[{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-09-08T06:41:14Z","article_number":"e202201568","keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"quality_controlled":"1","author":[{"full_name":"Daiß, Julia L","last_name":"Daiß","first_name":"Julia L"},{"first_name":"Michael","last_name":"Pilsl","full_name":"Pilsl, Michael"},{"full_name":"Straub, Kristina","last_name":"Straub","first_name":"Kristina"},{"first_name":"Andrea","last_name":"Bleckmann","full_name":"Bleckmann, Andrea"},{"last_name":"Höcherl","first_name":"Mona","full_name":"Höcherl, Mona"},{"first_name":"Florian B","last_name":"Heiss","full_name":"Heiss, Florian B"},{"full_name":"Abascal-Palacios, Guillermo","first_name":"Guillermo","last_name":"Abascal-Palacios"},{"first_name":"Ewan P","last_name":"Ramsay","full_name":"Ramsay, Ewan P"},{"last_name":"Tluckova","first_name":"Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","full_name":"Tluckova, Katarina"},{"last_name":"Mars","first_name":"Jean-Clement","full_name":"Mars, Jean-Clement"},{"full_name":"Fürtges, Torben","first_name":"Torben","last_name":"Fürtges"},{"first_name":"Astrid","last_name":"Bruckmann","full_name":"Bruckmann, Astrid"},{"full_name":"Rudack, Till","last_name":"Rudack","first_name":"Till"},{"orcid":"0000-0003-0893-7036","last_name":"Bernecky","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"},{"full_name":"Lamour, Valérie","first_name":"Valérie","last_name":"Lamour"},{"full_name":"Panov, Konstantin","first_name":"Konstantin","last_name":"Panov"},{"last_name":"Vannini","first_name":"Alessandro","full_name":"Vannini, Alessandro"},{"first_name":"Tom","last_name":"Moss","full_name":"Moss, Tom"},{"first_name":"Christoph","last_name":"Engel","full_name":"Engel, Christoph"}],"date_published":"2022-09-01T00:00:00Z","article_processing_charge":"No","doi":"10.26508/lsa.202201568","date_updated":"2023-08-03T13:39:36Z","intvolume":"         5","file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2022-09-08T06:41:14Z","success":1,"content_type":"application/pdf","file_id":"12062","date_updated":"2022-09-08T06:41:14Z","checksum":"4201d876a3e5e8b65e319d03300014ad","file_name":"2022_LifeScienceAlliance_Daiss.pdf","file_size":3183129}],"publication_status":"published","license":"https://creativecommons.org/licenses/by/4.0/","month":"09","isi":1,"language":[{"iso":"eng"}],"ddc":["570"],"day":"01","date_created":"2022-09-06T18:45:23Z","oa_version":"Published Version","publication":"Life Science Alliance","department":[{"_id":"CaBe"}],"title":"The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans","publisher":"Life Science Alliance","abstract":[{"text":"Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This “dock II” domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor–binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.","lang":"eng"}],"_id":"12051","has_accepted_license":"1","year":"2022","volume":5,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","citation":{"apa":"Daiß, J. L., Pilsl, M., Straub, K., Bleckmann, A., Höcherl, M., Heiss, F. B., … Engel, C. (2022). The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>","chicago":"Daiß, Julia L, Michael Pilsl, Kristina Straub, Andrea Bleckmann, Mona Höcherl, Florian B Heiss, Guillermo Abascal-Palacios, et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>. Life Science Alliance, 2022. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>.","ieee":"J. L. Daiß <i>et al.</i>, “The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans,” <i>Life Science Alliance</i>, vol. 5, no. 11. Life Science Alliance, 2022.","short":"J.L. Daiß, M. Pilsl, K. Straub, A. Bleckmann, M. Höcherl, F.B. Heiss, G. Abascal-Palacios, E.P. Ramsay, K. Tluckova, J.-C. Mars, T. Fürtges, A. Bruckmann, T. Rudack, C. Bernecky, V. Lamour, K. Panov, A. Vannini, T. Moss, C. Engel, Life Science Alliance 5 (2022).","ista":"Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios G, Ramsay EP, Tluckova K, Mars J-C, Fürtges T, Bruckmann A, Rudack T, Bernecky C, Lamour V, Panov K, Vannini A, Moss T, Engel C. 2022. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Science Alliance. 5(11), e202201568.","mla":"Daiß, Julia L., et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>, vol. 5, no. 11, e202201568, Life Science Alliance, 2022, doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>.","ama":"Daiß JL, Pilsl M, Straub K, et al. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. 2022;5(11). doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>"},"publication_identifier":{"issn":["2575-1077"]},"oa":1,"acknowledgement":"The authors especially thank Philip Gunkel for his contribution. We thank all\r\npast and present members of the Engel lab, Achim Griesenbeck, Colyn Crane-\r\nRobinson, Christophe Lotz, Marlene Vayssieres, Klaus Grasser, Herbert Tschochner, and Philipp Milkereit for help and discussion; Gerhard Lehmann and Nobert Eichner for IT support; Joost Zomerdijk for UBF-constructs, Volker Cordes for the Hela P2 cell line; Remco Sprangers for shared cell culture; Dina Grohmann and the Archaea Center for fermentation; and Thomas\r\nDresselhaus for access to fluorescence microscopes. This work was in part supported by the Emmy-Noether Programm (DFG grant no. EN 1204/1-1 to C Engel) of the German Research Council and Collaborative Research Center 960 (TP-A8 to C Engel).","status":"public","issue":"11","external_id":{"isi":["000972702600001"]},"article_type":"original"},{"abstract":[{"text":"To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.\r\nFor complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"date_created":"2023-01-12T11:56:38Z","title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"publication":"STAR Protocols","publisher":"Elsevier","citation":{"ama":"Hübschmann V, Korkut M, Siegert S. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>","ista":"Hübschmann V, Korkut M, Siegert S. 2022. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. STAR Protocols. 3(4), 101866.","mla":"Hübschmann, Verena, et al. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>, vol. 3, no. 4, 101866, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>.","short":"V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (2022).","chicago":"Hübschmann, Verena, Medina Korkut, and Sandra Siegert. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>.","ieee":"V. Hübschmann, M. Korkut, and S. Siegert, “Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay,” <i>STAR Protocols</i>, vol. 3, no. 4. Elsevier, 2022.","apa":"Hübschmann, V., Korkut, M., &#38; Siegert, S. (2022). Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>"},"publication_identifier":{"issn":["2666-1667"]},"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.). We thank Rouven Schulz and Alessandro Venturino for their insights into functional assays and data analysis, Verena Seiboth for insights into necessary institutional permission, and ISTA imaging & optics facility (IOF) especially Bernhard Hochreiter for their support.","oa":1,"status":"public","article_type":"letter_note","issue":"4","_id":"12117","has_accepted_license":"1","year":"2022","volume":3,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"quality_controlled":"1","author":[{"first_name":"Verena","last_name":"Hübschmann","full_name":"Hübschmann, Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Korkut, Medina","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","first_name":"Medina","orcid":"0000-0003-4309-2251","last_name":"Korkut"},{"full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877"}],"date_published":"2022-12-16T00:00:00Z","related_material":{"record":[{"status":"public","relation":"other","id":"11478"}]},"date_updated":"2023-11-02T12:21:32Z","doi":"10.1016/j.xpro.2022.101866","article_processing_charge":"No","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"acknowledged_ssus":[{"_id":"Bio"}],"file_date_updated":"2023-01-23T09:50:51Z","article_number":"101866","language":[{"iso":"eng"}],"project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571","call_identifier":"H2020"},{"name":"How human microglia shape developing neurons during health and inflammation","grant_number":"SC19-017","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A"}],"month":"12","day":"16","ddc":["570"],"intvolume":"         3","publication_status":"published","file":[{"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2023-01-23T09:50:51Z","success":1,"content_type":"application/pdf","file_id":"12340","date_updated":"2023-01-23T09:50:51Z","checksum":"3c71b8a60633d42c2f77c49025d5559b","file_name":"2022_STARProtocols_Huebschmann.pdf","file_size":6251945}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"abstract":[{"text":"Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.","lang":"eng"}],"publication":"Developmental Cell","department":[{"_id":"JiFr"}],"title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","publisher":"Elsevier","date_created":"2023-01-12T11:57:00Z","oa_version":"None","status":"public","acknowledgement":"The authors are grateful to Jörg Kudla, Ying Miao, Yu Zheng, Gang Li, and Jun Zheng for providing published materials and to Wenkun Zhou and Caifu Jiang for helpful discussions. This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), the Beijing Municipal Natural Science Foundation (5192011), and the Chinese Universities Scientific Fund (2022TC153).","issue":"23","article_type":"original","external_id":{"pmid":["36473460"],"isi":["000919603800005"]},"citation":{"apa":"Xiao, H., Hu, Y., Wang, Y., Cheng, J., Wang, J., Chen, G., … Zhang, J. (2022). Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>","ieee":"H. Xiao <i>et al.