by type I-D Cascade. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30402-8\">https://doi.org/10.1038/s41467-022-30402-8</a>","mla":"Schwartz, Evan A., et al. “Structural Rearrangements Allow Nucleic Acid Discrimination by Type I-D Cascade.” <i>Nature Communications</i>, vol. 13, 2829, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30402-8\">10.1038/s41467-022-30402-8</a>.","ieee":"E. A. Schwartz <i>et al.</i>, “Structural rearrangements allow nucleic acid discrimination by type I-D Cascade,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ista":"Schwartz EA, McBride TM, Bravo JPK, Wrapp D, Fineran PC, Fagerlund RD, Taylor DW. 2022. Structural rearrangements allow nucleic acid discrimination by type I-D Cascade. Nature Communications. 13, 2829.","short":"E.A. Schwartz, T.M. McBride, J.P.K. Bravo, D. Wrapp, P.C. Fineran, R.D. Fagerlund, D.W. Taylor, Nature Communications 13 (2022)."},"quality_controlled":"1","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41467-022-30402-8"},{"article_processing_charge":"No","isi":1,"scopus_import":"1","doi":"10.1103/physrevapplied.17.054031","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","volume":17,"citation":{"ieee":"V. Li, F. R. Diorico, and O. Hosten, “Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters,” <i>Physical Review Applied</i>, vol. 17, no. 5. American Physical Society, 2022.","short":"V. Li, F.R. Diorico, O. Hosten, Physical Review Applied 17 (2022).","ista":"Li V, Diorico FR, Hosten O. 2022. Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters. Physical Review Applied. 17(5), 054031.","chicago":"Li, Vyacheslav, Fritz R Diorico, and Onur Hosten. “Laser Frequency-Offset Locking at 10-Hz-Level Instability Using Hybrid Electronic Filters.” <i>Physical Review Applied</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">https://doi.org/10.1103/physrevapplied.17.054031</a>.","ama":"Li V, Diorico FR, Hosten O. Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters. <i>Physical Review Applied</i>. 2022;17(5). doi:<a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">10.1103/physrevapplied.17.054031</a>","apa":"Li, V., Diorico, F. R., &#38; Hosten, O. (2022). Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">https://doi.org/10.1103/physrevapplied.17.054031</a>","mla":"Li, Vyacheslav, et al. “Laser Frequency-Offset Locking at 10-Hz-Level Instability Using Hybrid Electronic Filters.” <i>Physical Review Applied</i>, vol. 17, no. 5, 054031, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">10.1103/physrevapplied.17.054031</a>."},"quality_controlled":"1","publication":"Physical Review Applied","date_published":"2022-05-19T00:00:00Z","month":"05","status":"public","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"type":"journal_article","issue":"5","date_updated":"2026-07-08T08:50:57Z","related_material":{"record":[{"relation":"dissertation_contains","id":"17225","status":"public"}]},"researchdata_availability":"no","corr_author":"1","acknowledgement":"This work was supported by IST Austria. The authors thank Yueheng Shi for technical contributions.","article_type":"original","author":[{"full_name":"Li, Vyacheslav","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Vyacheslav"},{"last_name":"Diorico","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","first_name":"Fritz R","full_name":"Diorico, Fritz R","orcid":"0000-0002-4947-8924"},{"first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur"}],"date_created":"2022-06-07T08:07:59Z","language":[{"iso":"eng"}],"day":"19","external_id":{"arxiv":["2111.13194"],"isi":["000880670300001"]},"supplementarymaterial":"no","publication_identifier":{"issn":["2331-7019"]},"publisher":"American Physical Society","article_number":"054031","oa":1,"intvolume":"        17","oa_version":"Preprint","title":"Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters","_id":"11438","publication_status":"published","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2111.13194","open_access":"1"}],"keyword":["General Physics and Astronomy"],"abstract":[{"lang":"eng","text":"Lasers with well-controlled relative frequencies are indispensable for many applications in science and technology. We present a frequency-offset locking method for lasers based on beat-frequency discrimination utilizing hybrid electronic LC filters. The method is specifically designed for decoupling the tightness of the lock from the broadness of its capture range. The presented demonstration locks two free-running diode lasers at 780 nm with a 5.5-GHz offset. It displays an offset frequency instability below 55 Hz for time scales in excess of 1000 s and a minimum of 12 Hz at 10-s averaging. The performance is complemented with a 190-MHz lock-capture range, a tuning range of up to 1 GHz, and a frequency ramp agility of 200kHz/μs."