[{"oa":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells."}],"doi":"10.1038/s41467-023-43168-4","file_date_updated":"2023-12-27T08:40:43Z","file":[{"access_level":"open_access","file_name":"2023_NatureComm_Curatolo.pdf","creator":"kschuh","file_size":1342319,"date_created":"2023-12-27T08:40:43Z","relation":"main_file","checksum":"fd9e9d527c2691f03fbc24031a75a3b3","file_id":"14714","content_type":"application/pdf","date_updated":"2023-12-27T08:40:43Z","success":1}],"citation":{"ama":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 2023;14. doi:10.1038/s41467-023-43168-4","short":"A.I. Curatolo, O. Kimchi, C.P. Goodrich, R.K. Krueger, M.P. Brenner, Nature Communications 14 (2023).","mla":"Curatolo, Agnese I., et al. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications, vol. 14, 8328, Springer Nature, 2023, doi:10.1038/s41467-023-43168-4.","ista":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. 2023. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 14, 8328.","chicago":"Curatolo, Agnese I., Ofer Kimchi, Carl Peter Goodrich, Ryan K. Krueger, and Michael P. Brenner. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-43168-4.","apa":"Curatolo, A. I., Kimchi, O., Goodrich, C. P., Krueger, R. K., & Brenner, M. P. (2023). A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-43168-4","ieee":"A. I. Curatolo, O. Kimchi, C. P. Goodrich, R. K. Krueger, and M. P. Brenner, “A computational toolbox for the assembly yield of complex and heterogeneous structures,” Nature Communications, vol. 14. Springer Nature, 2023."},"title":"A computational toolbox for the assembly yield of complex and heterogeneous structures","date_created":"2023-12-24T23:00:53Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","status":"public","department":[{"_id":"CaGo"}],"publication_status":"published","year":"2023","intvolume":" 14","publication":"Nature Communications","publisher":"Springer Nature","author":[{"last_name":"Curatolo","full_name":"Curatolo, Agnese I.","first_name":"Agnese I."},{"first_name":"Ofer","full_name":"Kimchi, Ofer","last_name":"Kimchi"},{"first_name":"Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"Krueger","full_name":"Krueger, Ryan K.","first_name":"Ryan K."},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."}],"has_accepted_license":"1","volume":14,"scopus_import":"1","type":"journal_article","article_processing_charge":"Yes","acknowledgement":"We thank Lucy Colwell for suggesting that we use covariance based methods to predict contacts and Yang Hsia, Scott Boyken, Zibo Chen, and David Baker for collaborations on designed protein complexes. We also thank Ned Wingreen for suggesting the alternative derivation of (11). This research was supported by the Office of Naval Research through ONR N00014-17-1-3029, the Simons Foundation the NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard (award number #1764269), the Peter B. Lewis ’55 Lewis-Sigler Institute/Genomics Fund through the Lewis-Sigler Institute of Integrative Genomics at Princeton University, and the National Science Foundation through the Center for the Physics of Biological Function (PHY-1734030).","quality_controlled":"1","publication_identifier":{"eissn":["20411723"]},"_id":"14710","ddc":["530"],"article_number":"8328","license":"https://creativecommons.org/licenses/by/4.0/","day":"01","date_updated":"2024-01-02T11:36:46Z","language":[{"iso":"eng"}],"date_published":"2023-12-01T00:00:00Z","month":"12"},{"oa":1,"article_type":"original","file":[{"creator":"dernst","file_name":"2022_NatureCommunications_Cheung.pdf","access_level":"open_access","relation":"main_file","file_size":7910519,"date_created":"2022-02-21T07:51:33Z","checksum":"51d580aff2327dd957946208a9749e1a","file_id":"10777","content_type":"application/pdf","success":1,"date_updated":"2022-02-21T07:51:33Z"}],"abstract":[{"text":"Presynaptic glutamate replenishment is fundamental to brain function. In high activity regimes, such as epileptic episodes, this process is thought to rely on the glutamate-glutamine cycle between neurons and astrocytes. However the presence of an astroglial glutamine supply, as well as its functional relevance in vivo in the healthy brain remain controversial, partly due to a lack of tools that can directly examine glutamine transfer. Here, we generated a fluorescent probe that tracks glutamine in live cells, which provides direct visual evidence of an activity-dependent glutamine supply from astroglial networks to presynaptic structures under physiological conditions. This mobilization is mediated by connexin43, an astroglial protein with both gap-junction and hemichannel functions, and is essential for synaptic transmission and object recognition memory. Our findings uncover an indispensable recruitment of astroglial glutamine in physiological synaptic activity and memory via an unconventional pathway, thus providing an astrocyte basis for cognitive processes.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-022-28331-7","file_date_updated":"2022-02-21T07:51:33Z","date_created":"2022-02-20T23:01:30Z","title":"Physiological synaptic activity and recognition memory require astroglial glutamine","citation":{"apa":"Cheung, G. T., Bataveljic, D., Visser, J., Kumar, N., Moulard, J., Dallérac, G., … Rouach, N. (2022). Physiological synaptic activity and recognition memory require astroglial glutamine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-28331-7","ieee":"G. T. Cheung et al., “Physiological synaptic activity and recognition memory require astroglial glutamine,” Nature Communications, vol. 13. Springer Nature, 2022.","chicago":"Cheung, Giselle T, Danijela Bataveljic, Josien Visser, Naresh Kumar, Julien Moulard, Glenn Dallérac, Daria Mozheiko, et al. “Physiological Synaptic Activity and Recognition Memory Require Astroglial Glutamine.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-28331-7.","ista":"Cheung GT, Bataveljic D, Visser J, Kumar N, Moulard J, Dallérac G, Mozheiko D, Rollenhagen A, Ezan P, Mongin C, Chever O, Bemelmans AP, Lübke J, Leray I, Rouach N. 2022. Physiological synaptic activity and recognition memory require astroglial glutamine. Nature Communications. 13, 753.","mla":"Cheung, Giselle T., et al. “Physiological Synaptic Activity and Recognition Memory Require Astroglial Glutamine.” Nature Communications, vol. 13, 753, Springer Nature, 2022, doi:10.1038/s41467-022-28331-7.","short":"G.T. Cheung, D. Bataveljic, J. Visser, N. Kumar, J. Moulard, G. Dallérac, D. Mozheiko, A. Rollenhagen, P. Ezan, C. Mongin, O. Chever, A.P. Bemelmans, J. Lübke, I. Leray, N. Rouach, Nature Communications 13 (2022).","ama":"Cheung GT, Bataveljic D, Visser J, et al. Physiological synaptic activity and recognition memory require astroglial glutamine. Nature Communications. 2022;13. doi:10.1038/s41467-022-28331-7"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","publication_status":"published","status":"public","department":[{"_id":"SiHi"}],"year":"2022","publication":"Nature Communications","intvolume":" 13","publisher":"Springer Nature","author":[{"full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","first_name":"Giselle T"},{"full_name":"Bataveljic, Danijela","last_name":"Bataveljic","first_name":"Danijela"},{"first_name":"Josien","last_name":"Visser","full_name":"Visser, Josien"},{"first_name":"Naresh","full_name":"Kumar, Naresh","last_name":"Kumar"},{"first_name":"Julien","full_name":"Moulard, Julien","last_name":"Moulard"},{"last_name":"Dallérac","full_name":"Dallérac, Glenn","first_name":"Glenn"},{"first_name":"Daria","full_name":"Mozheiko, Daria","last_name":"Mozheiko"},{"full_name":"Rollenhagen, Astrid","last_name":"Rollenhagen","first_name":"Astrid"},{"first_name":"Pascal","last_name":"Ezan","full_name":"Ezan, Pascal"},{"first_name":"Cédric","full_name":"Mongin, Cédric","last_name":"Mongin"},{"first_name":"Oana","last_name":"Chever","full_name":"Chever, Oana"},{"first_name":"Alexis Pierre","last_name":"Bemelmans","full_name":"Bemelmans, Alexis Pierre"},{"first_name":"Joachim","full_name":"Lübke, Joachim","last_name":"Lübke"},{"last_name":"Leray","full_name":"Leray, Isabelle","first_name":"Isabelle"},{"first_name":"Nathalie","last_name":"Rouach","full_name":"Rouach, Nathalie"}],"type":"journal_article","scopus_import":"1","volume":13,"has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"We thank D. Mazaud and. J. Cazères for technical assistance. This work was supported by grants from the European Research Council (Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD) to N.R. and from FP7-PEOPLE Marie Curie Intra-European Fellowship for career development (grant #622289) to G.C.","pmid":1,"ddc":["570"],"article_number":"753","publication_identifier":{"eissn":["20411723"]},"_id":"10764","day":"08","date_updated":"2023-08-02T14:25:01Z","date_published":"2022-02-08T00:00:00Z","external_id":{"isi":["000757297200017"],"pmid":["35136061"]},"language":[{"iso":"eng"}],"month":"02","isi":1},{"day":"08","date_updated":"2023-08-02T14:25:33Z","external_id":{"isi":["000757297200008"],"pmid":["35136046"]},"date_published":"2022-02-08T00:00:00Z","language":[{"iso":"eng"}],"month":"02","isi":1,"author":[{"first_name":"Beatriz","full_name":"Herguedas, Beatriz","last_name":"Herguedas"},{"full_name":"Kohegyi, Bianka K.","last_name":"Kohegyi","first_name":"Bianka K."},{"first_name":"Jan Niklas","full_name":"Dohrke, Jan Niklas","last_name":"Dohrke"},{"orcid":"0000-0002-8698-3823","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake","last_name":"Watson"},{"first_name":"Danyang","last_name":"Zhang","full_name":"Zhang, Danyang"},{"first_name":"Hinze","last_name":"Ho","full_name":"Ho, Hinze"},{"first_name":"Saher A.","full_name":"Shaikh, Saher A.","last_name":"Shaikh"},{"last_name":"Lape","full_name":"Lape, Remigijus","first_name":"Remigijus"},{"first_name":"James M.","full_name":"Krieger, James M.","last_name":"Krieger"},{"last_name":"Greger","full_name":"Greger, Ingo H.","first_name":"Ingo H."