</i>, “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” <i>Developmental Cell</i>, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022.","chicago":"Xiao, Huixin, Yumei Hu, Yaping Wang, Jinkui Cheng, Jinyi Wang, Guojingwei Chen, Qian Li, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>.","short":"H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang, S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental Cell 57 (2022) 2638–2651.e6.","ista":"Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6.","mla":"Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>.","ama":"Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. 2022;57(23):2638-2651.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>"},"publication_identifier":{"issn":["1534-5807"]},"volume":57,"page":"2638-2651.e6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"12120","year":"2022","author":[{"first_name":"Huixin","last_name":"Xiao","full_name":"Xiao, Huixin"},{"full_name":"Hu, Yumei","last_name":"Hu","first_name":"Yumei"},{"full_name":"Wang, Yaping","last_name":"Wang","first_name":"Yaping"},{"last_name":"Cheng","first_name":"Jinkui","full_name":"Cheng, Jinkui"},{"full_name":"Wang, Jinyi","first_name":"Jinyi","last_name":"Wang"},{"last_name":"Chen","first_name":"Guojingwei","full_name":"Chen, Guojingwei"},{"last_name":"Li","first_name":"Qian","full_name":"Li, Qian"},{"first_name":"Shuwei","last_name":"Wang","full_name":"Wang, Shuwei"},{"full_name":"Wang, Yalu","first_name":"Yalu","last_name":"Wang"},{"full_name":"Wang, Shao-Shuai","last_name":"Wang","first_name":"Shao-Shuai"},{"first_name":"Yi","last_name":"Wang","full_name":"Wang, Yi"},{"last_name":"Xuan","first_name":"Wei","full_name":"Xuan, Wei"},{"last_name":"Li","first_name":"Zhen","full_name":"Li, Zhen"},{"first_name":"Yan","last_name":"Guo","full_name":"Guo, Yan"},{"first_name":"Zhizhong","last_name":"Gong","full_name":"Gong, Zhizhong"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"},{"full_name":"Zhang, Jing","last_name":"Zhang","first_name":"Jing"}],"date_published":"2022-12-05T00:00:00Z","article_processing_charge":"No","date_updated":"2023-10-04T08:23:20Z","doi":"10.1016/j.devcel.2022.11.006","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"scopus_import":"1","quality_controlled":"1","pmid":1,"day":"05","isi":1,"month":"12","language":[{"iso":"eng"}],"intvolume":"        57","publication_status":"published"},{"has_accepted_license":"1","year":"2022","_id":"12121","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":221,"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"citation":{"short":"J. Zhao, M.T. Bui, J. Ma, F. Künzl, L. Picchianti, J.C. De La Concepcion, Y. Chen, S. Petsangouraki, A. Mohseni, M. García-Leon, M.S. Gomez, C. Giannini, D. Gwennogan, R. Kobylinska, M. Clavel, S. Schellmann, Y. Jaillais, J. Friml, B.-H. Kang, Y. Dagdas, Journal of Cell Biology 221 (2022).","ista":"Zhao J, Bui MT, Ma J, Künzl F, Picchianti L, De La Concepcion JC, Chen Y, Petsangouraki S, Mohseni A, García-Leon M, Gomez MS, Giannini C, Gwennogan D, Kobylinska R, Clavel M, Schellmann S, Jaillais Y, Friml J, Kang B-H, Dagdas Y. 2022. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. 221(12), e202203139.","mla":"Zhao, Jierui, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” <i>Journal of Cell Biology</i>, vol. 221, no. 12, e202203139, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202203139\">10.1083/jcb.202203139</a>.","ama":"Zhao J, Bui MT, Ma J, et al. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. <i>Journal of Cell Biology</i>. 2022;221(12). doi:<a href=\"https://doi.org/10.1083/jcb.202203139\">10.1083/jcb.202203139</a>","apa":"Zhao, J., Bui, M. T., Ma, J., Künzl, F., Picchianti, L., De La Concepcion, J. C., … Dagdas, Y. (2022). Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202203139\">https://doi.org/10.1083/jcb.202203139</a>","ieee":"J. Zhao <i>et al.</i>, “Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole,” <i>Journal of Cell Biology</i>, vol. 221, no. 12. Rockefeller University Press, 2022.","chicago":"Zhao, Jierui, Mai Thu Bui, Juncai Ma, Fabian Künzl, Lorenzo Picchianti, Juan Carlos De La Concepcion, Yixuan Chen, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202203139\">https://doi.org/10.1083/jcb.202203139</a>."},"external_id":{"isi":["000932958800001"],"pmid":["36260289"]},"article_type":"original","issue":"12","acknowledgement":"We thank Suayip Ustün, Karin Schumacher, Erika Isono, Gerd Juergens, Takashi Ueda, Daniel Hofius, and Liwen Jiang for sharing published materials.\r\nWe acknowledge funding from Austrian Academy of Sciences, Austrian Science Fund (FWF, P 32355, P 34944), Austrian Science Fund (FWF-SFB F79), Vienna Science and Technology\r\nFund (WWTF, LS17-047) to Y. Dagdas; Austrian Academy of Sciences DOC Fellowship to J. Zhao, Marie Curie VIP2 Fellowship to J.C. De La Concepcion and M. Clavel; Hong Kong Research Grant Council (GRF14121019, 14113921, AoE/M-05/12, C4002-17G) to B.-H. Kang. We thank Vienna Biocenter Core Facilities (VBCF) Protein Chemistry, Biooptics, Plant Sciences, Molecular Biology, and Protein Technologies. We thank J. Matthew Watson\r\nand members of the Dagdas lab for the critical reading and editing of the manuscript.","oa":1,"status":"public","oa_version":"Published Version","date_created":"2023-01-12T11:57:10Z","publisher":"Rockefeller University Press","department":[{"_id":"JiFr"}],"title":"Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole","publication":"Journal of Cell Biology","abstract":[{"text":"Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants.","lang":"eng"}],"publication_status":"published","file":[{"file_size":10365777,"checksum":"050b5cc4b25e6b94fe3e3cbfe0f5c06b","file_name":"2022_JCB_Zhao.pdf","date_updated":"2023-01-23T10:30:11Z","file_id":"12342","content_type":"application/pdf","date_created":"2023-01-23T10:30:11Z","success":1,"relation":"main_file","access_level":"open_access","creator":"dernst"}],"intvolume":"       221","language":[{"iso":"eng"}],"month":"12","isi":1,"day":"01","ddc":["580"],"pmid":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"e202203139","file_date_updated":"2023-01-23T10:30:11Z","quality_controlled":"1","scopus_import":"1","keyword":["Cell Biology"],"doi":"10.1083/jcb.202203139","date_updated":"2023-08-03T14:20:15Z","article_processing_charge":"No","author":[{"full_name":"Zhao, Jierui","last_name":"Zhao","first_name":"Jierui"},{"first_name":"Mai Thu","last_name":"Bui","full_name":"Bui, Mai Thu"},{"first_name":"Juncai","last_name":"Ma","full_name":"Ma, Juncai"},{"full_name":"Künzl, Fabian","first_name":"Fabian","last_name":"Künzl"},{"full_name":"Picchianti, Lorenzo","last_name":"Picchianti","first_name":"Lorenzo"},{"full_name":"De La Concepcion, Juan Carlos","last_name":"De La Concepcion","first_name":"Juan Carlos"},{"first_name":"Yixuan","last_name":"Chen","full_name":"Chen, Yixuan"},{"first_name":"Sofia","last_name":"Petsangouraki","full_name":"Petsangouraki, Sofia"},{"first_name":"Azadeh","last_name":"Mohseni","full_name":"Mohseni, Azadeh"},{"full_name":"García-Leon, Marta","last_name":"García-Leon","first_name":"Marta"},{"full_name":"Gomez, Marta Salas","last_name":"Gomez","first_name":"Marta Salas"},{"full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","last_name":"Giannini"},{"first_name":"Dubois","last_name":"Gwennogan","full_name":"Gwennogan, Dubois"},{"full_name":"Kobylinska, Roksolana","last_name":"Kobylinska","first_name":"Roksolana"},{"last_name":"Clavel","first_name":"Marion","full_name":"Clavel, Marion"},{"full_name":"Schellmann, Swen","last_name":"Schellmann","first_name":"Swen"},{"last_name":"Jaillais","first_name":"Yvon","full_name":"Jaillais, Yvon"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Byung-Ho","last_name":"Kang","full_name":"Kang, Byung-Ho"},{"full_name":"Dagdas, Yasin","first_name":"Yasin","last_name":"Dagdas"}],"date_published":"2022-12-01T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":221,"has_accepted_license":"1","year":"2022","_id":"12122","issue":"12","external_id":{"isi":["000932941400001"],"pmid":["36214847 "]},"article_type":"original","oa":1,"acknowledgement":"We thank Markéta Dalecká and Irena Krejzová for their support with FIB-SEM imaging, the Imaging Methods Core Facility at BIOCEV supported by the Ministry of Education, Youth and Sports Czech Republic (Large RI Project LM2018129 Czech-BioImaging), and European Regional Development Fund (project No. CZ.02.1.01/0.0/0.0/18_046/0016045) for their support with obtaining imaging data presented in this paper. The authors further thank Andreas Villunger, Florian Gärtner, Frank Bradke, and Sarah Förster for helpful discussions; Andy Zielinski for help with statistics; and Björn Weiershausen for assisting with figure illustration.\r\n\r\nThis work was funded by a fellowship of the Ministry of Innovation, Science and Research of North-Rhine-Westphalia (AZ: 421-8.03.03.02-137069) to E. Kiermaier and the Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy – EXC 2151 – 390873048. R. Hauschild was funded by grant number 2020-225401 from the Chan Zuckerberg Initiative Donor-Advised Fund, an advised fund of Silicon Valley Community Foundation. M. Hons is supported by Czech Science Foundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013.","status":"public","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"citation":{"ama":"Weier A-K, Homrich M, Ebbinghaus S, et al. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. <i>Journal of Cell Biology</i>. 2022;221(12). doi:<a href=\"https://doi.org/10.1083/jcb.202107134\">10.1083/jcb.202107134</a>","short":"A.-K. Weier, M. Homrich, S. Ebbinghaus, P. Juda, E. Miková, R. Hauschild, L. Zhang, T. Quast, E. Mass, A. Schlitzer, W. Kolanus, S. Burgdorf, O.J. Gruß, M. Hons, S. Wieser, E. Kiermaier, Journal of Cell Biology 221 (2022).","ista":"Weier A-K, Homrich M, Ebbinghaus S, Juda P, Miková E, Hauschild R, Zhang L, Quast T, Mass E, Schlitzer A, Kolanus W, Burgdorf S, Gruß OJ, Hons M, Wieser S, Kiermaier E. 2022. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. Journal of Cell Biology. 221(12), e202107134.","mla":"Weier, Ann-Kathrin, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” <i>Journal of Cell Biology</i>, vol. 221, no. 12, e202107134, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202107134\">10.1083/jcb.202107134</a>.","ieee":"A.-K. Weier <i>et al.</i>, “Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells,” <i>Journal of Cell Biology</i>, vol. 221, no. 12. Rockefeller University Press, 2022.","chicago":"Weier, Ann-Kathrin, Mirka Homrich, Stephanie Ebbinghaus, Pavel Juda, Eliška Miková, Robert Hauschild, Lili Zhang, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202107134\">https://doi.org/10.1083/jcb.202107134</a>.","apa":"Weier, A.-K., Homrich, M., Ebbinghaus, S., Juda, P., Miková, E., Hauschild, R., … Kiermaier, E. (2022). Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202107134\">https://doi.org/10.1083/jcb.202107134</a>"},"publisher":"Rockefeller University Press","publication":"Journal of Cell Biology","title":"Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells","department":[{"_id":"Bio"}],"date_created":"2023-01-12T12:01:09Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Centrosomes play a crucial role during immune cell interactions and initiation of the immune response. In proliferating cells, centrosome numbers are tightly controlled and generally limited to one in G1 and two prior to mitosis. Defects in regulating centrosome numbers have been associated with cell transformation and tumorigenesis. Here, we report the emergence of extra centrosomes in leukocytes during immune activation. Upon antigen encounter, dendritic cells pass through incomplete mitosis and arrest in the subsequent G1 phase leading to tetraploid cells with accumulated centrosomes. In addition, cell stimulation increases expression of polo-like kinase 2, resulting in diploid cells with two centrosomes in G1-arrested cells. During cell migration, centrosomes tightly cluster and act as functional microtubule-organizing centers allowing for increased persistent locomotion along gradients of chemotactic cues. Moreover, dendritic cells with extra centrosomes display enhanced secretion of inflammatory cytokines and optimized T cell responses. Together, these results demonstrate a previously unappreciated role of extra centrosomes for regular cell and tissue homeostasis."}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","success":1,"date_created":"2023-08-16T11:24:53Z","file_id":"14065","date_updated":"2023-08-16T11:24:53Z","file_size":11090179,"file_name":"2023_JCB_Weier.pdf","checksum":"0c9af38f82af30c6ce528f2caece4246"}],"publication_status":"published","intvolume":"       221","ddc":["570"],"day":"05","pmid":1,"month":"12","isi":1,"language":[{"iso":"eng"}],"project":[{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","grant_number":"CZI01","name":"Tools for automation and feedback microscopy"}],"article_number":"e202107134","file_date_updated":"2023-08-16T11:24:53Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"article_processing_charge":"No","doi":"10.1083/jcb.202107134","date_updated":"2023-08-16T11:29:12Z","date_published":"2022-12-05T00:00:00Z","author":[{"first_name":"Ann-Kathrin","last_name":"Weier","full_name":"Weier, Ann-Kathrin"},{"full_name":"Homrich, Mirka","first_name":"Mirka","last_name":"Homrich"},{"full_name":"Ebbinghaus, Stephanie","first_name":"Stephanie","last_name":"Ebbinghaus"},{"first_name":"Pavel","last_name":"Juda","full_name":"Juda, Pavel"},{"full_name":"Miková, Eliška","last_name":"Miková","first_name":"Eliška"},{"first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Lili","last_name":"Zhang","first_name":"Lili"},{"first_name":"Thomas","last_name":"Quast","full_name":"Quast, Thomas"},{"full_name":"Mass, Elvira","last_name":"Mass","first_name":"Elvira"},{"last_name":"Schlitzer","first_name":"Andreas","full_name":"Schlitzer, Andreas"},{"last_name":"Kolanus","first_name":"Waldemar","full_name":"Kolanus, Waldemar"},{"first_name":"Sven","last_name":"Burgdorf","full_name":"Burgdorf, Sven"},{"full_name":"Gruß, Oliver J.","last_name":"Gruß","first_name":"Oliver J."},{"full_name":"Hons, Miroslav","first_name":"Miroslav","last_name":"Hons"},{"full_name":"Wieser, Stefan","last_name":"Wieser","first_name":"Stefan"},{"full_name":"Kiermaier, Eva","last_name":"Kiermaier","first_name":"Eva"}],"quality_controlled":"1","keyword":["Cell Biology"],"scopus_import":"1"},{"ddc":["580"],"day":"15","pmid":1,"month":"11","isi":1,"language":[{"iso":"eng"}],"file":[{"file_name":"2022_NatureCommunications_Huang.pdf","checksum":"233922a7b9507d9d48591e6799e4526e","file_size":3375249,"file_id":"12346","date_updated":"2023-01-23T11:17:33Z","success":1,"date_created":"2023-01-23T11:17:33Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file"}],"publication_status":"published","intvolume":"        13","article_processing_charge":"No","doi":"10.1038/s41467-022-34723-6","date_updated":"2023-08-04T08:52:01Z","author":[{"first_name":"Jian","last_name":"Huang","full_name":"Huang, Jian"},{"full_name":"Zhao, Lei","last_name":"Zhao","first_name":"Lei"},{"full_name":"Malik, Shikha","first_name":"Shikha","last_name":"Malik"},{"full_name":"Gentile, Benjamin R.","last_name":"Gentile","first_name":"Benjamin R."},{"full_name":"Xiong, Va","first_name":"Va","last_name":"Xiong"},{"full_name":"Arazi, Tzahi","first_name":"Tzahi","last_name":"Arazi"},{"first_name":"Heather A.","last_name":"Owen","full_name":"Owen, Heather A."},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhao","first_name":"Dazhong","full_name":"Zhao, Dazhong"}],"date_published":"2022-11-15T00:00:00Z","quality_controlled":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"scopus_import":"1","article_number":"6960","file_date_updated":"2023-01-23T11:17:33Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","external_id":{"isi":["000884426700001"],"pmid":["36379956"]},"acknowledgement":"We thank A. Cheung,W. Lukowitz, V.Walbot, D.Weijers, and R. Yadegari for critically reading the manuscript; E. Xiong and G. Zhang for preparing some experiments, T. Schuck, J. Gonnering, and P. Engevold for plant care, the Arabidopsis Biological Resource Center (ABRC) for ARF10,ARF16, ARF17, EMS1,MIR160a BAC clones and cDNAs, the SALK_090804 seed, T. Nakagawa for pGBW vectors, Y. Zhao for the YUC1 cDNA, Q. Chen for the pHEE401E vector, R. Yadegari for pAT5G01860::n1GFP, pAT5G45980:n1GFP, pAT5G50490::n1GFP, pAT5G56200:n1GFP vectors, and D.Weijers for the pGreenII KAN SV40-3×GFP and R2D2 vectors, W. Yang for the splmutant, Y. Qin for the pKNU::KNU-VENUS vector and seed, G. Tang for the STTM160/160-48 vector, and L. Colombo for pPIN1::PIN1-GFP spl and pin1-5 seeds. This work was supported by the US National Science Foundation (NSF)-Israel Binational Science Foundation (BSF) research grant to D.Z. (IOS-1322796) and T.A. (2012756). D.Z. also\r\ngratefully acknowledges supports of the Shaw Scientist Award from the Greater Milwaukee Foundation, USDA National Institute of Food and Agriculture (NIFA, 2022-67013-36294), the UWM Discovery and Innovation Grant, the Bradley Catalyst Award from the UWM Research\r\nFoundation, and WiSys and UW System Applied Research Funding Programs.","oa":1,"status":"public","publication_identifier":{"issn":["2041-1723"]},"citation":{"mla":"Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>, vol. 13, 6960, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>.","ista":"Huang J, Zhao L, Malik S, Gentile BR, Xiong V, Arazi T, Owen HA, Friml J, Zhao D. 2022. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 13, 6960.","short":"J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen, J. Friml, D. Zhao, Nature Communications 13 (2022).","ama":"Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>","apa":"Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao, D. (2022). Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>","ieee":"J. Huang <i>et al.</i>, “Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","chicago":"Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":13,"year":"2022","has_accepted_license":"1","_id":"12130","abstract":[{"lang":"eng","text":"Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants."}],"publisher":"Springer Nature","publication":"Nature Communications","department":[{"_id":"JiFr"}],"title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","date_created":"2023-01-12T12:02:41Z","oa_version":"Published Version"},{"ddc":["570"],"day":"03","pmid":1,"month":"11","isi":1,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","success":1,"date_created":"2023-01-24T09:29:02Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_size":7368534,"file_name":"2022_MolecularCell_Zapletal.pdf","checksum":"999e443b54e4fdaa2542ca5a97619731","file_id":"12354","date_updated":"2023-01-24T09:29:02Z"}],"publication_status":"published","intvolume":"        82","article_processing_charge":"No","doi":"10.1016/j.molcel.2022.10.010","date_updated":"2023-08-04T08:57:17Z","date_published":"2022-11-03T00:00:00Z","author":[{"full_name":"Zapletal, David","first_name":"David","last_name":"Zapletal"},{"full_name":"Taborska, Eliska","first_name":"Eliska","last_name":"Taborska"},{"last_name":"Pasulka","first_name":"Josef","full_name":"Pasulka, Josef"},{"last_name":"Malik","first_name":"Radek","full_name":"Malik, Radek"},{"full_name":"Kubicek, Karel","first_name":"Karel","last_name":"Kubicek"},{"full_name":"Zanova, Martina","last_name":"Zanova","first_name":"Martina"},{"first_name":"Christian","last_name":"Much","full_name":"Much, Christian"},{"full_name":"Sebesta, Marek","last_name":"Sebesta","first_name":"Marek"},{"first_name":"Valeria","last_name":"Buccheri","full_name":"Buccheri, Valeria"},{"first_name":"Filip","last_name":"Horvat","full_name":"Horvat, Filip"},{"full_name":"Jenickova, Irena","first_name":"Irena","last_name":"Jenickova"},{"last_name":"Prochazkova","first_name":"Michaela","full_name":"Prochazkova, Michaela"},{"full_name":"Prochazka, Jan","first_name":"Jan","last_name":"Prochazka"},{"first_name":"Matyas","last_name":"Pinkas","full_name":"Pinkas, Matyas"},{"full_name":"Novacek, Jiri","last_name":"Novacek","first_name":"Jiri"},{"last_name":"Joseph","first_name":"Diego F.","full_name":"Joseph, Diego F."