}],"year":"2022","das_tickbox":"0","arxiv":1},{"dataavailabilitystatement":"All PYTHON scripts and simulation input files generated for the study are in the SI repository https://github.com/BingqingCheng/S0, Ref. 29.\r\n29. B. Cheng, https://github.com/BingqingCheng/S0 “Data repository for the S0 method” (2020).","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1063/5.0107059","quality_controlled":"1","citation":{"chicago":"Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure Factors.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0107059\">https://doi.org/10.1063/5.0107059</a>.","apa":"Cheng, B. (2022). Computing chemical potentials of solutions from structure factors. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0107059\">https://doi.org/10.1063/5.0107059</a>","ama":"Cheng B. Computing chemical potentials of solutions from structure factors. <i>The Journal of Chemical Physics</i>. 2022;157(12). doi:<a href=\"https://doi.org/10.1063/5.0107059\">10.1063/5.0107059</a>","mla":"Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure Factors.” <i>The Journal of Chemical Physics</i>, vol. 157, no. 12, 121101, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0107059\">10.1063/5.0107059</a>.","ieee":"B. Cheng, “Computing chemical potentials of solutions from structure factors,” <i>The Journal of Chemical Physics</i>, vol. 157, no. 12. AIP Publishing, 2022.","ista":"Cheng B. 2022. Computing chemical potentials of solutions from structure factors. The Journal of Chemical Physics. 157(12), 121101.","short":"B. Cheng, The Journal of Chemical Physics 157 (2022)."},"volume":157,"file":[{"checksum":"b0915b706568a663a9a372fca24adf35","creator":"dernst","date_updated":"2023-01-30T09:07:00Z","file_id":"12441","file_size":4402384,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_created":"2023-01-30T09:07:00Z","success":1,"file_name":"2022_JourChemPhysics_Cheng.pdf"}],"article_processing_charge":"No","isi":1,"scopus_import":"1","researchdata_availability":"yes","related_material":{"link":[{"url":"https://github.com/ BingqingCheng/S0","relation":"software"}]},"acknowledgement":"I thank Daan Frenkel for providing feedback on an early draft and for stimulating discussions, Debashish Mukherji and Robinson Cortes-Huerto for sharing the trajectories for urea–water mixtures, and Aleks Reinhardt for useful suggestions on the manuscript.","corr_author":"1","article_type":"original","author":[{"first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"}],"language":[{"iso":"eng"}],"date_created":"2023-01-16T09:56:20Z","day":"30","file_date_updated":"2023-01-30T09:07:00Z","date_published":"2022-09-30T00:00:00Z","month":"09","ddc":["530","540"],"publication":"The Journal of Chemical Physics","status":"public","type":"journal_article","issue":"12","has_accepted_license":"1","department":[{"_id":"BiCh"}],"date_updated":"2026-08-07T11:22:29Z","publisher":"AIP Publishing","article_number":"121101","external_id":{"pmid":["36182422"],"isi":["000862856000003"]},"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"supplementarymaterial":"yes","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"das_tickbox":"1","year":"2022","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"abstract":[{"lang":"eng","text":"The chemical potential of a component in a solution is defined as the free energy change as the amount of that component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. This Communication presents the so-called S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal–isobaric ensemble. This new method is demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures, a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. "}],"intvolume":"       157","oa":1,"pmid":1,"oa_version":"Published Version","publication_status":"published","_id":"12249","title":"Computing chemical potentials of solutions from structure factors"},{"year":"2022","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"abstract":[{"text":"The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ.","lang":"eng"}],"intvolume":"        13","ec_funded":1,"oa":1,"oa_version":"Published Version","publication_status":"published","_id":"11373","title":"In vitro reconstitution of