}],"publisher":"Springer Nature","scopus_import":"1","type":"journal_article","has_accepted_license":"1","volume":13,"quality_controlled":"1","pmid":1,"acknowledgement":"We thank Ondrej Cais for critical reading of the manuscript. We are grateful to LMB\r\nscientific computing and the EM facility for support, Paul Emsley for help with model\r\nbuilding and Takanori Nakane for helpful comments with Relion 3.1. This work was\r\nsupported by grants from the Medical Research Council (MC_U105174197) and BBSRC\r\n(BB/N002113/1) to I.H.G, and grants from the MCIN/AEI/ 10.13039/501100011033 and\r\n“ESF Investing in your future” to B.H (PID2019-106284GA-I00 and RYC2018-025720-I).","article_processing_charge":"No","ddc":["570"],"article_number":"734","_id":"10763","publication_identifier":{"eissn":["20411723"]},"publication_status":"published","department":[{"_id":"PeJo"}],"status":"public","year":"2022","publication":"Nature Communications","intvolume":" 13","oa":1,"article_type":"original","file":[{"content_type":"application/pdf","date_updated":"2022-02-21T07:59:32Z","success":1,"file_name":"2022_NatureCommunications_Herguedas.pdf","access_level":"open_access","creator":"dernst","file_size":2625540,"date_created":"2022-02-21T07:59:32Z","relation":"main_file","checksum":"d86ee8eabe8b794730729ffbb1a8832e","file_id":"10778"}],"file_date_updated":"2022-02-21T07:59:32Z","doi":"10.1038/s41467-022-28404-7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory\r\nsynapses in the brain. Glutamate binding to the receptor’s ligand-binding domains (LBDs)\r\nleads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission\r\nand are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs)\r\nthrough currently incompletely resolved mechanisms. Here, electron cryo-microscopy\r\nstructures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states\r\n(at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop (‘β1’),\r\nelucidating how this TARP stabilizes specific gating states. We further show how TARPs alter\r\nchannel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we\r\nreveal that the Q/R-editing site couples the channel constriction at the filter entrance to the\r\ngate, and forms the major cation binding site in the conduction path. Our results provide a\r\nmechanistic framework of how TARPs modulate AMPAR gating and conductance.","lang":"eng"}],"date_created":"2022-02-20T23:01:30Z","title":"Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor","citation":{"ama":"Herguedas B, Kohegyi BK, Dohrke JN, et al. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nature Communications. 2022;13. doi:10.1038/s41467-022-28404-7","short":"B. Herguedas, B.K. Kohegyi, J.N. Dohrke, J. Watson, D. Zhang, H. Ho, S.A. Shaikh, R. Lape, J.M. Krieger, I.H. Greger, Nature Communications 13 (2022).","mla":"Herguedas, Beatriz, et al. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8 AMPA Receptor.” Nature Communications, vol. 13, 734, Springer Nature, 2022, doi:10.1038/s41467-022-28404-7.","ista":"Herguedas B, Kohegyi BK, Dohrke JN, Watson J, Zhang D, Ho H, Shaikh SA, Lape R, Krieger JM, Greger IH. 2022. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nature Communications. 13, 734.","chicago":"Herguedas, Beatriz, Bianka K. Kohegyi, Jan Niklas Dohrke, Jake Watson, Danyang Zhang, Hinze Ho, Saher A. Shaikh, Remigijus Lape, James M. Krieger, and Ingo H. Greger. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8 AMPA Receptor.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-28404-7.","ieee":"B. Herguedas et al., “Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor,” Nature Communications, vol. 13. Springer Nature, 2022.","apa":"Herguedas, B., Kohegyi, B. K., Dohrke, J. N., Watson, J., Zhang, D., Ho, H., … Greger, I. H. (2022). Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-28404-7"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"}},{"author":[{"full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","orcid":"0000-0001-6264-2162","first_name":"Rishabh"},{"first_name":"William J","full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease"},{"last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","orcid":"0000-0001-6249-5860"},{"first_name":"Georg M","full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold"},{"full_name":"Qiu, Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","orcid":"0000-0003-4345-4267","first_name":"Liu"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"publisher":"Springer Nature","scopus_import":"1","type":"journal_article","volume":13,"has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"The authors thank S. Wald and F. Diorico for their help with optical filtering, O. Hosten\r\nand M. Aspelmeyer for equipment, H.G.L. Schwefel for materials and discussions, L.\r\nDrmic and P. Zielinski for software support, and the MIBA workshop at IST Austria for\r\nmachining the microwave cavity. This work was supported by the European Research\r\nCouncil under grant agreement no. 758053 (ERC StG QUNNECT) and the European\r\nUnion’s Horizon 2020 research and innovation program under grant agreement no.\r\n899354 (FETopen SuperQuLAN). W.H. is the recipient of an ISTplus postdoctoral fellowship\r\nwith funding from the European Union’s Horizon 2020 research and innovation\r\nprogram under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the\r\nrecipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F.\r\nacknowledges support from the Austrian Science Fund (FWF) through BeyondC (F7105)\r\nand the European Union’s Horizon 2020 research and innovation programs under grant\r\nagreement no. 862644 (FETopen QUARTET).","ddc":["530"],"article_number":"1276","_id":"10924","publication_identifier":{"eissn":["20411723"]},"day":"11","date_updated":"2023-08-03T06:21:11Z","external_id":{"arxiv":["2107.08303"],"isi":["000767892300013"]},"date_published":"2022-03-11T00:00:00Z","language":[{"iso":"eng"}],"month":"03","isi":1,"oa":1,"article_type":"original","file":[{"checksum":"7c5176db7b8e2ed18a4e0c5aca70a72c","file_id":"10929","access_level":"open_access","file_name":"2022_NatureCommunications_Sahu.pdf","creator":"dernst","file_size":1167492,"date_created":"2022-03-28T08:02:12Z","relation":"main_file","date_updated":"2022-03-28T08:02:12Z","success":1,"content_type":"application/pdf"}],"project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Integrating superconducting quantum circuits","grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862644","name":"Quantum readout techniques and technologies"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"file_date_updated":"2022-03-28T08:02:12Z","doi":"10.1038/s41467-022-28924-2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Solid-state microwave systems offer strong interactions for fast quantum logic and sensing but photons at telecom wavelength are the ideal choice for high-density low-loss quantum interconnects. A general-purpose interface that can make use of single photon effects requires < 1 input noise quanta, which has remained elusive due to either low efficiency or pump induced heating. Here we demonstrate coherent electro-optic modulation on nanosecond-timescales with only 0.16+0.02−0.01 microwave input noise photons with a total bidirectional transduction efficiency of 8.7% (or up to 15% with 0.41+0.02−0.02), as required for near-term heralded quantum network protocols. The use of short and high-power optical pump pulses also enables near-unity cooperativity of the electro-optic interaction leading to an internal pure conversion efficiency of up to 99.5%. Together with the low mode occupancy this provides evidence for electro-optic laser cooling and vacuum amplification as predicted a decade ago."}],"title":"Quantum-enabled operation of a microwave-optical interface","date_created":"2022-03-27T22:01:45Z","citation":{"ama":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. Quantum-enabled operation of a microwave-optical interface. Nature Communications. 2022;13. doi:10.1038/s41467-022-28924-2","mla":"Sahu, Rishabh, et al. “Quantum-Enabled Operation of a Microwave-Optical Interface.” Nature Communications, vol. 13, 1276, Springer Nature, 2022, doi:10.1038/s41467-022-28924-2.","short":"R. Sahu, W.J. Hease, A.R. Rueda Sanchez, G.M. Arnold, L. Qiu, J.M. Fink, Nature Communications 13 (2022).","ista":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. 2022. Quantum-enabled operation of a microwave-optical interface. Nature Communications. 13, 1276.","chicago":"Sahu, Rishabh, William J Hease, Alfredo R Rueda Sanchez, Georg M Arnold, Liu Qiu, and Johannes M Fink. “Quantum-Enabled Operation of a Microwave-Optical Interface.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-28924-2.","apa":"Sahu, R., Hease, W. J., Rueda Sanchez, A. R., Arnold, G. M., Qiu, L., & Fink, J. M. (2022). Quantum-enabled operation of a microwave-optical interface. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-28924-2","ieee":"R. Sahu, W. J. Hease, A. R. Rueda Sanchez, G. M. Arnold, L. Qiu, and J. M. Fink, “Quantum-enabled operation of a microwave-optical interface,” Nature Communications, vol. 13. Springer Nature, 2022."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"status":"public","id":"12900","relation":"dissertation_contains"},{"status":"public","id":"13175","relation":"dissertation_contains"}]},"ec_funded":1,"publication_status":"published","status":"public","department":[{"_id":"JoFi"}],"year":"2022","publication":"Nature Communications","intvolume":" 13"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"While recent advancements in computation and modelling have improved the analysis of complex traits, our understanding of the genetic basis of the time at symptom onset remains limited. Here, we develop a Bayesian approach (BayesW) that provides probabilistic inference of the genetic architecture of age-at-onset phenotypes in a sampling scheme that facilitates biobank-scale time-to-event analyses. We show in extensive simulation work the benefits BayesW provides in terms of number of discoveries, model performance and genomic prediction. In the UK Biobank, we find many thousands of common genomic regions underlying the age-at-onset of high blood pressure (HBP), cardiac disease (CAD), and type-2 diabetes (T2D), and for the genetic basis of onset reflecting the underlying genetic liability to disease. Age-at-menopause and age-at-menarche are also highly polygenic, but with higher variance contributed by low frequency variants. Genomic prediction into the Estonian Biobank data shows that BayesW gives higher prediction accuracy than other approaches.","lang":"eng"}],"file_date_updated":"2021-05-04T15:07:50Z","doi":"10.1038/s41467-021-22538-w","project":[{"name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"file":[{"file_id":"9372","checksum":"eca8b9ae713835c5b785211dd08d8a2e","relation":"main_file","file_size":6474239,"date_created":"2021-05-04T15:07:50Z","creator":"kschuh","access_level":"open_access","file_name":"2021_nature_communications_Ojavee.pdf","success":1,"date_updated":"2021-05-04T15:07:50Z","content_type":"application/pdf"}],"oa":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/predicting-the-onset-of-diseases/","relation":"press_release","description":"News on IST Homepage"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"mla":"Ojavee, Sven E., et al. “Genomic Architecture and Prediction of Censored Time-to-Event Phenotypes with a Bayesian Genome-Wide Analysis.” Nature Communications, vol. 12, no. 1, 2337, Nature Research, 2021, doi:10.1038/s41467-021-22538-w.","short":"S.E. Ojavee, A. Kousathanas, D. Trejo Banos, E.J. Orliac, M. Patxot, K. Lall, R. Magi, K. Fischer, Z. Kutalik, M.R. Robinson, Nature Communications 12 (2021).","ama":"Ojavee SE, Kousathanas A, Trejo Banos D, et al. Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-22538-w","apa":"Ojavee, S. E., Kousathanas, A., Trejo Banos, D., Orliac, E. J., Patxot, M., Lall, K., … Robinson, M. R. (2021). Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-22538-w","ieee":"S. E. Ojavee et al., “Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis,” Nature Communications, vol. 12, no. 1. Nature Research, 2021.","ista":"Ojavee SE, Kousathanas A, Trejo Banos D, Orliac EJ, Patxot M, Lall K, Magi R, Fischer K, Kutalik Z, Robinson MR. 2021. Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis. Nature Communications. 12(1), 2337.","chicago":"Ojavee, Sven E, Athanasios Kousathanas, Daniel Trejo Banos, Etienne J Orliac, Marion Patxot, Kristi Lall, Reedik Magi, Krista Fischer, Zoltan Kutalik, and Matthew Richard Robinson. “Genomic Architecture and Prediction of Censored Time-to-Event Phenotypes with a Bayesian Genome-Wide Analysis.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-22538-w."},"title":"Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis","date_created":"2020-09-17T10:53:00Z","year":"2021","department":[{"_id":"MaRo"}],"status":"public","publication_status":"published","intvolume":" 12","publication":"Nature Communications","issue":"1","has_accepted_license":"1","volume":12,"type":"journal_article","scopus_import":"1","publisher":"Nature Research","author":[{"full_name":"Ojavee, Sven E","last_name":"Ojavee","first_name":"Sven E"},{"first_name":"Athanasios","last_name":"Kousathanas","full_name":"Kousathanas, Athanasios"},{"last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel","first_name":"Daniel"},{"last_name":"Orliac","full_name":"Orliac, Etienne J","first_name":"Etienne J"},{"first_name":"Marion","full_name":"Patxot, Marion","last_name":"Patxot"},{"first_name":"Kristi","last_name":"Lall","full_name":"Lall, Kristi"},{"last_name":"Magi","full_name":"Magi, Reedik","first_name":"Reedik"},{"last_name":"Fischer","full_name":"Fischer, Krista","first_name":"Krista"},{"first_name":"Zoltan","full_name":"Kutalik, Zoltan","last_name":"Kutalik"},{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"publication_identifier":{"eissn":["20411723"]},"_id":"8430","ddc":["570"],"article_number":"2337","acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria and the University of Lausanne; the work of KF was supported by the grant PUT1665 by the Estonian Research Council. We would like to thank Mike Goddard for comments which greatly improved the work, the participants of the cohort studies, and the Ecole Polytechnique Federal Lausanne (EPFL) SCITAS for their excellent compute resources, their generosity with their time and the kindness of their support.","article_processing_charge":"No","quality_controlled":"1","date_updated":"2023-08-04T11:00:17Z","day":"20","isi":1,"month":"04","language":[{"iso":"eng"}],"date_published":"2021-04-20T00:00:00Z","external_id":{"isi":["000642509600006"]}},{"_id":"9254","publication_identifier":{"eissn":["20411723"]},"article_number":"1657","ddc":["580"],"pmid":1,"acknowledgement":"This work was supported by grants from the Israel Science Foundation (2378/19 to E.S.), the Joint NSFC-ISF Research Grant (3419/20 to E.S. and Z.D.), the Human Frontier Science Program (HFSP—LIY000540/2020 to E.S.), the European Research Council Starting Grant (757683- RobustHormoneTrans to E.S.), PBC postdoctoral fellowships (to Y.H. and M.O.), NIH (GM114660 to Y.Z.), Breast Cancer Research Foundation (BCRF to I.T.).","article_processing_charge":"No","quality_controlled":"1","has_accepted_license":"1","volume":12,"scopus_import":"1","type":"journal_article","author":[{"full_name":"Hu, Yangjie","last_name":"Hu","first_name":"Yangjie"},{"last_name":"Omary","full_name":"Omary, Moutasem","first_name":"Moutasem"},{"last_name":"Hu","full_name":"Hu, Yun","first_name":"Yun"},{"full_name":"Doron, Ohad","last_name":"Doron","first_name":"Ohad"},{"first_name":"Lukas","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer"},{"full_name":"Chen, Qingguo","last_name":"Chen","first_name":"Qingguo"},{"full_name":"Megides, Or","last_name":"Megides","first_name":"Or"},{"full_name":"Chekli, Ori","last_name":"Chekli","first_name":"Ori"},{"first_name":"Zhaojun","full_name":"Ding, Zhaojun","last_name":"Ding"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Zhao","full_name":"Zhao, Yunde","first_name":"Yunde"},{"first_name":"Ilan","last_name":"Tsarfaty","full_name":"Tsarfaty, Ilan"},{"last_name":"Shani","full_name":"Shani, Eilon","first_name":"Eilon"}],"publisher":"Springer Nature","isi":1,"month":"03","language":[{"iso":"eng"}],"external_id":{"pmid":["33712581"],"isi":["000630419400048"]},"date_published":"2021-03-12T00:00:00Z","date_updated":"2023-08-07T14:17:55Z","day":"12","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"short":"Y. Hu, M. Omary, Y. Hu, O. Doron, L. Hörmayer, Q. Chen, O. Megides, O. Chekli, Z. Ding, J. Friml, Y. Zhao, I. Tsarfaty, E. Shani, Nature Communications 12 (2021).","mla":"Hu, Yangjie, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” Nature Communications, vol. 12, 1657, Springer Nature, 2021, doi:10.1038/s41467-021-21802-3.","ama":"Hu Y, Omary M, Hu Y, et al. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 2021;12. doi:10.1038/s41467-021-21802-3","ieee":"Y. Hu et al., “Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing,” Nature Communications, vol. 12. Springer Nature, 2021.","apa":"Hu, Y., Omary, M., Hu, Y., Doron, O., Hörmayer, L., Chen, Q., … Shani, E. (2021). Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-21802-3","ista":"Hu Y, Omary M, Hu Y, Doron O, Hörmayer L, Chen Q, Megides O, Chekli O, Ding Z, Friml J, Zhao Y, Tsarfaty I, Shani E. 2021. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 12, 1657.","chicago":"Hu, Yangjie, Moutasem Omary, Yun Hu, Ohad Doron, Lukas Hörmayer, Qingguo Chen, Or Megides, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-21802-3."},"date_created":"2021-03-21T23:01:19Z","title":"Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing","doi":"10.1038/s41467-021-21802-3","file_date_updated":"2021-03-22T11:18:58Z","abstract":[{"text":"Auxin is a key regulator of plant growth and development. Local auxin biosynthesis and intercellular transport generates regional gradients in the root that are instructive for processes such as specification of developmental zones that maintain root growth and tropic responses. Here we present a toolbox to study auxin-mediated root development that features: (i) the ability to control auxin synthesis with high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic analysis infrastructure. Integration of these two features enables cutting-edge analysis of root development at single-cell resolution based on morphokinetic parameters under normal growth conditions and during cell-type-specific induction of auxin biosynthesis. We show directional auxin flow in the root and refine the contributions of key players in this process. In addition, we determine the quantitative kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic insights into root development, the tools developed here will enable biologists to study kinetics and morphology of various critical processes at the single cell-level in whole organisms.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"9275","checksum":"e1022f3aee349853ded2b2b3e092362d","relation":"main_file","file_size":8602096,"date_created":"2021-03-22T11:18:58Z","creator":"dernst","access_level":"open_access","file_name":"2021_NatureComm_Hu.pdf","success":1,"date_updated":"2021-03-22T11:18:58Z","content_type":"application/pdf"}],"article_type":"original","oa":1,"intvolume":" 12","publication":"Nature Communications","year":"2021","department":[{"_id":"JiFr"}],"status":"public","publication_status":"published"},{"status":"public","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2021","issue":"1","intvolume":" 12","publication":"Nature Communications","oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"High impact epidemics constitute one of the largest threats humanity is facing in the 21st century. In the absence of pharmaceutical interventions, physical distancing together with testing, contact tracing and quarantining are crucial in slowing down epidemic dynamics. Yet, here we show that if testing capacities are limited, containment may fail dramatically because such combined countermeasures drastically change the rules of the epidemic transition: Instead of continuous, the response to countermeasures becomes discontinuous. Rather than following the conventional exponential growth, the outbreak that is initially strongly suppressed eventually accelerates and scales faster than exponential during an explosive growth period. As a consequence, containment measures either suffice to stop the outbreak at low total case numbers or fail catastrophically if marginally too weak, thus implying large uncertainties in reliably estimating overall epidemic dynamics, both during initial phases and during second wave scenarios."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-05-25T14:18:40Z","doi":"10.1038/s41467-021-22725-9","file":[{"relation":"main_file","date_created":"2021-05-25T14:18:40Z","file_size":1176573,"creator":"kschuh","file_name":"2021_NatureCommunications_Scarselli.pdf","access_level":"open_access","file_id":"9426","checksum":"fe26c1b8a7da1ae07a6c03f80ff06ea1","content_type":"application/pdf","success":1,"date_updated":"2021-05-25T14:18:40Z"}],"citation":{"mla":"Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications, vol. 12, no. 1, 2586, Springer Nature, 2021, doi:10.1038/s41467-021-22725-9.","short":"D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021).","ama":"Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition due to limited testing. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-22725-9","apa":"Scarselli, D., Budanur, N. B., Timme, M., & Hof, B. (2021). Discontinuous epidemic transition due to limited testing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-22725-9","ieee":"D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic transition due to limited testing,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ista":"Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition due to limited testing. Nature Communications. 12(1), 2586.","chicago":"Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-22725-9."},"date_created":"2021-05-23T22:01:42Z","title":"Discontinuous epidemic transition due to limited testing","related_material":{"link":[{"url":"https://ist.ac.at/en/news/smashing-the-covid-curve/","relation":"press_release","description":"News on IST Homepage"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","day":"10","date_updated":"2023-08-08T13:45:13Z","language":[{"iso":"eng"}],"date_published":"2021-05-10T00:00:00Z","external_id":{"isi":["000687305500044"]},"isi":1,"month":"05","publisher":"Springer Nature","author":[{"orcid":"0000-0001-5227-4271","first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","full_name":"Scarselli, Davide","last_name":"Scarselli"},{"first_name":"Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B"},{"full_name":"Timme, Marc","last_name":"Timme","first_name":"Marc"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn"}],"volume":12,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","article_processing_charge":"No","acknowledgement":"The authors thank Malte Schröder for valuable discussions and creating the scale-free network topologies. B.H. thanks Mukund Vasudevan for helpful discussion. The research by M.T. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy–EXC-2068–390729961–Cluster of Excellence Physics of Life of TU Dresden.","quality_controlled":"1","publication_identifier":{"eissn":["20411723"]},"_id":"9407","article_number":"2586","ddc":["570"]},{"article_type":"original","oa":1,"file":[{"file_id":"9608","checksum":"75dd89d09945185b2d14b2434a0bcb50","date_created":"2021-06-28T08:04:22Z","file_size":2156554,"relation":"main_file","file_name":"2021_NatureCommunications_Santini.pdf","access_level":"open_access","creator":"asandaue","date_updated":"2021-06-28T08:04:22Z","success":1,"content_type":"application/pdf"}],"abstract":[{"text":"In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-021-23510-4","file_date_updated":"2021-06-28T08:04:22Z","title":"Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3","date_created":"2021-06-27T22:01:46Z","citation":{"mla":"Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications, vol. 12, no. 1, 3804, Springer Nature, 2021, doi:10.1038/s41467-021-23510-4.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma, J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021).","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23510-4","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma, X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23510-4","ieee":"L. Santini et al., “Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 12(1), 3804.","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23510-4."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","publication_status":"published","status":"public","department":[{"_id":"SiHi"}],"year":"2021","issue":"1","publication":"Nature Communications","intvolume":" 12","publisher":"Springer Nature","author":[{"first_name":"Laura","full_name":"Santini, Laura","last_name":"Santini"},{"first_name":"Florian","last_name":"Halbritter","full_name":"Halbritter, Florian"},{"first_name":"Fabian","last_name":"Titz-Teixeira","full_name":"Titz-Teixeira, Fabian"},{"full_name":"Suzuki, Toru","last_name":"Suzuki","first_name":"Toru"},{"first_name":"Maki","last_name":"Asami","full_name":"Asami, Maki"},{"full_name":"Ma, Xiaoyan","last_name":"Ma","first_name":"Xiaoyan"},{"full_name":"Ramesmayer, Julia","last_name":"Ramesmayer","first_name":"Julia"},{"last_name":"Lackner","full_name":"Lackner, Andreas","first_name":"Andreas"},{"first_name":"Nick","last_name":"Warr","full_name":"Warr, Nick"},{"last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","first_name":"Florian","orcid":"0000-0002-7462-0048"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"last_name":"Laue","full_name":"Laue, Ernest","first_name":"Ernest"},{"last_name":"Farlik","full_name":"Farlik, Matthias","first_name":"Matthias"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"first_name":"Andreas","full_name":"Beyer, Andreas","last_name":"Beyer"},{"first_name":"Anthony C.F.","full_name":"Perry, Anthony C.F.","last_name":"Perry"},{"first_name":"Martin","full_name":"Leeb, Martin","last_name":"Leeb"}],"scopus_import":"1","type":"journal_article","volume":12,"has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"The authors thank Robert Feil and Anton Wutz for helpful discussions and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates, and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF) for support with next-generation sequencing. We are grateful to animal care teams at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship. M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006) by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund FWF (I3786 and P31334).","ddc":["570"],"article_number":"3804","publication_identifier":{"eissn":["20411723"]},"_id":"9601","day":"12","date_updated":"2023-08-10T13:53:23Z","date_published":"2021-07-12T00:00:00Z","external_id":{"isi":["000667248600005"]},"language":[{"iso":"eng"}],"month":"07","isi":1},{"date_published":"2021-06-29T00:00:00Z","external_id":{"isi":["000671752100003"],"pmid":["34188036"]},"language":[{"iso":"eng"}],"month":"06","isi":1,"day":"29","date_updated":"2023-08-10T14:05:09Z","quality_controlled":"1","article_processing_charge":"No","acknowledgement":"K.C. acknowledges support from ERC Start grant no. (279307: Graph Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF) grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","pmid":1,"ddc":["510"],"article_number":"4009","publication_identifier":{"eissn":["20411723"]},"_id":"9640","publisher":"Springer Nature","author":[{"full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","orcid":"0000-0002-1097-9684","first_name":"Josef"},{"orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"scopus_import":"1","type":"journal_article","has_accepted_license":"1","volume":12,"issue":"1","publication":"Nature Communications","intvolume":" 12","publication_status":"published","department":[{"_id":"KrCh"}],"status":"public","year":"2021","title":"Fast and strong amplifiers of natural selection","date_created":"2021-07-11T22:01:15Z","citation":{"ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009.","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-24271-w.","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-24271-w","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-24271-w","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021).","mla":"Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:10.1038/s41467-021-24271-w."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"oa":1,"article_type":"original","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"file":[{"creator":"cziletti","file_name":"2021_NatCoom_Tkadlec.pdf","access_level":"open_access","relation":"main_file","file_size":628992,"date_created":"2021-07-19T13:02:20Z","checksum":"5767418926a7f7fb76151de29473dae0","file_id":"9692","content_type":"application/pdf","success":1,"date_updated":"2021-07-19T13:02:20Z"}],"abstract":[{"lang":"eng","text":"Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-07-19T13:02:20Z","doi":"10.1038/s41467-021-24271-w"},{"citation":{"ama":"Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26234-7","short":"S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah, M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez, M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021).","mla":"Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:10.1038/s41467-021-26234-7.","chicago":"Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma, Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26234-7.","ista":"Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 12(1), 6094.","apa":"Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S., … Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26234-7","ieee":"S. J. Pradhan et al., “Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021."},"date_created":"2021-10-31T23:01:29Z","title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","related_material":{"link":[{"url":"https://doi.org/10.1101/2020.11.23.394171 ","description":"Preprint","relation":"earlier_version"}]},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"article_type":"original","oa":1,"doi":"10.1038/s41467-021-26234-7","file_date_updated":"2021-11-09T13:59:26Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant."}],"file":[{"content_type":"application/pdf","success":1,"date_updated":"2021-11-09T13:59:26Z","creator":"cziletti","access_level":"open_access","file_name":"2021_NatureComm_Pradhan.pdf","relation":"main_file","file_size":7144437,"date_created":"2021-11-09T13:59:26Z","checksum":"c40a69ae94435ecd3a30c9874a11ef2b","file_id":"10262"}],"issue":"1","intvolume":" 12","publication":"Nature Communications","department":[{"_id":"CaHe"}],"status":"public","publication_status":"published","year":"2021","pmid":1,"article_processing_charge":"Yes","acknowledgement":"We are grateful to the members of C.-P.H. and SG lab for discussions. Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10: GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments. We would also like to thank Chaitanya Dingare for valuable suggestions. We thank Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the manuscript. This work was supported by the Centre of Excellence in Epigenetics program of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07) to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship (JCB/2019/000013) from Science and Engineering Research Board, Government of India to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The work using animal models was partly supported by the infrastructure support grants from the Department of Biotechnology (National Facility for Laboratory Model Organisms: BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015). S.J.P. was supported by Fellowship from the Council of Scientific and Industrial Research, India and travel fellowship from the Company of Biologists, UK. P.C.R. was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance (IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India. M.S. was supported by core funding from the Tata Institute of Fundamental Research (TIFR 12P-121).","quality_controlled":"1","_id":"10202","publication_identifier":{"eissn":["20411723"]},"ddc":["570"],"article_number":"6094","author":[{"last_name":"Pradhan","full_name":"Pradhan, Saurabh J.","first_name":"Saurabh J."},{"first_name":"Puli Chandramouli","last_name":"Reddy","full_name":"Reddy, Puli Chandramouli"},{"last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","full_name":"Smutny, Michael","first_name":"Michael","orcid":"0000-0002-5920-9090"},{"first_name":"Ankita","full_name":"Sharma, Ankita","last_name":"Sharma"},{"first_name":"Keisuke","orcid":"0000-0002-6453-8075","last_name":"Sako","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","full_name":"Sako, Keisuke"},{"first_name":"Meghana S.","full_name":"Oak, Meghana S.","last_name":"Oak"},{"first_name":"Rini","full_name":"Shah, Rini","last_name":"Shah"},{"first_name":"Mrinmoy","last_name":"Pal","full_name":"Pal, Mrinmoy"},{"first_name":"Ojas","full_name":"Deshpande, Ojas","last_name":"Deshpande"},{"first_name":"Greg","full_name":"Dsilva, Greg","last_name":"Dsilva"},{"full_name":"Tang, Yin","last_name":"Tang","first_name":"Yin"},{"first_name":"Rakesh","full_name":"Mishra, Rakesh","last_name":"Mishra"},{"full_name":"Deshpande, Girish","last_name":"Deshpande","first_name":"Girish"},{"first_name":"Antonio J.","last_name":"Giraldez","full_name":"Giraldez, Antonio J."},{"full_name":"Sonawane, Mahendra","last_name":"Sonawane","first_name":"Mahendra"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"last_name":"Galande","full_name":"Galande, Sanjeev","first_name":"Sanjeev"}],"publisher":"Springer Nature","volume":12,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000709050300016"],"pmid":["34667153"]},"date_published":"2021-10-19T00:00:00Z","isi":1,"month":"10","day":"19","date_updated":"2023-08-14T10:32:48Z"},{"citation":{"chicago":"Turoňová, Beata, Wim J.H. Hagen, Martin Obr, Shyamal Mosalaganti, J. Wouter Beugelink, Christian E. Zimmerli, Hans Georg Kräusslich, and Martin Beck. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-14535-2.","ista":"Turoňová B, Hagen WJH, Obr M, Mosalaganti S, Beugelink JW, Zimmerli CE, Kräusslich HG, Beck M. 2020. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 11, 876.","ieee":"B. Turoňová et al., “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Turoňová, B., Hagen, W. J. H., Obr, M., Mosalaganti, S., Beugelink, J. W., Zimmerli, C. E., … Beck, M. (2020). Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-14535-2","ama":"Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 2020;11. doi:10.1038/s41467-020-14535-2","mla":"Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” Nature Communications, vol. 11, 876, Springer Nature, 2020, doi:10.1038/s41467-020-14535-2.","short":"B. Turoňová, W.J.H. Hagen, M. Obr, S. Mosalaganti, J.W. Beugelink, C.E. Zimmerli, H.G. Kräusslich, M. Beck, Nature Communications 11 (2020)."},"date_created":"2020-02-23T23:00:35Z","title":"Benchmarking tomographic acquisition schemes for high-resolution structural biology","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","oa":1,"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:59Z","doi":"10.1038/s41467-020-14535-2","file":[{"file_id":"7517","checksum":"2c8d10475e1b0d397500760e28bdf561","relation":"main_file","date_created":"2020-02-24T14:00:54Z","file_size":2027529,"creator":"dernst","file_name":"2020_NatureComm_Turonova.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf"}],"intvolume":" 11","publication":"Nature Communications","status":"public","department":[{"_id":"FlSc"}],"publication_status":"published","year":"2020","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["20411723"]},"_id":"7511","article_number":"876","ddc":["570"],"publisher":"Springer Nature","author":[{"first_name":"Beata","full_name":"Turoňová, Beata","last_name":"Turoňová"},{"first_name":"Wim J.H.","last_name":"Hagen","full_name":"Hagen, Wim J.H."},{"orcid":"0000-0003-1756-6564","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","last_name":"Obr"},{"full_name":"Mosalaganti, Shyamal","last_name":"Mosalaganti","first_name":"Shyamal"},{"first_name":"J. Wouter","last_name":"Beugelink","full_name":"Beugelink, J. Wouter"},{"first_name":"Christian E.","full_name":"Zimmerli, Christian E.","last_name":"Zimmerli"},{"first_name":"Hans Georg","full_name":"Kräusslich, Hans Georg","last_name":"Kräusslich"},{"full_name":"Beck, Martin","last_name":"Beck","first_name":"Martin"}],"volume":11,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2020-02-13T00:00:00Z","external_id":{"isi":["000514928000017"]},"isi":1,"month":"02","day":"13","date_updated":"2023-08-18T06:36:41Z"},{"author":[{"first_name":"Andrej","orcid":"0000-0003-3638-1426","last_name":"Hurny","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Hurny, Andrej"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela","last_name":"Cuesta","orcid":"0000-0003-1923-2410","first_name":"Candela"},{"last_name":"Cavallari","full_name":"Cavallari, Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola"},{"orcid":"0000-0002-5503-4983","first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","full_name":"Ötvös, Krisztina","last_name":"Ötvös"},{"first_name":"Jerome","last_name":"Duclercq","full_name":"Duclercq, Jerome"},{"first_name":"Ladislav","last_name":"Dokládal","full_name":"Dokládal, Ladislav"},{"orcid":"0000-0001-9179-6099","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C","last_name":"Montesinos López"},{"orcid":"0000-0003-4675-6893","first_name":"Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal","last_name":"Gallemi"},{"first_name":"Hana","last_name":"Semeradova","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","full_name":"Semeradova, Hana"},{"id":"A0385D1A-9376-11EA-A47D-9862C5E3AB22","full_name":"Rauter, Thomas","last_name":"Rauter","first_name":"Thomas"},{"full_name":"Stenzel, Irene","last_name":"Stenzel","first_name":"Irene"},{"first_name":"Geert","last_name":"Persiau","full_name":"Persiau, Geert"},{"first_name":"Freia","full_name":"Benade, Freia","last_name":"Benade"},{"full_name":"Bhalearo, Rishikesh","last_name":"Bhalearo","first_name":"Rishikesh"},{"first_name":"Eva","last_name":"Sýkorová","full_name":"Sýkorová, Eva"},{"first_name":"András","full_name":"Gorzsás, András","last_name":"Gorzsás"},{"full_name":"Sechet, Julien","last_name":"Sechet","first_name":"Julien"},{"first_name":"Gregory","last_name":"Mouille","full_name":"Mouille, Gregory"},{"first_name":"Ingo","full_name":"Heilmann, Ingo","last_name":"Heilmann"},{"first_name":"Geert","last_name":"De Jaeger","full_name":"De Jaeger, Geert"},{"first_name":"Jutta","full_name":"Ludwig-Müller, Jutta","last_name":"Ludwig-Müller"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","scopus_import":"1","type":"journal_article","volume":11,"has_accepted_license":"1","quality_controlled":"1","pmid":1,"acknowledgement":"We thank Daria Siekhaus, Jiri Friml and Alexander Johnson for critical reading of the manuscript, Peter Pimpl, Christian Luschnig and Liwen Jiang for sharing published material, Lesia Rodriguez Solovey for technical assistance. This work was supported by the Austrian Science Fund (FWF01_I1774S) to A.H., K.Ö., and E.B., the German Research Foundation (DFG; He3424/6-1 to I.H.), by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] (to N.C.), by the EU in the framework of the Marie-Curie FP7 COFUND People Programme through the award of an AgreenSkills+ fellowship No. 609398 (to J.S.) and by the Scientific Service Units of IST-Austria through resources provided by the Bioimaging Facility, the Life Science Facility. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","article_processing_charge":"No","ddc":["570"],"article_number":"2170","_id":"7805","publication_identifier":{"eissn":["20411723"]},"day":"01","date_updated":"2023-08-21T06:21:56Z","external_id":{"pmid":["32358503"],"isi":["000531425900012"]},"date_published":"2020-05-01T00:00:00Z","language":[{"iso":"eng"}],"month":"05","isi":1,"article_type":"original","oa":1,"file":[{"content_type":"application/pdf","success":1,"date_updated":"2020-10-06T07:47:53Z","creator":"dernst","file_name":"2020_NatureComm_Hurny.pdf","access_level":"open_access","relation":"main_file","date_created":"2020-10-06T07:47:53Z","file_size":4743576,"checksum":"2cba327c9e9416d75cb96be54b0fb441","file_id":"8614"}],"project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"file_date_updated":"2020-10-06T07:47:53Z","doi":"10.1038/s41467-020-15895-5","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance","date_created":"2020-05-10T22:00:48Z","citation":{"ieee":"A. Hurny et al., “Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Hurny, A., Cuesta, C., Cavallari, N., Ötvös, K., Duclercq, J., Dokládal, L., … Benková, E. (2020). Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-15895-5","chicago":"Hurny, Andrej, Candela Cuesta, Nicola Cavallari, Krisztina Ötvös, Jerome Duclercq, Ladislav Dokládal, Juan C Montesinos López, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15895-5.","ista":"Hurny A, Cuesta C, Cavallari N, Ötvös K, Duclercq J, Dokládal L, Montesinos López JC, Gallemi M, Semerádová H, Rauter T, Stenzel I, Persiau G, Benade F, Bhalearo R, Sýkorová E, Gorzsás A, Sechet J, Mouille G, Heilmann I, De Jaeger G, Ludwig-Müller J, Benková E. 2020. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 11, 2170.","mla":"Hurny, Andrej, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” Nature Communications, vol. 11, 2170, Springer Nature, 2020, doi:10.1038/s41467-020-15895-5.","short":"A. Hurny, C. Cuesta, N. Cavallari, K. Ötvös, J. Duclercq, L. Dokládal, J.C. Montesinos López, M. Gallemi, H. Semerádová, T. Rauter, I. Stenzel, G. Persiau, F. Benade, R. Bhalearo, E. Sýkorová, A. Gorzsás, J. Sechet, G. Mouille, I. Heilmann, G. De Jaeger, J. Ludwig-Müller, E. Benková, Nature Communications 11 (2020).","ama":"Hurny A, Cuesta C, Cavallari N, et al. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 2020;11. doi:10.1038/s41467-020-15895-5"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1,"publication_status":"published","status":"public","department":[{"_id":"EvBe"}],"year":"2020","publication":"Nature Communications","intvolume":" 11"},{"ddc":["570"],"article_number":"2099","_id":"7804","publication_identifier":{"eissn":["20411723"]},"quality_controlled":"1","article_processing_charge":"No","scopus_import":"1","type":"journal_article","volume":11,"has_accepted_license":"1","author":[{"last_name":"Flynn","full_name":"Flynn, Sean M.","first_name":"Sean M."},{"full_name":"Chen, Changchun","last_name":"Chen","first_name":"Changchun"},{"orcid":"0000-0001-8945-6992","first_name":"Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","full_name":"Artan, Murat","last_name":"Artan"},{"last_name":"Barratt","full_name":"Barratt, Stephen","first_name":"Stephen"},{"full_name":"Crisp, Alastair","last_name":"Crisp","first_name":"Alastair"},{"first_name":"Geoffrey M.","full_name":"Nelson, Geoffrey M.","last_name":"Nelson"},{"first_name":"Sew Yeu","last_name":"Peak-Chew","full_name":"Peak-Chew, Sew Yeu"},{"last_name":"Begum","full_name":"Begum, Farida","first_name":"Farida"},{"full_name":"Skehel, Mark","last_name":"Skehel","first_name":"Mark"},{"orcid":"0000-0001-8347-0443","first_name":"Mario","full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono"}],"publisher":"Springer Nature","month":"04","isi":1,"external_id":{"isi":["000531855500029"]},"date_published":"2020-04-29T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2023-08-21T06:21:14Z","day":"29","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"title":"MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity","date_created":"2020-05-10T22:00:47Z","citation":{"mla":"Flynn, Sean M., et al. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” Nature Communications, vol. 11, 2099, Springer Nature, 2020, doi:10.1038/s41467-020-15872-y.","short":"S.M. Flynn, C. Chen, M. Artan, S. Barratt, A. Crisp, G.M. Nelson, S.Y. Peak-Chew, F. Begum, M. Skehel, M. de Bono, Nature Communications 11 (2020).","ama":"Flynn SM, Chen C, Artan M, et al. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 2020;11. doi:10.1038/s41467-020-15872-y","ieee":"S. M. Flynn et al., “MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Flynn, S. M., Chen, C., Artan, M., Barratt, S., Crisp, A., Nelson, G. M., … de Bono, M. (2020). MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-15872-y","ista":"Flynn SM, Chen C, Artan M, Barratt S, Crisp A, Nelson GM, Peak-Chew SY, Begum F, Skehel M, de Bono M. 2020. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 11, 2099.","chicago":"Flynn, Sean M., Changchun Chen, Murat Artan, Stephen Barratt, Alastair Crisp, Geoffrey M. Nelson, Sew Yeu Peak-Chew, Farida Begum, Mark Skehel, and Mario de Bono. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15872-y."},"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:48:03Z","file_name":"2020_NatureComm_Flynn.pdf","access_level":"open_access","creator":"dernst","date_created":"2020-05-11T10:36:33Z","file_size":4609120,"relation":"main_file","checksum":"dce367abf2c1a1d15f58fe6f7de82893","file_id":"7817"}],"file_date_updated":"2020-07-14T12:48:03Z","doi":"10.1038/s41467-020-15872-y","abstract":[{"lang":"eng","text":"Besides pro-inflammatory roles, the ancient cytokine interleukin-17 (IL-17) modulates neural circuit function. We investigate IL-17 signaling in neurons, and the extent it can alter organismal phenotypes. We combine immunoprecipitation and mass spectrometry to biochemically characterize endogenous signaling complexes that function downstream of IL-17 receptors in C. elegans neurons. We identify the paracaspase MALT-1 as a critical output of the pathway. MALT1 mediates signaling from many immune receptors in mammals, but was not previously implicated in IL-17 signaling or nervous system function. C. elegans MALT-1 forms a complex with homologs of Act1 and IRAK and appears to function both as a scaffold and a protease. MALT-1 is expressed broadly in the C. elegans nervous system, and neuronal IL-17–MALT-1 signaling regulates multiple phenotypes, including escape behavior, associative learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating neural circuit function downstream of IL-17 to remodel physiology and behavior."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","oa":1,"publication":"Nature Communications","intvolume":" 11","year":"2020","publication_status":"published","department":[{"_id":"MaDe"}],"status":"public"},{"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"chicago":"Lukacisinova, Marta, Booshini Fernando, and Mark Tobias Bollenbach. “Highly Parallel Lab Evolution Reveals That Epistasis Can Curb the Evolution of Antibiotic Resistance.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16932-z.","ista":"Lukacisinova M, Fernando B, Bollenbach MT. 2020. Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. 11, 3105.","ieee":"M. Lukacisinova, B. Fernando, and M. T. Bollenbach, “Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Lukacisinova, M., Fernando, B., & Bollenbach, M. T. (2020). Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16932-z","ama":"Lukacisinova M, Fernando B, Bollenbach MT. Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications. 2020;11. doi:10.1038/s41467-020-16932-z","short":"M. Lukacisinova, B. Fernando, M.T. Bollenbach, Nature Communications 11 (2020).","mla":"Lukacisinova, Marta, et al. “Highly Parallel Lab Evolution Reveals That Epistasis Can Curb the Evolution of Antibiotic Resistance.” Nature Communications, vol. 11, 3105, Springer Nature, 2020, doi:10.1038/s41467-020-16932-z."},"date_created":"2020-06-29T07:59:35Z","title":"Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance","file_date_updated":"2020-07-14T12:48:08Z","doi":"10.1038/s41467-020-16932-z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics."}],"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"}],"file":[{"date_updated":"2020-07-14T12:48:08Z","content_type":"application/pdf","file_id":"8071","checksum":"4f5f49d63add331d5eb8a2bae477b396","relation":"main_file","date_created":"2020-06-30T09:58:50Z","file_size":1546491,"creator":"cziletti","file_name":"2020_NatureComm_Lukacisinova.pdf","access_level":"open_access"}],"article_type":"original","oa":1,"intvolume":" 11","publication":"Nature Communications","year":"2020","status":"public","publication_status":"published","_id":"8037","publication_identifier":{"eissn":["20411723"]},"article_number":"3105","ddc":["570"],"pmid":1,"article_processing_charge":"No","quality_controlled":"1","volume":11,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","author":[{"orcid":"0000-0002-2519-8004","first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","last_name":"Lukacisinova"},{"first_name":"Booshini","last_name":"Fernando","full_name":"Fernando, Booshini"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"}],"publisher":"Springer Nature","isi":1,"month":"06","language":[{"iso":"eng"}],"external_id":{"pmid":["32561723"],"isi":["000545685100002"]},"date_published":"2020-06-19T00:00:00Z","extern":"1","date_updated":"2023-08-22T07:48:30Z","day":"19"},{"intvolume":" 11","publication":"Nature Communications","issue":"1","year":"2020","department":[{"_id":"LeSa"}],"status":"public","publication_status":"published","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/"}]},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:10.1038/s41467-020-17957-0.","ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17957-0","ieee":"J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer Nature, 2020.","apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17957-0","chicago":"Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0.","ista":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135."},"date_created":"2020-08-30T22:01:10Z","title":"Key role of quinone in the mechanism of respiratory complex I","doi":"10.1038/s41467-020-17957-0","file_date_updated":"2020-08-31T13:40:00Z","abstract":[{"lang":"eng","text":"Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_size":7527373,"date_created":"2020-08-31T13:40:00Z","creator":"cziletti","access_level":"open_access","file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","file_id":"8326","checksum":"52b96f41d7d0db9728064c08da00d030","content_type":"application/pdf","success":1,"date_updated":"2020-08-31T13:40:00Z"}],"article_type":"original","oa":1,"isi":1,"month":"08","language":[{"iso":"eng"}],"external_id":{"pmid":["32811817"],"isi":["000607072900001"]},"date_published":"2020-08-18T00:00:00Z","date_updated":"2023-08-22T09:03:00Z","day":"18","_id":"8318","publication_identifier":{"eissn":["20411723"]},"article_number":"4135","ddc":["570"],"pmid":1,"acknowledgement":"This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster.","article_processing_charge":"No","quality_controlled":"1","has_accepted_license":"1","volume":11,"scopus_import":"1","type":"journal_article","author":[{"first_name":"Javier","last_name":"Gutierrez-Fernandez","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","full_name":"Gutierrez-Fernandez, Javier"},{"last_name":"Kaszuba","full_name":"Kaszuba, Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","first_name":"Karol"},{"last_name":"Minhas","full_name":"Minhas, Gurdeep S.","first_name":"Gurdeep S."},{"last_name":"Baradaran","full_name":"Baradaran, Rozbeh","first_name":"Rozbeh"},{"last_name":"Tambalo","id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","full_name":"Tambalo, Margherita","first_name":"Margherita"},{"first_name":"David T.","full_name":"Gallagher, David T.","last_name":"Gallagher"},{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"publisher":"Springer Nature"},{"year":"2020","department":[{"_id":"EvBe"}],"status":"public","publication_status":"published","intvolume":" 11","publication":"Nature Communications","abstract":[{"text":"Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-020-17949-0","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2020-09-10T08:05:19Z","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis."},{"grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}],"file":[{"file_id":"8357","checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","file_size":3455704,"date_created":"2020-09-10T08:05:19Z","relation":"main_file","access_level":"open_access","file_name":"2020_NatureComm_Kubiasova.pdf","creator":"dernst","date_updated":"2020-09-10T08:05:19Z","success":1,"content_type":"application/pdf"}],"article_type":"original","oa":1,"ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"mla":"Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0.","short":"K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová, L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal, P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications 11 (2020).","ama":"Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0","apa":"Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V., Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0","ieee":"K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature Communications, vol. 11. Springer Nature, 2020.","ista":"Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 11, 4285.","chicago":"Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler, Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0."},"date_created":"2020-09-06T22:01:12Z","title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","date_updated":"2023-08-22T09:09:06Z","day":"27","isi":1,"month":"08","language":[{"iso":"eng"}],"date_published":"2020-08-27T00:00:00Z","external_id":{"pmid":["32855390"],"isi":["000567931000002"]},"volume":11,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","publisher":"Springer Nature","author":[{"last_name":"Kubiasova","full_name":"Kubiasova, Karolina","id":"946011F4-3E71-11EA-860B-C7A73DDC885E","first_name":"Karolina","orcid":"0000-0001-5630-9419"},{"first_name":"Juan C","orcid":"0000-0001-9179-6099","last_name":"Montesinos López","full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olga","last_name":"Šamajová","full_name":"Šamajová, Olga"},{"first_name":"Jaroslav","last_name":"Nisler","full_name":"Nisler, Jaroslav"},{"first_name":"Václav","full_name":"Mik, Václav","last_name":"Mik"},{"first_name":"Hana","full_name":"Semeradova, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semeradova"},{"first_name":"Lucie","full_name":"Plíhalová, Lucie","last_name":"Plíhalová"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"first_name":"Peter","orcid":"0000-0001-5227-5741","last_name":"Marhavý","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavý, Peter"},{"first_name":"Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola"},{"last_name":"Zalabák","full_name":"Zalabák, David","first_name":"David"},{"first_name":"Karel","full_name":"Berka, Karel","last_name":"Berka"},{"first_name":"Karel","full_name":"Doležal, Karel","last_name":"Doležal"},{"full_name":"Galuszka, Petr","last_name":"Galuszka","first_name":"Petr"},{"last_name":"Šamaj","full_name":"Šamaj, Jozef","first_name":"Jozef"},{"last_name":"Strnad","full_name":"Strnad, Miroslav","first_name":"Miroslav"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva"},{"first_name":"Ondřej","full_name":"Plíhal, Ondřej","last_name":"Plíhal"},{"first_name":"Lukáš","last_name":"Spíchal","full_name":"Spíchal, Lukáš"}],"publication_identifier":{"eissn":["20411723"]},"_id":"8336","ddc":["580"],"article_number":"4285","acknowledgement":"This paper is dedicated to deceased P. Galuszka for his support and contribution to the project. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material. The work was supported from ERDF project “Plants as a tool for sustainable global development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S (K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria (H.S.).","article_processing_charge":"No","pmid":1,"quality_controlled":"1"},{"oa":1,"article_type":"original","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"file":[{"creator":"dernst","file_name":"2020_NatureComm_Antoniadi.pdf","access_level":"open_access","relation":"main_file","file_size":3526415,"date_created":"2020-12-10T12:23:56Z","checksum":"5b96f39b598de7510cfefefb819b9a6d","file_id":"8936","content_type":"application/pdf","success":1,"date_updated":"2020-12-10T12:23:56Z"}],"abstract":[{"text":"Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-020-17700-9","acknowledged_ssus":[{"_id":"Bio"}],"file_date_updated":"2020-12-10T12:23:56Z","date_created":"2020-09-06T22:01:13Z","title":"Cell-surface receptors enable perception of extracellular cytokinins","citation":{"apa":"Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský, R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17700-9","ieee":"I. Antoniadi et al., “Cell-surface receptors enable perception of extracellular cytokinins,” Nature Communications, vol. 11. Springer Nature, 2020.","ista":"Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 11, 4284.","chicago":"Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17700-9.","short":"I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský, V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian, J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications 11 (2020).","mla":"Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications, vol. 11, 4284, Springer Nature, 2020, doi:10.1038/s41467-020-17700-9.","ama":"Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 2020;11. doi:10.1038/s41467-020-17700-9"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"publication_status":"published","department":[{"_id":"JiFr"}],"status":"public","year":"2020","publication":"Nature Communications","intvolume":" 11","publisher":"Springer Nature","author":[{"last_name":"Antoniadi","full_name":"Antoniadi, Ioanna","first_name":"Ioanna"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","full_name":"Gelová, Zuzana","last_name":"Gelová","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"first_name":"Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Plíhal","full_name":"Plíhal, Ondřej","first_name":"Ondřej"},{"first_name":"Radim","last_name":"Simerský","full_name":"Simerský, Radim"},{"full_name":"Mik, Václav","last_name":"Mik","first_name":"Václav"},{"first_name":"Thomas","full_name":"Vain, Thomas","last_name":"Vain"},{"first_name":"Eduardo","last_name":"Mateo-Bonmatí","full_name":"Mateo-Bonmatí, Eduardo"},{"first_name":"Michal","last_name":"Karady","full_name":"Karady, Michal"},{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"full_name":"Plačková, Lenka","last_name":"Plačková","first_name":"Lenka"},{"first_name":"Korawit","full_name":"Opassathian, Korawit","last_name":"Opassathian"},{"first_name":"Jan","full_name":"Hejátko, Jan","last_name":"Hejátko"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"last_name":"Doležal","full_name":"Doležal, Karel","first_name":"Karel"},{"first_name":"Karin","full_name":"Ljung, Karin","last_name":"Ljung"},{"first_name":"Colin","full_name":"Turnbull, Colin","last_name":"Turnbull"}],"scopus_import":"1","type":"journal_article","volume":11,"has_accepted_license":"1","quality_controlled":"1","acknowledgement":"We thank Bruno Müller and Aaron Rashotte for critical discussions and provision of plant lines used in this work, Roger Granbom and Tamara Hernández Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic) for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre and the IST Austria Bio-Imaging facility are acknowledged for support. The work was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.), Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.), the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811) (E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic via the European Regional Development Fund-Project “Plants as a tool for sustainable global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M., L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P., K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J. was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading to these results received funding from European Union’s Horizon 2020 programme (ERC grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.","article_processing_charge":"No","ddc":["580"],"article_number":"4284","publication_identifier":{"eissn":["20411723"]},"_id":"8337","day":"27","date_updated":"2023-08-22T09:10:32Z","date_published":"2020-08-27T00:00:00Z","external_id":{"isi":["000567931000001"]},"language":[{"iso":"eng"}],"month":"08","isi":1},{"date_updated":"2023-08-22T10:18:17Z","day":"07","month":"10","isi":1,"external_id":{"pmid":["33028844"],"isi":["000577244600003"]},"date_published":"2020-10-07T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","scopus_import":"1","volume":11,"has_accepted_license":"1","author":[{"first_name":"Magdalena K.","last_name":"Sznurkowska","full_name":"Sznurkowska, Magdalena K."},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Azzarelli","full_name":"Azzarelli, Roberta","first_name":"Roberta"},{"full_name":"Chatzeli, Lemonia","last_name":"Chatzeli","first_name":"Lemonia"},{"first_name":"Tatsuro","full_name":"Ikeda, Tatsuro","last_name":"Ikeda"},{"last_name":"Yoshida","full_name":"Yoshida, Shosei","first_name":"Shosei"},{"full_name":"Philpott, Anna","last_name":"Philpott","first_name":"Anna"},{"first_name":"Benjamin D","full_name":"Simons, Benjamin D","last_name":"Simons"}],"publisher":"Springer Nature","ddc":["570"],"article_number":"5037","_id":"8669","publication_identifier":{"eissn":["20411723"]},"quality_controlled":"1","pmid":1,"article_processing_charge":"No","year":"2020","publication_status":"published","status":"public","department":[{"_id":"EdHa"}],"publication":"Nature Communications","intvolume":" 11","file":[{"success":1,"date_updated":"2020-10-19T11:27:46Z","content_type":"application/pdf","file_id":"8677","checksum":"0ecc0eab72d2d50694852579611a6624","relation":"main_file","date_created":"2020-10-19T11:27:46Z","file_size":5540540,"creator":"dernst","access_level":"open_access","file_name":"2020_NatureComm_Sznurkowska.pdf"}],"doi":"10.1038/s41467-020-18837-3","file_date_updated":"2020-10-19T11:27:46Z","abstract":[{"lang":"eng","text":"Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","oa":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"title":"Tracing the cellular basis of islet specification in mouse pancreas","date_created":"2020-10-18T22:01:35Z","citation":{"mla":"Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature, 2020, doi:10.1038/s41467-020-18837-3.","short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020).","ama":"Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 2020;11. doi:10.1038/s41467-020-18837-3","ieee":"M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T., Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3","chicago":"Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3.","ista":"Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 11, 5037."