},{"first_name":"Radislav","last_name":"Sedlacek","full_name":"Sedlacek, Radislav"},{"last_name":"Bernecky","orcid":"0000-0003-0893-7036","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"},{"full_name":"O’Carroll, Dónal","first_name":"Dónal","last_name":"O’Carroll"},{"full_name":"Stefl, Richard","first_name":"Richard","last_name":"Stefl"},{"full_name":"Svoboda, Petr","last_name":"Svoboda","first_name":"Petr"}],"quality_controlled":"1","keyword":["Cell Biology","Molecular Biology"],"scopus_import":"1","file_date_updated":"2023-01-24T09:29:02Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"21","external_id":{"pmid":["36332606"],"isi":["000898565300011"]},"article_type":"original","acknowledgement":"We thank Kristian Vlahovicek (University of Zagreb) for support of bioinformatics analyses and Vladimir Benes (EMBL Sequencing Facility) and Genomics and Bioinformatics Core Facility at the Institute of Molecular Genetics for help with RNA sequencing. The main funding was provided by the Czech Science Foundation (EXPRO grant 20-03950X to P.S. and 22-19896S to R. Stefl). Early stages of the work were supported by European Research Council grants under the European Union’s Horizon 2020 Research and Innovation Programme (grants 647403 to P.S. and 649030 to R. Stefl). V.B., D.F.J., and F.H. were in part supported by PhD student fellowships from the Charles University; this work will be in part fulfilling requirements for a PhD degree as “school work.” Funding of D.Z. included the OP RDE project “Internal Grant Agency of Masaryk University” no. CZ.02.2.69/0.0/0.0/19_073/0016943. The Ministry of Education, Youth, and Sports of the Czech Republic (MEYS CR) provided institutional support for CEITEC 2020 project LQ1601. For technical support, we acknowledge EMBL Monterotondo’s genome engineering and transgenic core facilities, the Czech Centre for Phenogenomics at the Institute of Molecular Genetics (supported by RVO 68378050 from the Czech Academy of Sciences and LM2018126 and CZ.02.1.01/0.0/0.0/18_046/0015861 CCP Infrastructure Upgrade II from MEYS CR), the Cryo-EM and Proteomics Core Facilities (CEITEC, Masaryk University) supported by the CIISB research infrastructure (LM2018127 from MEYS CR), and support from the Scientific Service Units of ISTA through resources from the Electron Microscopy Facility. Computational resources included e-Infrastruktura CZ (LM2018140) and ELIXIR-CZ (LM2018131) projects by MEYS CR and the Croatian National Centres of Research Excellence in Personalized Healthcare (#KK.01.1.1.01.0010) and Data Science and Advanced Cooperative Systems (#KK.01.1.1.01.0009) projects funded by the European Structural and Investment Funds grants.","status":"public","oa":1,"publication_identifier":{"issn":["1097-2765"]},"citation":{"ista":"Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek J, Joseph DF, Sedlacek R, Bernecky C, O’Carroll D, Stefl R, Svoboda P. 2022. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. 82(21), 4064–4079.e13.","short":"D. Zapletal, E. Taborska, J. Pasulka, R. Malik, K. Kubicek, M. Zanova, C. Much, M. Sebesta, V. Buccheri, F. Horvat, I. Jenickova, M. Prochazkova, J. Prochazka, M. Pinkas, J. Novacek, D.F. Joseph, R. Sedlacek, C. Bernecky, D. O’Carroll, R. Stefl, P. Svoboda, Molecular Cell 82 (2022) 4064–4079.e13.","mla":"Zapletal, David, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” <i>Molecular Cell</i>, vol. 82, no. 21, Elsevier, 2022, p. 4064–4079.e13, doi:<a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">10.1016/j.molcel.2022.10.010</a>.","ama":"Zapletal D, Taborska E, Pasulka J, et al. Structural and functional basis of mammalian microRNA biogenesis by Dicer. <i>Molecular Cell</i>. 2022;82(21):4064-4079.e13. doi:<a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">10.1016/j.molcel.2022.10.010</a>","apa":"Zapletal, D., Taborska, E., Pasulka, J., Malik, R., Kubicek, K., Zanova, M., … Svoboda, P. (2022). Structural and functional basis of mammalian microRNA biogenesis by Dicer. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">https://doi.org/10.1016/j.molcel.2022.10.010</a>","chicago":"Zapletal, David, Eliska Taborska, Josef Pasulka, Radek Malik, Karel Kubicek, Martina Zanova, Christian Much, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” <i>Molecular Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">https://doi.org/10.1016/j.molcel.2022.10.010</a>.","ieee":"D. Zapletal <i>et al.</i>, “Structural and functional basis of mammalian microRNA biogenesis by Dicer,” <i>Molecular Cell</i>, vol. 82, no. 21. Elsevier, p. 4064–4079.e13, 2022."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":82,"page":"4064-4079.e13","has_accepted_license":"1","year":"2022","_id":"12143","abstract":[{"text":"MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.","lang":"eng"}],"publisher":"Elsevier","publication":"Molecular Cell","department":[{"_id":"CaBe"}],"title":"Structural and functional basis of mammalian microRNA biogenesis by Dicer","date_created":"2023-01-12T12:05:36Z","oa_version":"Published Version"},{"file_date_updated":"2023-01-24T10:45:01Z","article_number":"e1010586","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2022-10-17T00:00:00Z","author":[{"first_name":"Xiuyun","last_name":"Jiang","full_name":"Jiang, Xiuyun"},{"full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck","first_name":"Lena"},{"first_name":"Christian Eduardo","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"full_name":"Pfitzner, Anna-Katharina","last_name":"Pfitzner","first_name":"Anna-Katharina"},{"full_name":"Lominadze, Elene","last_name":"Lominadze","first_name":"Elene"},{"first_name":"Aurélien","last_name":"Roux","full_name":"Roux, Aurélien"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"doi":"10.1371/journal.pcbi.1010586","date_updated":"2023-08-04T09:03:21Z","related_material":{"link":[{"relation":"software","url":"https://github.com/sharonJXY/3-filament-model"}]},"article_processing_charge":"No","scopus_import":"1","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"quality_controlled":"1","intvolume":"        18","publication_status":"published","file":[{"content_type":"application/pdf","success":1,"date_created":"2023-01-24T10:45:01Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_size":2641067,"file_name":"2022_PLoSCompBio_Jiang.pdf","checksum":"bada6a7865e470cf42bbdfa67dd471d2","date_updated":"2023-01-24T10:45:01Z","file_id":"12359"}],"day":"17","ddc":["570"],"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"},{"_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","name":"The evolution of trafficking: from archaea to eukaryotes","grant_number":"96752"}],"language":[{"iso":"eng"}],"month":"10","isi":1,"title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","department":[{"_id":"AnSa"}],"publication":"PLOS Computational Biology","publisher":"Public Library of Science","oa_version":"Published Version","ec_funded":1,"date_created":"2023-01-12T12:08:10Z","abstract":[{"lang":"eng","text":"ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks."}],"volume":18,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12152","has_accepted_license":"1","year":"2022","status":"public","oa":1,"acknowledgement":"A.S . received an award from European Research Council (https://erc.europa.eu, “NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org, UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open, Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation, Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc, MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research (https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and an award from the European Research Council\r\nConsolidator (https://erc.europa.eu, 311536). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","article_type":"original","external_id":{"isi":["000924885500005"]},"issue":"10","citation":{"ieee":"X. Jiang <i>et al.</i>, “Modelling membrane reshaping by staged polymerization of ESCRT-III filaments,” <i>PLOS Computational Biology</i>, vol. 18, no. 10. Public Library of Science, 2022.","chicago":"Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos, Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>.","apa":"Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K., Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>","ama":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. 2022;18(10). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>","ista":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586.","mla":"Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>, vol. 18, no. 10, e1010586, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>.","short":"X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E. Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022)."},"publication_identifier":{"issn":["1553-7358"]}},{"oa_version":"Published Version","date_created":"2023-01-12T12:08:51Z","title":"Eukaryotic gene regulation at equilibrium, or non?","department":[{"_id":"GaTk"}],"publication":"Current Opinion in Systems Biology","publisher":"Elsevier","abstract":[{"text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.","lang":"eng"}],"_id":"12156","has_accepted_license":"1","year":"2022","volume":31,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9, 100435, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>.","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. 