Escherichia coli divisome activation","publisher":"Springer Nature","article_number":"2635","external_id":{"isi":["000795171100037"]},"publication_identifier":{"issn":["2041-1723"]},"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","grant_number":"679239"},{"name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-34485-1","relation":"erratum"}],"record":[{"relation":"research_data","id":"10934","status":"public"},{"id":"14280","status":"public","relation":"dissertation_contains"}]},"article_type":"original","acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","corr_author":"1","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","first_name":"Philipp","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 "},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","first_name":"Natalia S.","full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124"},{"first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"full_name":"Lopez Pelegrin, Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Pelegrin","first_name":"Maria D"},{"id":"B9577E20-AA38-11E9-AC9A-0930E6697425","last_name":"Michalik","first_name":"David","full_name":"Michalik, David"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"}],"language":[{"iso":"eng"}],"day":"12","date_created":"2022-05-13T09:06:28Z","file_date_updated":"2022-05-13T09:10:51Z","date_published":"2022-05-12T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"05","ddc":["570"],"publication":"Nature Communications","status":"public","type":"journal_article","department":[{"_id":"MaLo"}],"has_accepted_license":"1","date_updated":"2026-08-24T22:30:11Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-022-30301-y","citation":{"ista":"Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635.","short":"P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>","apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., &#38; Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>","mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>, vol. 13, 2635, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>.","chicago":"Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>."},"quality_controlled":"1","volume":13,"file":[{"date_updated":"2022-05-13T09:10:51Z","checksum":"5af863ee1b95a0710f6ee864d68dc7a6","creator":"dernst","content_type":"application/pdf","file_size":6945191,"file_id":"11374","access_level":"open_access","date_created":"2022-05-13T09:10:51Z","relation":"main_file","file_name":"2022_NatureCommunications_Radler.pdf","success":1}],"article_processing_charge":"No","isi":1,"scopus_import":"1"},{"article_type":"original","author":[{"first_name":"Evan","last_name":"Miles","full_name":"Miles, Evan"},{"full_name":"McCarthy, Michael","first_name":"Michael","last_name":"McCarthy"},{"full_name":"Dehecq, Amaury","last_name":"Dehecq","first_name":"Amaury"},{"full_name":"Kneib, Marin","last_name":"Kneib","first_name":"Marin"},{"first_name":"Stefan","last_name":"Fugger","full_name":"Fugger, Stefan"},{"first_name":"Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"}],"date_created":"2023-02-20T08:11:29Z","language":[{"iso":"eng"}],"day":"17","publication":"Nature Communications","month":"05","date_published":"2021-05-17T00:00:00Z","status":"public","type":"journal_article","date_updated":"2023-02-28T13:21:51Z","extern":"1","doi":"10.1038/s41467-021-23073-4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":12,"citation":{"short":"E. Miles, M. McCarthy, A. Dehecq, M. Kneib, S. Fugger, F. Pellicciotti, Nature Communications 12 (2021).","ista":"Miles E, McCarthy M, Dehecq A, Kneib M, Fugger S, Pellicciotti F. 2021. Health and sustainability of glaciers in High Mountain Asia. Nature Communications. 12, 2868.","ieee":"E. Miles, M. McCarthy, A. Dehecq, M. Kneib, S. Fugger, and F. Pellicciotti, “Health and sustainability of glaciers in High Mountain Asia,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","mla":"Miles, Evan, et al. “Health and Sustainability of Glaciers in High Mountain Asia.” <i>Nature Communications</i>, vol. 12, 2868, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23073-4\">10.1038/s41467-021-23073-4</a>.","ama":"Miles E, McCarthy M, Dehecq A, Kneib M, Fugger S, Pellicciotti F. Health and sustainability of glaciers in High Mountain Asia. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-23073-4\">10.1038/s41467-021-23073-4</a>","apa":"Miles, E., McCarthy, M., Dehecq, A., Kneib, M., Fugger, S., &#38; Pellicciotti, F. (2021). Health and sustainability of glaciers in High Mountain Asia. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23073-4\">https://doi.org/10.1038/s41467-021-23073-4</a>","chicago":"Miles, Evan, Michael McCarthy, Amaury Dehecq, Marin Kneib, Stefan Fugger, and Francesca Pellicciotti. “Health and Sustainability of Glaciers in High Mountain Asia.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23073-4\">https://doi.org/10.1038/s41467-021-23073-4</a>."},"quality_controlled":"1","article_processing_charge":"No","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41467-021-23073-4","open_access":"1"}],"abstract":[{"text":"Glaciers in High Mountain Asia generate meltwater that supports the water needs of 250 million people, but current knowledge of annual accumulation and ablation is limited to sparse field measurements biased in location and glacier size. Here, we present altitudinally-resolved specific mass balances (surface, internal, and basal combined) for 5527 glaciers in High Mountain Asia for 2000–2016, derived by correcting observed glacier thinning patterns for mass redistribution due to ice flow. We find that 41% of glaciers accumulated mass over less than 20% of their area, and only 60% ± 10% of regional annual ablation was compensated by accumulation. Even without 21st century warming, 21% ± 1% of ice volume will be lost by 2100 due to current climatic-geometric imbalance, representing a reduction in glacier ablation into rivers of 28% ± 1%. The ablation of glaciers in the Himalayas and Tien Shan was mostly unsustainable and ice volume in these regions will reduce by at least 30% by 2100. The most important and vulnerable glacier-fed river basins (Amu Darya, Indus, Syr Darya, Tarim Interior) were supplied with >50% sustainable glacier ablation but will see long-term reductions in ice mass and glacier meltwater supply regardless of the Karakoram Anomaly.","lang":"eng"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"year":"2021","oa":1,"intvolume":"        12","oa_version":"Published Version","title":"Health and sustainability of glaciers in High Mountain Asia","_id":"12585","publication_status":"published","publisher":"Springer Nature","article_number":"2868","publication_identifier":{"issn":["2041-1723"]}},{"article_processing_charge":"Yes","scopus_import":"1","doi":"10.1038/s41467-021-25337-5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","volume":12,"quality_controlled":"1","citation":{"chicago":"Steens, Jurre A., Yifan Zhu, David W. Taylor, Jack Peter Kelly Bravo, Stijn H. P. Prinsen, Cor D. Schoen, Bart J. F. Keijser, et al. “SCOPE Enables Type III CRISPR-Cas Diagnostics Using Flexible Targeting and Stringent CARF Ribonuclease Activation.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-25337-5\">https://doi.org/10.1038/s41467-021-25337-5</a>.","mla":"Steens, Jurre A., et al. “SCOPE Enables Type III CRISPR-Cas Diagnostics Using Flexible Targeting and Stringent CARF Ribonuclease Activation.” <i>Nature Communications</i>, vol. 12, 5033, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-25337-5\">10.1038/s41467-021-25337-5</a>.","apa":"Steens, J. A., Zhu, Y., Taylor, D. W., Bravo, J. P. K., Prinsen, S. H. P., Schoen, C. D., … Staals, R. H. J. (2021). SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-25337-5\">https://doi.org/10.1038/s41467-021-25337-5</a>","ama":"Steens JA, Zhu Y, Taylor DW, et al. SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-25337-5\">10.1038/s41467-021-25337-5</a>","ieee":"J. A. Steens <i>et al.</i>, “SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","ista":"Steens JA, Zhu Y, Taylor DW, Bravo JPK, Prinsen SHP, Schoen CD, Keijser BJF, Ossendrijver M, Hofstra LM, Brouns SJJ, Shinkai A, van der Oost J, Staals RHJ. 2021. SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. Nature Communications. 12, 5033.","short":"J.A. Steens, Y. Zhu, D.W. Taylor, J.P.K. Bravo, S.H.P. Prinsen, C.D. Schoen, B.J.F. Keijser, M. Ossendrijver, L.M. Hofstra, S.J.J. Brouns, A. Shinkai, J. van der Oost, R.H.J. Staals, Nature Communications 12 (2021)."},"status":"public","publication":"Nature Communications","date_published":"2021-08-19T00:00:00Z","month":"08","date_updated":"2024-06-04T06:11:54Z","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"date_created":"2024-03-20T10:42:33Z","day":"19","author":[{"full_name":"Steens, Jurre A.","first_name":"Jurre A.","last_name":"Steens"},{"full_name":"Zhu, Yifan","first_name":"Yifan","last_name":"Zhu"},{"full_name":"Taylor, David W.","first_name":"David W.","last_name":"Taylor"},{"last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753"},{"full_name":"Prinsen, Stijn H. P.","last_name":"Prinsen","first_name":"Stijn H. P."