}},{"year":"2020","status":"public","department":[{"_id":"MiSi"},{"_id":"EM-Fac"}],"publication_status":"published","intvolume":" 11","publication":"Nature Communications","file_date_updated":"2020-11-23T13:29:49Z","doi":"10.1038/s41467-020-19515-0","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation. While spatio-temporal dynamics of clot formation are well characterized, the cell-biological mechanisms of platelet recruitment to inflammatory micro-environments remain incompletely understood. Here we identify Arp2/3-dependent lamellipodia formation as a prominent morphological feature of immune-responsive platelets. Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand. Platelet-specific abrogation of Arp2/3 interferes with haptotactic repositioning of platelets to microlesions, thus impairing vascular sealing and provoking inflammatory microbleeding. During infection, haptotaxis promotes capture of bacteria and prevents hematogenic dissemination, rendering platelets gate-keepers of the inflamed microvasculature. Consequently, these findings identify haptotaxis as a key effector function of immune-responsive platelets."}],"project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"file":[{"checksum":"485b7b6cf30198ba0ce126491a28f125","file_id":"8798","file_name":"2020_NatureComm_Nicolai.pdf","access_level":"open_access","creator":"dernst","file_size":7035340,"date_created":"2020-11-23T13:29:49Z","relation":"main_file","date_updated":"2020-11-23T13:29:49Z","success":1,"content_type":"application/pdf"}],"article_type":"original","oa":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-31310-7","relation":"erratum"}]},"ec_funded":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ista":"Nicolai L, Schiefelbein K, Lipsky S, Leunig A, Hoffknecht M, Pekayvaz K, Raude B, Marx C, Ehrlich A, Pircher J, Zhang Z, Saleh I, Marel A-K, Löf A, Petzold T, Lorenz M, Stark K, Pick R, Rosenberger G, Weckbach L, Uhl B, Xia S, Reichel CA, Walzog B, Schulz C, Zheden V, Bender M, Li R, Massberg S, Gärtner FR. 2020. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 11, 5778.","chicago":"Nicolai, Leo, Karin Schiefelbein, Silvia Lipsky, Alexander Leunig, Marie Hoffknecht, Kami Pekayvaz, Ben Raude, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19515-0.","ieee":"L. Nicolai et al., “Vascular surveillance by haptotactic blood platelets in inflammation and infection,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Nicolai, L., Schiefelbein, K., Lipsky, S., Leunig, A., Hoffknecht, M., Pekayvaz, K., … Gärtner, F. R. (2020). Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19515-0","ama":"Nicolai L, Schiefelbein K, Lipsky S, et al. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 2020;11. doi:10.1038/s41467-020-19515-0","short":"L. Nicolai, K. Schiefelbein, S. Lipsky, A. Leunig, M. Hoffknecht, K. Pekayvaz, B. Raude, C. Marx, A. Ehrlich, J. Pircher, Z. Zhang, I. Saleh, A.-K. Marel, A. Löf, T. Petzold, M. Lorenz, K. Stark, R. Pick, G. Rosenberger, L. Weckbach, B. Uhl, S. Xia, C.A. Reichel, B. Walzog, C. Schulz, V. Zheden, M. Bender, R. Li, S. Massberg, F.R. Gärtner, Nature Communications 11 (2020).","mla":"Nicolai, Leo, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications, vol. 11, 5778, Springer Nature, 2020, doi:10.1038/s41467-020-19515-0."},"title":"Vascular surveillance by haptotactic blood platelets in inflammation and infection","date_created":"2020-11-22T23:01:23Z","date_updated":"2023-08-22T13:26:26Z","day":"13","isi":1,"month":"11","language":[{"iso":"eng"}],"external_id":{"pmid":["33188196"],"isi":["000594648000014"]},"date_published":"2020-11-13T00:00:00Z","has_accepted_license":"1","volume":11,"type":"journal_article","scopus_import":"1","author":[{"first_name":"Leo","full_name":"Nicolai, Leo","last_name":"Nicolai"},{"first_name":"Karin","full_name":"Schiefelbein, Karin","last_name":"Schiefelbein"},{"first_name":"Silvia","last_name":"Lipsky","full_name":"Lipsky, Silvia"},{"first_name":"Alexander","full_name":"Leunig, Alexander","last_name":"Leunig"},{"first_name":"Marie","full_name":"Hoffknecht, Marie","last_name":"Hoffknecht"},{"first_name":"Kami","full_name":"Pekayvaz, Kami","last_name":"Pekayvaz"},{"first_name":"Ben","last_name":"Raude","full_name":"Raude, Ben"},{"full_name":"Marx, Charlotte","last_name":"Marx","first_name":"Charlotte"},{"first_name":"Andreas","full_name":"Ehrlich, Andreas","last_name":"Ehrlich"},{"last_name":"Pircher","full_name":"Pircher, Joachim","first_name":"Joachim"},{"full_name":"Zhang, Zhe","last_name":"Zhang","first_name":"Zhe"},{"full_name":"Saleh, Inas","last_name":"Saleh","first_name":"Inas"},{"first_name":"Anna-Kristina","last_name":"Marel","full_name":"Marel, Anna-Kristina"},{"full_name":"Löf, Achim","last_name":"Löf","first_name":"Achim"},{"first_name":"Tobias","last_name":"Petzold","full_name":"Petzold, Tobias"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"first_name":"Konstantin","last_name":"Stark","full_name":"Stark, Konstantin"},{"full_name":"Pick, Robert","last_name":"Pick","first_name":"Robert"},{"full_name":"Rosenberger, Gerhild","last_name":"Rosenberger","first_name":"Gerhild"},{"last_name":"Weckbach","full_name":"Weckbach, Ludwig","first_name":"Ludwig"},{"last_name":"Uhl","full_name":"Uhl, Bernd","first_name":"Bernd"},{"last_name":"Xia","full_name":"Xia, Sheng","first_name":"Sheng"},{"first_name":"Christoph Andreas","last_name":"Reichel","full_name":"Reichel, Christoph Andreas"},{"first_name":"Barbara","full_name":"Walzog, Barbara","last_name":"Walzog"},{"last_name":"Schulz","full_name":"Schulz, Christian","first_name":"Christian"},{"first_name":"Vanessa","orcid":"0000-0002-9438-4783","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa"},{"last_name":"Bender","full_name":"Bender, Markus","first_name":"Markus"},{"first_name":"Rong","full_name":"Li, Rong","last_name":"Li"},{"first_name":"Steffen","full_name":"Massberg, Steffen","last_name":"Massberg"},{"first_name":"Florian R","orcid":"0000-0001-6120-3723","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R"}],"publisher":"Springer Nature","_id":"8787","publication_identifier":{"eissn":["20411723"]},"article_number":"5778","ddc":["570"],"pmid":1,"acknowledgement":"We thank Sebastian Helmer, Nicole Blount, Christine Mann, and Beate Jantz for technical assistance; Hellen Ishikawa-Ankerhold for help and advice; Michael Sixt for critical\r\ndiscussions. This study was supported by the DFG SFB 914 (S.M. [B02 and Z01], K.Sch.\r\n[B02], B.W. [A02 and Z03], C.A.R. [B03], C.S. [A10], J.P. [Gerok position]), the DFG\r\nSFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Center for\r\nCardiovascular Research (DZHK) (Clinician Scientist Program [L.N.], MHA 1.4VD\r\n[S.M.], Postdoc Start-up Grant, 81×3600213 [F.G.]), FP7 program (project 260309,\r\nPRESTIGE [S.M.]), FöFoLe project 1015/1009 (L.N.), FöFoLe project 947 (F.G.), the\r\nFriedrich-Baur-Stiftung project 41/16 (F.G.), and LMUexcellence NFF (F.G.). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no.\r\n833440) (S.M.). F.G. received funding from the European Union’s Horizon 2020 research\r\nand innovation program under the Marie Skłodowska-Curie grant agreement no.\r\n747687.","article_processing_charge":"No","quality_controlled":"1"},{"volume":10,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","publisher":"Springer Nature","author":[{"first_name":"Hagar F.","last_name":"Moussa","full_name":"Moussa, Hagar F."},{"last_name":"Bsteh","full_name":"Bsteh, Daniel","first_name":"Daniel"},{"first_name":"Ramesh","full_name":"Yelagandula, Ramesh","last_name":"Yelagandula"},{"first_name":"Carina","full_name":"Pribitzer, Carina","last_name":"Pribitzer"},{"first_name":"Karin","full_name":"Stecher, Karin","last_name":"Stecher"},{"id":"4D883232-F248-11E8-B48F-1D18A9856A87","full_name":"Bartalska, Katarina","last_name":"Bartalska","first_name":"Katarina"},{"last_name":"Michetti","full_name":"Michetti, Luca","first_name":"Luca"},{"full_name":"Wang, Jingkui","last_name":"Wang","first_name":"Jingkui"},{"first_name":"Jorge A.","full_name":"Zepeda-Martinez, Jorge A.","last_name":"Zepeda-Martinez"},{"first_name":"Ulrich","last_name":"Elling","full_name":"Elling, Ulrich"},{"first_name":"Jacob I.","full_name":"Stuckey, Jacob I.","last_name":"Stuckey"},{"last_name":"James","full_name":"James, Lindsey I.","first_name":"Lindsey I."},{"last_name":"Frye","full_name":"Frye, Stephen V.","first_name":"Stephen V."},{"first_name":"Oliver","last_name":"Bell","full_name":"Bell, Oliver"}],"publication_identifier":{"eissn":["20411723"]},"_id":"6412","article_number":"1931","ddc":["570"],"article_processing_charge":"No","quality_controlled":"1","date_updated":"2023-08-25T10:31:56Z","day":"29","isi":1,"month":"04","language":[{"iso":"eng"}],"date_published":"2019-04-29T00:00:00Z","external_id":{"isi":["000466118700002"]},"abstract":[{"text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-019-09628-6","file_date_updated":"2020-07-14T12:47:29Z","file":[{"creator":"dernst","access_level":"open_access","file_name":"2019_NatureComm_Moussa.pdf","relation":"main_file","date_created":"2019-05-14T08:45:51Z","file_size":1223647,"checksum":"6550a328335396c856db4cbdda7d2994","file_id":"6448","content_type":"application/pdf","date_updated":"2020-07-14T12:47:29Z"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09628-6","short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019).","mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6.","ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931.","chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6.","ieee":"H. F. Moussa et al., “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09628-6"},"title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","date_created":"2019-05-13T07:58:35Z","year":"2019","department":[{"_id":"SaSi"}],"status":"public","publication_status":"published","intvolume":" 10","publication":"Nature Communications","issue":"1"}]