2022;31(9). doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>","apa":"Zoller, B., Gregor, T., &#38; Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>.","ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9. Elsevier, 2022."},"publication_identifier":{"issn":["2452-3100"]},"acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","status":"public","oa":1,"article_type":"original","issue":"9","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-01-24T12:14:10Z","article_number":"100435","scopus_import":"1","keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"quality_controlled":"1","author":[{"last_name":"Zoller","first_name":"Benjamin","full_name":"Zoller, Benjamin"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"1","first_name":"Gašper"}],"date_published":"2022-09-01T00:00:00Z","doi":"10.1016/j.coisb.2022.100435","date_updated":"2023-02-13T09:20:34Z","article_processing_charge":"Yes (via OA deal)","intvolume":"        31","publication_status":"published","file":[{"checksum":"97ef01e0cc60cdc84f45640a0f248fb0","file_name":"2022_CurrentBiology_Zoller.pdf","file_size":2214944,"date_updated":"2023-01-24T12:14:10Z","file_id":"12362","date_created":"2023-01-24T12:14:10Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file"}],"language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"month":"09","day":"01","ddc":["570"]},{"quality_controlled":"1","scopus_import":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"doi":"10.7554/elife.66697","date_updated":"2023-08-04T09:04:58Z","article_processing_charge":"No","date_published":"2022-09-26T00:00:00Z","author":[{"full_name":"Hayward, Laura","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","first_name":"Laura","last_name":"Hayward"},{"last_name":"Sella","first_name":"Guy","full_name":"Sella, Guy"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"66697","file_date_updated":"2023-01-24T12:21:32Z","language":[{"iso":"eng"}],"isi":1,"month":"09","day":"26","ddc":["570"],"publication_status":"published","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2023-01-24T12:21:32Z","success":1,"file_id":"12363","date_updated":"2023-01-24T12:21:32Z","file_size":18935612,"checksum":"28de155b231ac1c8d4501c98b2fb359a","file_name":"2022_eLife_Hayward.pdf"}],"intvolume":"        11","abstract":[{"text":"Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.","lang":"eng"}],"oa_version":"Published Version","date_created":"2023-01-12T12:09:00Z","publisher":"eLife Sciences Publications","title":"Polygenic adaptation after a sudden change in environment","department":[{"_id":"NiBa"}],"publication":"eLife","publication_identifier":{"eissn":["2050-084X"]},"citation":{"ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>.","apa":"Hayward, L., &#38; Sella, G. (2022). Polygenic adaptation after a sudden change in environment. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>","ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>","mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>, vol. 11, 66697, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>.","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","short":"L. Hayward, G. Sella, ELife 11 (2022)."},"article_type":"original","external_id":{"isi":["000890735600001"]},"status":"public","oa":1,"acknowledgement":"We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372 Laura Katharine Hayward","year":"2022","has_accepted_license":"1","_id":"12157","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":11},{"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"scopus_import":"1","quality_controlled":"1","date_published":"2022-10-24T00:00:00Z","author":[{"full_name":"Prehal, Christian","last_name":"Prehal","first_name":"Christian"},{"full_name":"von Mentlen, Jean-Marc","first_name":"Jean-Marc","last_name":"von Mentlen"},{"last_name":"Drvarič Talian","first_name":"Sara","full_name":"Drvarič Talian, Sara"},{"last_name":"Vizintin","first_name":"Alen","full_name":"Vizintin, Alen"},{"full_name":"Dominko, Robert","first_name":"Robert","last_name":"Dominko"},{"full_name":"Amenitsch, Heinz","last_name":"Amenitsch","first_name":"Heinz"},{"full_name":"Porcar, Lionel","last_name":"Porcar","first_name":"Lionel"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander"},{"full_name":"Wood, Vanessa","first_name":"Vanessa","last_name":"Wood"}],"article_processing_charge":"No","date_updated":"2023-08-04T09:15:31Z","doi":"10.1038/s41467-022-33931-4","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-01-27T07:19:11Z","article_number":"6326","isi":1,"month":"10","language":[{"iso":"eng"}],"pmid":1,"ddc":["540"],"day":"24","intvolume":"        13","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2023-01-27T07:19:11Z","success":1,"date_updated":"2023-01-27T07:19:11Z","file_id":"12411","file_size":4216931,"checksum":"5034336dbf0f860030ef745c08df9e0e","file_name":"2022_NatureCommunications_Prehal.pdf"}],"publication_status":"published","abstract":[{"text":"The inadequate understanding of the mechanisms that reversibly convert molecular sulfur (S) into lithium sulfide (Li<jats:sub>2</jats:sub>S) via soluble polysulfides (PSs) formation impedes the development of high-performance lithium-sulfur (Li-S) batteries with non-aqueous electrolyte solutions. Here, we use operando small and wide angle X-ray scattering and operando small angle neutron scattering (SANS) measurements to track the nucleation, growth and dissolution of solid deposits from atomic to sub-micron scales during real-time Li-S cell operation. In particular, stochastic modelling based on the SANS data allows quantifying the nanoscale phase evolution during battery cycling. We show that next to nano-crystalline Li<jats:sub>2</jats:sub>S the deposit comprises solid short-chain PSs particles. The analysis of the experimental data suggests that initially, Li<jats:sub>2</jats:sub>S<jats:sub>2</jats:sub> precipitates from the solution and then is partially converted via solid-state electroreduction to Li<jats:sub>2</jats:sub>S. We further demonstrate that mass transport, rather than electron transport through a thin passivating film, limits the discharge capacity and rate performance in Li-S cells.","lang":"eng"}],"date_created":"2023-01-16T09:45:09Z","oa_version":"Published Version","publication":"Nature Communications","department":[{"_id":"StFr"}],"title":"On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering","publisher":"Springer Nature","citation":{"apa":"Prehal, C., von Mentlen, J.-M., Drvarič Talian, S., Vizintin, A., Dominko, R., Amenitsch, H., … Wood, V. (2022). On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-33931-4\">https://doi.org/10.1038/s41467-022-33931-4</a>","chicago":"Prehal, Christian, Jean-Marc von Mentlen, Sara Drvarič Talian, Alen Vizintin, Robert Dominko, Heinz Amenitsch, Lionel Porcar, Stefan Alexander Freunberger, and Vanessa Wood. “On the Nanoscale Structural Evolution of Solid Discharge Products in Lithium-Sulfur Batteries Using Operando Scattering.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-33931-4\">https://doi.org/10.1038/s41467-022-33931-4</a>.","ieee":"C. Prehal <i>et al.</i>, “On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ista":"Prehal C, von Mentlen J-M, Drvarič Talian S, Vizintin A, Dominko R, Amenitsch H, Porcar L, Freunberger SA, Wood V. 2022. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. Nature Communications. 13, 6326.","mla":"Prehal, Christian, et al. “On the Nanoscale Structural Evolution of Solid Discharge Products in Lithium-Sulfur Batteries Using Operando Scattering.” <i>Nature Communications</i>, vol. 13, 6326, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-33931-4\">10.1038/s41467-022-33931-4</a>.","short":"C. Prehal, J.-M. von Mentlen, S. Drvarič Talian, A. Vizintin, R. Dominko, H. Amenitsch, L. Porcar, S.A. Freunberger, V. Wood, Nature Communications 13 (2022).","ama":"Prehal C, von Mentlen J-M, Drvarič Talian S, et al. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-33931-4\">10.1038/s41467-022-33931-4</a>"},"publication_identifier":{"issn":["2041-1723"]},"oa":1,"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant NanoEvolution, grant agreement No 894042. The authors acknowledge the CERIC-ERIC Consortium for the access to the Austrian SAXS beamline and TU Graz for support through the Lead Project LP-03.\r\nLikewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. In addition, the authors acknowledge access to the D-22SANS beamline at the ILL neutron source. Electron microscopy measurements were performed at the Scientific Scenter for Optical and Electron Microscopy (ScopeM) of the Swiss Federal Institute of Technology. C.P. and J.M.M. thank A. Senol for her support with the SANS\r\nbeamtime preparation. S.D.T, A.V. and R.D. acknowledge the financial support by the Slovenian Research Agency (ARRS) research core funding P2-0393 and P2-0423. Furthermore, A.V. acknowledge the funding from the Slovenian Research Agency, research project Z2−1863.\r\nS.A.F. is indebted to IST Austria for support. ","status":"public","external_id":{"pmid":["36280671"],"isi":["000871563700006"]},"article_type":"original","_id":"12208","year":"2022","has_accepted_license":"1","volume":13,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article"},{"quality_controlled":"1","scopus_import":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"doi":"10.1038/s41467-022-32806-y","related_material":{"record":[{"status":"public","relation":"research_data","id":"13068"}]},"date_updated":"2023-08-04T09:25:23Z","article_processing_charge":"No","date_published":"2022-09-05T00:00:00Z","author":[{"first_name":"S.","last_name":"Randriamanantsoa","full_name":"Randriamanantsoa, S."