},{"full_name":"Schoen, Cor D.","first_name":"Cor D.","last_name":"Schoen"},{"last_name":"Keijser","first_name":"Bart J. F.","full_name":"Keijser, Bart J. F."},{"full_name":"Ossendrijver, Michel","last_name":"Ossendrijver","first_name":"Michel"},{"first_name":"L. Marije","last_name":"Hofstra","full_name":"Hofstra, L. Marije"},{"full_name":"Brouns, Stan J. J.","first_name":"Stan J. J.","last_name":"Brouns"},{"first_name":"Akeo","last_name":"Shinkai","full_name":"Shinkai, Akeo"},{"full_name":"van der Oost, John","last_name":"van der Oost","first_name":"John"},{"first_name":"Raymond H. J.","last_name":"Staals","full_name":"Staals, Raymond H. J."}],"publication_identifier":{"issn":["2041-1723"]},"external_id":{"pmid":["34413302"]},"publisher":"Springer Nature","article_number":"5033","pmid":1,"oa":1,"intvolume":"        12","title":"SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation","_id":"15137","publication_status":"published","oa_version":"Published Version","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"abstract":[{"lang":"eng","text":"Characteristic properties of type III CRISPR-Cas systems include recognition of target RNA and the subsequent induction of a multifaceted immune response. This involves sequence-specific cleavage of the target RNA and production of cyclic oligoadenylate (cOA) molecules. Here we report that an exposed seed region at the 3′ end of the crRNA is essential for target RNA binding and cleavage, whereas cOA production requires base pairing at the 5′ end of the crRNA. Moreover, we uncover that the variation in the size and composition of type III complexes within a single host results in variable seed regions. This may prevent escape by invading genetic elements, while controlling cOA production tightly to prevent unnecessary damage to the host. Lastly, we use these findings to develop a new diagnostic tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples, revealing sensitivities in the atto-molar range."}],"year":"2021","main_file_link":[{"url":"https://doi.org/10.1038/s41467-021-25337-5","open_access":"1"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000709050300001"]},"publication_identifier":{"eissn":["2041-1723"]},"article_number":"6078","publisher":"Springer Nature","oa_version":"Published Version","title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","publication_status":"published","_id":"10163","oa":1,"intvolume":"        12","abstract":[{"lang":"eng","text":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay."}],"keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"year":"2021","scopus_import":"1","article_processing_charge":"No","file":[{"file_id":"10169","content_type":"application/pdf","file_size":5111706,"creator":"cchlebak","checksum":"d99fcd51aebde19c21314e3de0148007","date_updated":"2021-10-21T13:51:49Z","file_name":"2021_NatComm_Appel.pdf","success":1,"access_level":"open_access","date_created":"2021-10-21T13:51:49Z","relation":"main_file"}],"isi":1,"volume":12,"quality_controlled":"1","citation":{"ieee":"L.-M. Appel <i>et al.</i>, “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","short":"L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021).","ista":"Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.","chicago":"Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>.","mla":"Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>.","apa":"Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>","ama":"Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>"},"doi":"10.1038/s41467-021-26360-2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"CaBe"}],"has_accepted_license":"1","issue":"1","type":"journal_article","date_updated":"2024-10-21T06:02:05Z","publication":"Nature Communications","ddc":["610"],"month":"10","date_published":"2021-10-19T00:00:00Z","status":"public","author":[{"full_name":"Appel, Lisa-Marie","last_name":"Appel","first_name":"Lisa-Marie"},{"first_name":"Vedran","last_name":"Franke","full_name":"Franke, Vedran"},{"last_name":"Bruno","first_name":"Melania","full_name":"Bruno, Melania"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"last_name":"Kasiliauskaite","first_name":"Aiste","full_name":"Kasiliauskaite, Aiste"},{"full_name":"Kaufmann, Tanja","first_name":"Tanja","last_name":"Kaufmann"},{"first_name":"Ursula E.","last_name":"Schoeberl","full_name":"Schoeberl, Ursula E."