},{"full_name":"Papargyriou, A.","first_name":"A.","last_name":"Papargyriou"},{"full_name":"Maurer, H. C.","first_name":"H. C.","last_name":"Maurer"},{"last_name":"Peschke","first_name":"K.","full_name":"Peschke, K."},{"full_name":"Schuster, M.","last_name":"Schuster","first_name":"M."},{"last_name":"Zecchin","first_name":"G.","full_name":"Zecchin, G."},{"last_name":"Steiger","first_name":"K.","full_name":"Steiger, K."},{"first_name":"R.","last_name":"Öllinger","full_name":"Öllinger, R."},{"first_name":"D.","last_name":"Saur","full_name":"Saur, D."},{"full_name":"Scheel, C.","last_name":"Scheel","first_name":"C."},{"first_name":"R.","last_name":"Rad","full_name":"Rad, R."},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"last_name":"Reichert","first_name":"M.","full_name":"Reichert, M."},{"full_name":"Bausch, A. R.","last_name":"Bausch","first_name":"A. R."}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"5219","file_date_updated":"2023-01-27T08:14:48Z","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"language":[{"iso":"eng"}],"isi":1,"month":"09","day":"05","ddc":["570"],"publication_status":"published","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2023-01-27T08:14:48Z","date_updated":"2023-01-27T08:14:48Z","file_id":"12416","file_size":22645149,"file_name":"2022_NatureCommunications_Randriamanantsoa.pdf","checksum":"295261b5172274fd5b8f85a6a6058828"}],"intvolume":"        13","abstract":[{"lang":"eng","text":"The development dynamics and self-organization of glandular branched epithelia is of utmost importance for our understanding of diverse processes ranging from normal tissue growth to the growth of cancerous tissues. Using single primary murine pancreatic ductal adenocarcinoma (PDAC) cells embedded in a collagen matrix and adapted media supplementation, we generate organoids that self-organize into highly branched structures displaying a seamless lumen connecting terminal end buds, replicating in vivo PDAC architecture. We identify distinct morphogenesis phases, each characterized by a unique pattern of cell invasion, matrix deformation, protein expression, and respective molecular dependencies. We propose a minimal theoretical model of a branching and proliferating tissue, capturing the dynamics of the first phases. Observing the interaction of morphogenesis, mechanical environment and gene expression in vitro sets a benchmark for the understanding of self-organization processes governing complex organoid structure formation processes and branching morphogenesis."}],"oa_version":"Published Version","date_created":"2023-01-16T09:46:53Z","ec_funded":1,"publisher":"Springer Nature","title":"Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids","department":[{"_id":"EdHa"}],"publication":"Nature Communications","publication_identifier":{"issn":["2041-1723"]},"citation":{"ama":"Randriamanantsoa S, Papargyriou A, Maurer HC, et al. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32806-y\">10.1038/s41467-022-32806-y</a>","ista":"Randriamanantsoa S, Papargyriou A, Maurer HC, Peschke K, Schuster M, Zecchin G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch AR. 2022. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. Nature Communications. 13, 5219.","mla":"Randriamanantsoa, S., et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” <i>Nature Communications</i>, vol. 13, 5219, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32806-y\">10.1038/s41467-022-32806-y</a>.","short":"S. Randriamanantsoa, A. Papargyriou, H.C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo, M. Reichert, A.R. Bausch, Nature Communications 13 (2022).","ieee":"S. Randriamanantsoa <i>et al.</i>, “Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","chicago":"Randriamanantsoa, S., A. Papargyriou, H. C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32806-y\">https://doi.org/10.1038/s41467-022-32806-y</a>.","apa":"Randriamanantsoa, S., Papargyriou, A., Maurer, H. C., Peschke, K., Schuster, M., Zecchin, G., … Bausch, A. R. (2022). Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32806-y\">https://doi.org/10.1038/s41467-022-32806-y</a>"},"article_type":"original","external_id":{"isi":["000850348400025"]},"status":"public","acknowledgement":"A.R.B. acknowledges the financial support of the European Research Council (ERC) through the funding of the grant Principles of Integrin Mechanics and Adhesion (PoINT) and the German Research Foundation (DFG, SFB 1032, project ID 201269156). E.H. was supported by the European Union (European Research Council Starting Grant 851288). D.S., M.R., and R.R. acknowledge the support by the German Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project S01, project ID 329628492). C.S. and M.R. acknowledge the support by the German Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project 12, project ID 329628492). M.R. was supported by the German Research Foundation (DFG RE 3723/4-1). A.P. and M.R. were supported by the German Cancer Aid (Max-Eder Program 111273 and 70114328).\r\nOpen Access funding enabled and organized by Projekt DEAL.","oa":1,"year":"2022","has_accepted_license":"1","_id":"12217","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":13},{"article_number":"589","file_date_updated":"2023-01-27T08:23:46Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s42003-022-03446-1","date_updated":"2023-08-04T09:25:59Z","article_processing_charge":"No","author":[{"id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d","full_name":"Muhia, Mary W","last_name":"Muhia","first_name":"Mary W"},{"full_name":"YuanXiang, PingAn","last_name":"YuanXiang","first_name":"PingAn"},{"full_name":"Sedlacik, Jan","first_name":"Jan","last_name":"Sedlacik"},{"full_name":"Schwarz, Jürgen R.","last_name":"Schwarz","first_name":"Jürgen R."},{"last_name":"Heisler","first_name":"Frank F.","full_name":"Heisler, Frank F."},{"first_name":"Kira V.","last_name":"Gromova","full_name":"Gromova, Kira V."},{"last_name":"Thies","first_name":"Edda","full_name":"Thies, Edda"},{"full_name":"Breiden, Petra","last_name":"Breiden","first_name":"Petra"},{"first_name":"Yvonne","last_name":"Pechmann","full_name":"Pechmann, Yvonne"},{"last_name":"Kreutz","first_name":"Michael R.","full_name":"Kreutz, Michael R."},{"full_name":"Kneussel, Matthias","last_name":"Kneussel","first_name":"Matthias"}],"date_published":"2022-06-15T00:00:00Z","quality_controlled":"1","scopus_import":"1","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"publication_status":"published","file":[{"file_id":"12417","date_updated":"2023-01-27T08:23:46Z","file_name":"2022_CommBiology_Muhia.pdf","checksum":"bd95be1e77090208b79bc45ea8785d0b","file_size":3968356,"creator":"dernst","access_level":"open_access","relation":"main_file","success":1,"date_created":"2023-01-27T08:23:46Z","content_type":"application/pdf"}],"intvolume":"         5","day":"15","ddc":["570"],"language":[{"iso":"eng"}],"month":"06","isi":1,"publisher":"Springer Nature","title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","department":[{"_id":"PreCl"}],"publication":"Communications Biology","oa_version":"Published Version","date_created":"2023-01-16T09:48:19Z","abstract":[{"text":"Muskelin (Mkln1) is implicated in neuronal function, regulating plasma membrane receptor trafficking. However, its influence on intrinsic brain activity and corresponding behavioral processes remains unclear. Here we show that murine <jats:italic>Mkln1</jats:italic> knockout causes non-habituating locomotor activity, increased exploratory drive, and decreased locomotor response to amphetamine. Muskelin deficiency impairs social novelty detection while promoting the retention of spatial reference memory and fear extinction recall. This is strongly mirrored in either weaker or stronger resting-state functional connectivity between critical circuits mediating locomotor exploration and cognition. We show that <jats:italic>Mkln1</jats:italic> deletion alters dendrite branching and spine structure, coinciding with enhanced AMPAR-mediated synaptic transmission but selective impairment in synaptic potentiation maintenance. We identify muskelin at excitatory synapses and highlight its role in regulating dendritic spine actin stability. Our findings point to aberrant spine actin modulation and changes in glutamatergic synaptic function as critical mechanisms that contribute to the neurobehavioral phenotype arising from <jats:italic>Mkln1</jats:italic> ablation.","lang":"eng"}],"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":5,"year":"2022","has_accepted_license":"1","_id":"12224","external_id":{"isi":["000811777900003"]},"article_type":"original","oa":1,"acknowledgement":"The authors are grateful to the UKE Animal Facilities (Hamburg) for animal husbandry and Dr. Bastian Tiemann for his veterinary expertise and supervision of animal care. We thank Dr. Franco Lombino for critically reading the manuscript and for helpful discussion. This work was supported by grants from the Deutsche Forschungsgemeinschaft (DFG) (FOR2419-KN556/11-1, FOR2419-KN556/11-2, KN556/12-1) and the Landesforschungsförderung Hamburg (LFF-FV76) to M.K.\r\nOpen Access funding enabled and organized by Projekt DEAL.","status":"public","publication_identifier":{"issn":["2399-3642"]},"citation":{"apa":"Muhia, M. W., YuanXiang, P., Sedlacik, J., Schwarz, J. R., Heisler, F. F., Gromova, K. V., … Kneussel, M. (2022). Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03446-1\">https://doi.org/10.1038/s42003-022-03446-1</a>","chicago":"Muhia, Mary W, PingAn YuanXiang, Jan Sedlacik, Jürgen R. Schwarz, Frank F. Heisler, Kira V. Gromova, Edda Thies, et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03446-1\">https://doi.org/10.1038/s42003-022-03446-1</a>.","ieee":"M. W. Muhia <i>et al.</i>, “Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes,” <i>Communications Biology</i>, vol. 5. Springer Nature, 2022.","ista":"Muhia MW, YuanXiang P, Sedlacik J, Schwarz JR, Heisler FF, Gromova KV, Thies E, Breiden P, Pechmann Y, Kreutz MR, Kneussel M. 2022. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. 5, 589.","short":"M.W. Muhia, P. YuanXiang, J. Sedlacik, J.R. Schwarz, F.F. Heisler, K.V. Gromova, E. Thies, P. Breiden, Y. Pechmann, M.R. Kreutz, M. Kneussel, Communications Biology 5 (2022).","mla":"Muhia, Mary W., et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” <i>Communications Biology</i>, vol. 5, 589, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03446-1\">10.1038/s42003-022-03446-1</a>.","ama":"Muhia MW, YuanXiang P, Sedlacik J, et al. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. <i>Communications Biology</i>. 2022;5. doi:<a href=\"https://doi.org/10.1038/s42003-022-03446-1\">10.1038/s42003-022-03446-1</a>"}},{"keyword":["Developmental Biology","Molecular Biology"],"scopus_import":"1","quality_controlled":"1","author":[{"full_name":"Kogure, Yuki S.","last_name":"Kogure","first_name":"Yuki S."},{"full_name":"Muraoka, Hiromochi","last_name":"Muraoka","first_name":"Hiromochi"},{"last_name":"Koizumi","first_name":"Wataru C.","full_name":"Koizumi, Wataru C."},{"full_name":"Gelin-alessi, Raphaël","first_name":"Raphaël","last_name":"Gelin-alessi"},{"last_name":"Godard","first_name":"Benoit G","id":"3263621A-F248-11E8-B48F-1D18A9856A87","full_name":"Godard, Benoit G"},{"full_name":"Oka, Kotaro","last_name":"Oka","first_name":"Kotaro"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"full_name":"Hotta, Kohji","first_name":"Kohji","last_name":"Hotta"}],"date_published":"2022-11-01T00:00:00Z","article_processing_charge":"No","doi":"10.1242/dev.200215","date_updated":"2023-08-04T09:33:24Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-01-27T10:36:50Z","article_number":"dev200215","month":"11","isi":1,"language":[{"iso":"eng"}],"pmid":1,"ddc":["570"],"day":"01","intvolume":"       149","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2023-01-27T10:36:50Z","success":1,"date_updated":"2023-01-27T10:36:50Z","file_id":"12423","file_size":9160451,"checksum":"871b9c58eb79b9e60752de25a46938d6","file_name":"2022_Development_Kogure.pdf"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Ventral tail bending, which is transient but pronounced, is found in many chordate embryos and constitutes an interesting model of how tissue interactions control embryo shape. Here, we identify one key upstream regulator of ventral tail bending in embryos of the ascidian Ciona. We show that during the early tailbud stages, ventral epidermal cells exhibit a boat-shaped morphology (boat cell) with a narrow apical surface where phosphorylated myosin light chain (pMLC) accumulates. We further show that interfering with the function of the BMP ligand Admp led to pMLC localizing to the basal instead of the apical side of ventral epidermal cells and a reduced number of boat cells. Finally, we show that cutting ventral epidermal midline cells at their apex using an ultraviolet laser relaxed ventral tail bending. Based on these results, we propose a previously unreported function for Admp in localizing pMLC to the apical side of ventral epidermal cells, which causes the tail to bend ventrally by resisting antero-posterior notochord extension at the ventral side of the tail."}],"date_created":"2023-01-16T09:50:12Z","oa_version":"Published Version","publication":"Development","title":"Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona","department":[{"_id":"CaHe"}],"publisher":"The Company of Biologists","citation":{"ista":"Kogure YS, Muraoka H, Koizumi WC, Gelin-alessi R, Godard BG, Oka K, Heisenberg C-PJ, Hotta K. 2022. Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. Development. 149(21), dev200215.","short":"Y.S. Kogure, H. Muraoka, W.C. Koizumi, R. Gelin-alessi, B.G. Godard, K. Oka, C.-P.J. Heisenberg, K. Hotta, Development 149 (2022).","mla":"Kogure, Yuki S., et al. “Admp Regulates Tail Bending by Controlling Ventral Epidermal Cell Polarity via Phosphorylated Myosin Localization in Ciona.” <i>Development</i>, vol. 149, no. 21, dev200215, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/dev.200215\">10.1242/dev.200215</a>.","ama":"Kogure YS, Muraoka H, Koizumi WC, et al. Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. <i>Development</i>. 2022;149(21). doi:<a href=\"https://doi.org/10.1242/dev.200215\">10.1242/dev.200215</a>","apa":"Kogure, Y. S., Muraoka, H., Koizumi, W. C., Gelin-alessi, R., Godard, B. G., Oka, K., … Hotta, K. (2022). Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.200215\">https://doi.org/10.1242/dev.200215</a>","ieee":"Y. S. Kogure <i>et al.</i>, “Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona,” <i>Development</i>, vol. 149, no. 21. The Company of Biologists, 2022.","chicago":"Kogure, Yuki S., Hiromochi Muraoka, Wataru C. Koizumi, Raphaël Gelin-alessi, Benoit G Godard, Kotaro Oka, Carl-Philipp J Heisenberg, and Kohji Hotta. “Admp Regulates Tail Bending by Controlling Ventral Epidermal Cell Polarity via Phosphorylated Myosin Localization in Ciona.” <i>Development</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/dev.200215\">https://doi.org/10.1242/dev.200215</a>."},"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"status":"public","oa":1,"acknowledgement":"iona intestinalis adults were provided by Dr Yutaka Satou (Kyoto University) and Dr Manabu Yoshida (the University of Tokyo) with support from the National Bio-Resource Project of AMED, Japan. We thank Dr Hidehiko Hashimoto and Dr Yuji Mizotani for technical information about 1P-myosin antibody staining. We thank Dr Kaoru Imai and Dr Yutaka Satou for valuable discussion about Admp and for the DNA construct of Bmp2/4 under the Dlx.b upstream sequence. We thank Ms Maki Kogure for constructing the FUSION360 of the intercalating epidermal cell.\r\nThis work was supported by funding from the Japan Society for the Promotion of Science (JP16H01451, JP21H00440). Open Access funding provided by Keio University: Keio Gijuku Daigaku.","issue":"21","external_id":{"isi":["000903991700002"],"pmid":["36227591"]},"article_type":"original","_id":"12231","year":"2022","has_accepted_license":"1","volume":149,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article"},{"intvolume":"        57","publication_status":"published","pmid":1,"day":"01","language":[{"iso":"eng"}],"month":"10","isi":1,"date_published":"2022-10-01T00:00:00Z","author":[{"id":"5299a9ce-7679-11eb-a7bc-d1e62b936307","full_name":"Hino, Naoya","last_name":"Hino","first_name":"Naoya"},{"full_name":"Matsuda, Kimiya","first_name":"Kimiya","last_name":"Matsuda"},{"last_name":"Jikko","first_name":"Yuya","full_name":"Jikko, Yuya"},{"full_name":"Maryu, Gembu","first_name":"Gembu","last_name":"Maryu"},{"full_name":"Sakai, Katsuya","last_name":"Sakai","first_name":"Katsuya"},{"full_name":"Imamura, Ryu","last_name":"Imamura","first_name":"Ryu"},{"full_name":"Tsukiji, Shinya","last_name":"Tsukiji","first_name":"Shinya"},{"last_name":"Aoki","first_name":"Kazuhiro","full_name":"Aoki, Kazuhiro"},{"first_name":"Kenta","last_name":"Terai","full_name":"Terai, Kenta"},{"last_name":"Hirashima","first_name":"Tsuyoshi","full_name":"Hirashima, Tsuyoshi"},{"full_name":"Trepat, Xavier","first_name":"Xavier","last_name":"Trepat"},{"first_name":"Michiyuki","last_name":"Matsuda","full_name":"Matsuda, Michiyuki"}],"date_updated":"2023-08-04T09:38:53Z","doi":"10.1016/j.devcel.2022.09.003","article_processing_charge":"No","scopus_import":"1","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"quality_controlled":"1","page":"2290-2304.e7","volume":57,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12238","year":"2022","acknowledgement":"We thank the members of the Matsuda Laboratory for their helpful discussion and encouragement, and we thank K. Hirano and K. Takakura for their technical assistance. This work was supported by the Kyoto University Live Imaging Center. Financial support was provided in the form of JSPS KAKENHI grants (nos. 17J02107 and 20K22653 to N.H., and 20H05898 and 19H00993 to M.M.), a JST CREST grant (no. JPMJCR1654 to M.M.), a Moonshot R&D grant (no. JPMJPS2022-11 to M.M.), Generalitat de Catalunya and the CERCA Programme (no. SGR-2017-01602 to X.T.), MICCINN/FEDER (no. PGC2018-099645-B-I00 to X.T.), and European Research Council (no. Adv-883739 to X.T.). IBEC is a recipient of a Severo Ochoa Award of Excellence from the MINECO. This work was partly supported by an Extramural Collaborative Research Grant of Cancer Research Institute, Kanazawa University.","status":"public","article_type":"original","external_id":{"isi":["000898428700006"],"pmid":["36174555"]},"issue":"19","citation":{"mla":"Hino, Naoya, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.” <i>Developmental Cell</i>, vol. 57, no. 19, Elsevier, 2022, p. 2290–2304.e7, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">10.1016/j.devcel.2022.09.003</a>.","ista":"Hino N, Matsuda K, Jikko Y, Maryu G, Sakai K, Imamura R, Tsukiji S, Aoki K, Terai K, Hirashima T, Trepat X, Matsuda M. 2022. A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. Developmental Cell. 57(19), 2290–2304.e7.","short":"N. Hino, K. Matsuda, Y. Jikko, G. Maryu, K. Sakai, R. Imamura, S. Tsukiji, K. Aoki, K. Terai, T. Hirashima, X. Trepat, M. Matsuda, Developmental Cell 57 (2022) 2290–2304.e7.","ama":"Hino N, Matsuda K, Jikko Y, et al. A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. <i>Developmental Cell</i>. 