},{"last_name":"Puchinger","first_name":"Martin G.","full_name":"Puchinger, Martin G."},{"full_name":"Kostrhon, Sebastian","first_name":"Sebastian","last_name":"Kostrhon"},{"first_name":"Carmen","last_name":"Ebenwaldner","full_name":"Ebenwaldner, Carmen"},{"full_name":"Sebesta, Marek","first_name":"Marek","last_name":"Sebesta"},{"full_name":"Beltzung, Etienne","first_name":"Etienne","last_name":"Beltzung"},{"last_name":"Mechtler","first_name":"Karl","full_name":"Mechtler, Karl"},{"first_name":"Gen","last_name":"Lin","full_name":"Lin, Gen"},{"last_name":"Vlasova","first_name":"Anna","full_name":"Vlasova, Anna"},{"full_name":"Leeb, Martin","last_name":"Leeb","first_name":"Martin"},{"full_name":"Pavri, Rushad","first_name":"Rushad","last_name":"Pavri"},{"full_name":"Stark, Alexander","first_name":"Alexander","last_name":"Stark"},{"full_name":"Akalin, Altuna","first_name":"Altuna","last_name":"Akalin"},{"full_name":"Stefl, Richard","last_name":"Stefl","first_name":"Richard"},{"orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky"},{"full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo","first_name":"Kristina"},{"full_name":"Slade, Dea","first_name":"Dea","last_name":"Slade"}],"file_date_updated":"2021-10-21T13:51:49Z","date_created":"2021-10-20T14:40:32Z","day":"19","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159","description":"Preprint ","relation":"earlier_version"}]},"article_type":"original","acknowledgement":"D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S."},{"author":[{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg"},{"last_name":"Holder","first_name":"Tobias","full_name":"Holder, Tobias"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"first_name":"Erez","last_name":"Berg","full_name":"Berg, Erez"}],"date_created":"2021-12-10T07:51:33Z","day":"09","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/","relation":"press_release","description":"News on IST Webpage"}]},"article_type":"original","acknowledgement":"We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young for many stimulating discussions and for their comments on the manuscript. E.B. thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","department":[{"_id":"MaSe"}],"type":"journal_article","issue":"24","date_updated":"2025-04-14T07:43:47Z","publication":"Physical Review Letters","month":"12","date_published":"2021-12-09T00:00:00Z","status":"public","volume":127,"citation":{"chicago":"Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.247001\">https://doi.org/10.1103/physrevlett.127.247001</a>.","mla":"Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” <i>Physical Review Letters</i>, vol. 127, no. 24, 247001, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.247001\">10.1103/physrevlett.127.247001</a>.","apa":"Ghazaryan, A., Holder, T., Serbyn, M., &#38; Berg, E. (2021). Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.127.247001\">https://doi.org/10.1103/physrevlett.127.247001</a>","ama":"Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. <i>Physical Review Letters</i>. 2021;127(24). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.247001\">10.1103/physrevlett.127.247001</a>","ieee":"A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,” <i>Physical Review Letters</i>, vol. 127, no. 24. American Physical Society, 2021.","short":"A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127 (2021).","ista":"Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 127(24), 247001."},"quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1103/physrevlett.127.247001","scopus_import":"1","article_processing_charge":"No","isi":1,"arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/2109.00011","open_access":"1"}],"abstract":[{"lang":"eng","text":"We show that in a two-dimensional electron gas with an annular Fermi surface, long-range Coulomb interactions can lead to unconventional superconductivity by the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the inner and outer Fermi surfaces are close to each other. The most prevalent state has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible. We discuss these results in the context of rhombohedral trilayer graphene, where superconductivity was recently discovered in regimes where the normal state has an annular Fermi surface. Using realistic parameters, our mechanism can account for the order of magnitude of Tc, as well as its trends as a function of electron density and perpendicular displacement field. Moreover, it naturally explains some of the outstanding puzzles in this material, that include the weak temperature dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity to the ferromagnetic phase."}],"keyword":["general physics and astronomy"],"year":"2021","oa_version":"Preprint","title":"Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene","_id":"10527","publication_status":"published","oa":1,"ec_funded":1,"intvolume":"       127","article_number":"247001","publisher":"American Physical Society","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"external_id":{"arxiv":["2109.00011"],"isi":["000923819400004"]},"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]}},{"author":[{"id":"42832B76-F248-11E8-B48F-1D18A9856A87","last_name":"De Nicola","first_name":"Stefano","full_name":"De Nicola, Stefano","orcid":"0000-0002-4842-6671"},{"first_name":"Alexios","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"day":"29","language":[{"iso":"eng"}],"date_created":"2021-02-01T09:20:00Z","file_date_updated":"2021-02-03T12:47:04Z","acknowledgement":"S. D. N. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. M. and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and\r\nInnovation Programme (Grant Agreement No. 850899).","article_type":"original","type":"journal_article","issue":"4","department":[{"_id":"MaSe"}],"has_accepted_license":"1","date_updated":"2025-04-14T07:43:50Z","date_published":"2021-01-29T00:00:00Z","ddc":["530"],"month":"01","publication":"Physical Review Letters","status":"public","citation":{"mla":"De Nicola, Stefano, et al. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>, vol. 126, no. 4, 040602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>.","apa":"De Nicola, S., Michailidis, A., &#38; Serbyn, M. (2021). Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>","ama":"De Nicola S, Michailidis A, Serbyn M. Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. 2021;126(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>","chicago":"De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>.","ista":"De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 126(4), 040602.","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021).","ieee":"S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement view of dynamical quantum phase transitions,” <i>Physical Review Letters</i>, vol. 126, no. 4. American Physical Society, 2021."},"quality_controlled":"1","volume":126,"doi":"10.1103/physrevlett.126.040602","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","date_created":"2021-02-03T12:47:04Z","success":1,"file_name":"2021_PhysicalRevLett_DeNicola.pdf","date_updated":"2021-02-03T12:47:04Z","checksum":"d9acbc502390ed7a97e631d23ae19ecd","creator":"dernst","content_type":"application/pdf","file_size":398075,"file_id":"9074"}],"article_processing_charge":"Yes","isi":1,"arxiv":1,"year":"2021","abstract":[{"lang":"eng","text":"The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology."}],"keyword":["General Physics and Astronomy"],"oa_version":"Published Version","publication_status":"published","_id":"9048","title":"Entanglement view of dynamical quantum phase transitions","intvolume":"       126","ec_funded":1,"oa":1,"article_number":"040602","publisher":"American Physical Society","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["2008.04894"],"isi":["000613148200001"]},"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]}},{"isi":1,"file":[{"file_name":"2021_NatureCommunications_Obr.pdf","success":1,"relation":"main_file","date_created":"2021-06-09T15:21:14Z","access_level":"open_access","content_type":"application/pdf","file_size":6166295,"file_id":"9538","date_updated":"2021-06-09T15:21:14Z","creator":"kschuh","checksum":"53ccc53d09a9111143839dbe7784e663"}],"article_processing_charge":"No","scopus_import":"1","doi":"10.1038/s41467-021-23506-0","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","citation":{"ieee":"M. Obr <i>et al.</i>, “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” <i>Nature Communications</i>, vol. 12, no. 1. Nature Research, 2021.","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226.","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).","chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>.","mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>, vol. 12, no. 1, 3226, Nature Research, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>.","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>","apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>"},"volume":12,"status":"public","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"date_published":"2021-05-28T00:00:00Z","month":"05","ddc":["570"],"publication":"Nature Communications","date_updated":"2025-04-15T08:24:49Z","issue":"1","type":"journal_article","has_accepted_license":"1","department":[{"_id":"FlSc"}],"article_type":"original","acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF).","corr_author":"1","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/"}]},"language":[{"iso":"eng"}],"date_created":"2021-05-28T14:25:50Z","day":"28","file_date_updated":"2021-06-09T15:21:14Z","author":[{"full_name":"Obr, Martin","orcid":"0000-0003-1756-6564","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"last_name":"Ricana","first_name":"Clifton L.","full_name":"Ricana, Clifton L."},{"last_name":"Nikulin","first_name":"Nadia","full_name":"Nikulin, Nadia"},{"last_name":"Feathers","first_name":"Jon-Philip R.","full_name":"Feathers, Jon-Philip R."},{"full_name":"Klanschnig, Marco","first_name":"Marco","last_name":"Klanschnig"},{"full_name":"Thader, Andreas","first_name":"Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Johnson","first_name":"Marc C.","full_name":"Johnson, Marc C."},{"full_name":"Vogt, Volker M.","first_name":"Volker M.","last_name":"Vogt"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"},{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"}],"publication_identifier":{"eissn":["2041-1723"]},"external_id":{"isi":["000659145000011"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445"}],"publisher":"Nature Research","article_number":"3226","intvolume":"        12","oa":1,"_id":"9431","publication_status":"published","title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","oa_version":"Published Version","year":"2021","abstract":[{"text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.","lang":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"]},{"scopus_import":"1","isi":1,"article_processing_charge":"No","file":[{"file_name":"2021_NatureComm_Prattes.pdf","success":1,"relation":"main_file","date_created":"2021-06-15T18:55:59Z","access_level":"open_access","file_id":"9556","file_size":3397292,"content_type":"application/pdf","creator":"cziletti","checksum":"40fc24c1310930990b52a8ad1142ee97","date_updated":"2021-06-15T18:55:59Z"}],"volume":12,"quality_controlled":"1","citation":{"apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>","mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>.","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021).","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483.","ieee":"M. Prattes <i>et al.</i>, “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-021-23854-x","date_updated":"2024-10-21T06:02:01Z","department":[{"_id":"EM-Fac"}],"has_accepted_license":"1","issue":"1","type":"journal_article","status":"public","publication":"Nature Communications","ddc":["570"],"date_published":"2021-06-09T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"06","file_date_updated":"2021-06-15T18:55:59Z","date_created":"2021-06-10T14:57:45Z","day":"09","language":[{"iso":"eng"}],"author":[{"first_name":"Michael","last_name":"Prattes","full_name":"Prattes, Michael"},{"full_name":"Grishkovskaya, Irina","last_name":"Grishkovskaya","first_name":"Irina"},{"last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","orcid":"0000-0003-3904-947X"},{"last_name":"Rössler","first_name":"Ingrid","full_name":"Rössler, Ingrid"},{"first_name":"Isabella","last_name":"Klein","full_name":"Klein, Isabella"},{"first_name":"Christina","last_name":"Hetzmannseder","full_name":"Hetzmannseder, Christina"},{"first_name":"Gertrude","last_name":"Zisser","full_name":"Zisser, Gertrude"},{"full_name":"Gruber, Christian C.","last_name":"Gruber","first_name":"Christian C."},{"first_name":"Karl","last_name":"Gruber","full_name":"Gruber, Karl"},{"full_name":"Haselbach, David","last_name":"Haselbach","first_name":"David"},{"last_name":"Bergler","first_name":"Helmut","full_name":"Bergler, Helmut"}],"article_type":"original","acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["2041-1723"]},"external_id":{"isi":["000664874700014"],"pmid":["34108481"]},"article_number":"3483","publisher":"Springer Nature","title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","_id":"9540","publication_status":"published","oa_version":"Published Version","pmid":1,"oa":1,"intvolume":"        12","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"abstract":[{"lang":"eng","text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases."}],"year":"2021"}]