2022;57(19):2290-2304.e7. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">10.1016/j.devcel.2022.09.003</a>","apa":"Hino, N., Matsuda, K., Jikko, Y., Maryu, G., Sakai, K., Imamura, R., … Matsuda, M. (2022). A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">https://doi.org/10.1016/j.devcel.2022.09.003</a>","chicago":"Hino, Naoya, Kimiya Matsuda, Yuya Jikko, Gembu Maryu, Katsuya Sakai, Ryu Imamura, Shinya Tsukiji, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.09.003\">https://doi.org/10.1016/j.devcel.2022.09.003</a>.","ieee":"N. Hino <i>et al.</i>, “A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration,” <i>Developmental Cell</i>, vol. 57, no. 19. Elsevier, p. 2290–2304.e7, 2022."},"publication_identifier":{"issn":["1534-5807"]},"title":"A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration","department":[{"_id":"CaHe"}],"publication":"Developmental Cell","publisher":"Elsevier","oa_version":"None","date_created":"2023-01-16T09:51:39Z","abstract":[{"text":"Upon the initiation of collective cell migration, the cells at the free edge are specified as leader cells; however, the mechanism underlying the leader cell specification remains elusive. Here, we show that lamellipodial extension after the release from mechanical confinement causes sustained extracellular signal-regulated kinase (ERK) activation and underlies the leader cell specification. Live-imaging of Madin-Darby canine kidney (MDCK) cells and mouse epidermis through the use of Förster resonance energy transfer (FRET)-based biosensors showed that leader cells exhibit sustained ERK activation in a hepatocyte growth factor (HGF)-dependent manner. Meanwhile, follower cells exhibit oscillatory ERK activation waves in an epidermal growth factor (EGF) signaling-dependent manner. Lamellipodial extension at the free edge increases the cellular sensitivity to HGF. The HGF-dependent ERK activation, in turn, promotes lamellipodial extension, thereby forming a positive feedback loop between cell extension and ERK activation and specifying the cells at the free edge as the leader cells. Our findings show that the integration of physical and biochemical cues underlies the leader cell specification during collective cell migration.","lang":"eng"}]},{"publication_status":"published","file":[{"file_id":"12435","date_updated":"2023-01-30T07:46:51Z","checksum":"04d5c12490052d03e4dc4412338a43dd","file_name":"2022_MolecularPlant_Johnson.pdf","file_size":2307251,"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2023-01-30T07:46:51Z","success":1,"content_type":"application/pdf"}],"intvolume":"        15","project":[{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"month":"10","isi":1,"day":"03","ddc":["580"],"pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-01-30T07:46:51Z","quality_controlled":"1","scopus_import":"1","keyword":["Plant Science","Molecular Biology"],"doi":"10.1016/j.molp.2022.09.003","date_updated":"2023-08-04T09:39:24Z","article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","orcid":"0000-0001-9732-3815","last_name":"Costanzo"},{"full_name":"Dahhan, Dana A.","last_name":"Dahhan","first_name":"Dana A."},{"first_name":"Sebastian Y.","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"date_published":"2022-10-03T00:00:00Z","year":"2022","has_accepted_license":"1","_id":"12239","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"1533-1542","volume":15,"publication_identifier":{"issn":["1674-2052"]},"citation":{"mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>.","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. 2022;15(10):1533-1542. doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., &#38; Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>","ieee":"A. J. Johnson <i>et al.</i>, “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” <i>Molecular Plant</i>, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>."},"external_id":{"isi":["000882769800009"],"pmid":["36081349"]},"article_type":"original","issue":"10","acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","oa":1,"status":"public","oa_version":"Published Version","date_created":"2023-01-16T09:51:49Z","publisher":"Elsevier","title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"publication":"Molecular Plant","abstract":[{"lang":"eng","text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs."}]},{"volume":149,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"12245","has_accepted_license":"1","year":"2022","acknowledgement":"We are grateful to Dr Tom Pettini for the advice on smiFISH technique and Dr Laure Bally-Cuif for sharing plasmids. The authors also thank the Biological Services Facility, Bioimaging and Systems Microscopy Facilities of the University of Manchester for technical support.\r\nThis work was supported by a Wellcome Trust Senior Research Fellowship (090868/Z/09/Z) and a Wellcome Trust Investigator Award (224394/Z/21/Z) to N.P. and a Medical Research Council Career Development Award to C.S.M. (MR/V032534/1). J.B. was supported by a Wellcome Trust Four-Year PhD Studentship in Basic Science (219992/Z/19/Z). Open Access funding provided by The University of Manchester. Deposited in PMC for immediate release.","status":"public","oa":1,"issue":"19","external_id":{"pmid":["36189829"],"isi":["000918161000003"]},"article_type":"original","citation":{"apa":"Soto, X., Burton, J., Manning, C. S., Minchington, T., Lea, R., Lee, J., … Papalopulu, N. (2022). Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>","ieee":"X. Soto <i>et al.</i>, “Sequential and additive expression of miR-9 precursors control timing of neurogenesis,” <i>Development</i>, vol. 149, no. 19. The Company of Biologists, 2022.","chicago":"Soto, Ximena, Joshua Burton, Cerys S. Manning, Thomas Minchington, Robert Lea, Jessica Lee, Jochen Kursawe, Magnus Rattray, and Nancy Papalopulu. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>.","mla":"Soto, Ximena, et al. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>, vol. 149, no. 19, dev200474, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>.","short":"X. Soto, J. Burton, C.S. Manning, T. Minchington, R. Lea, J. Lee, J. Kursawe, M. Rattray, N. Papalopulu, Development 149 (2022).","ista":"Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray M, Papalopulu N. 2022. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. Development. 149(19), dev200474.","ama":"Soto X, Burton J, Manning CS, et al. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. 2022;149(19). doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>"},"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"publication":"Development","department":[{"_id":"AnKi"}],"title":"Sequential and additive expression of miR-9 precursors control timing of neurogenesis","publisher":"The Company of Biologists","date_created":"2023-01-16T09:53:17Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state."}],"intvolume":"       149","file":[{"file_size":9348839,"file_name":"2022_Development_Soto.pdf","checksum":"d7c29b74e9e4032308228cc704a30e88","date_updated":"2023-01-30T08:35:44Z","file_id":"12438","content_type":"application/pdf","success":1,"date_created":"2023-01-30T08:35:44Z","relation":"main_file","access_level":"open_access","creator":"dernst"}],"publication_status":"published","pmid":1,"ddc":["570"],"day":"01","month":"10","isi":1,"language":[{"iso":"eng"}],"file_date_updated":"2023-01-30T08:35:44Z","article_number":"dev200474","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Soto, Ximena","first_name":"Ximena","last_name":"Soto"},{"first_name":"Joshua","last_name":"Burton","full_name":"Burton, Joshua"},{"full_name":"Manning, Cerys S.","last_name":"Manning","first_name":"Cerys S."},{"id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","last_name":"Minchington","first_name":"Thomas"},{"first_name":"Robert","last_name":"Lea","full_name":"Lea, Robert"},{"full_name":"Lee, Jessica","first_name":"Jessica","last_name":"Lee"},{"first_name":"Jochen","last_name":"Kursawe","full_name":"Kursawe, Jochen"},{"full_name":"Rattray, Magnus","first_name":"Magnus","last_name":"Rattray"},{"full_name":"Papalopulu, Nancy","first_name":"Nancy","last_name":"Papalopulu"}],"date_published":"2022-10-01T00:00:00Z","article_processing_charge":"No","doi":"10.1242/dev.200474","related_material":{"link":[{"url":" https://github.com/burtonjosh/StepwiseMir9","relation":"software"}]},"date_updated":"2023-08-04T09:41:08Z","keyword":["Developmental Biology","Molecular Biology"],"scopus_import":"1","quality_controlled":"1"},{"isi":1,"month":"09","language":[{"iso":"eng"}],"ddc":["570"],"day":"01","intvolume":"        18","file":[{"checksum":"8b1d8f5ea20c8408acf466435fb6ae01","file_name":"2022_MolecularSystemsBio_Angermayr.pdf","file_size":1098812,"date_updated":"2023-01-30T09:49:55Z","file_id":"12446","date_created":"2023-01-30T09:49:55Z","success":1,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file"}],"publication_status":"published","keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"scopus_import":"1","quality_controlled":"1","date_published":"2022-09-01T00:00:00Z","author":[{"orcid":"0000-0001-8619-2223","last_name":"Angermayr","first_name":"Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","full_name":"Angermayr, Andreas"},{"last_name":"Pang","first_name":"Tin Yau","full_name":"Pang, Tin Yau"},{"last_name":"Chevereau","first_name":"Guillaume","full_name":"Chevereau, Guillaume"},{"last_name":"Mitosch","first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","full_name":"Mitosch, Karin"},{"full_name":"Lercher, Martin J","first_name":"Martin J","last_name":"Lercher"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"}],"article_processing_charge":"No","doi":"10.15252/msb.202110490","date_updated":"2023-08-04T09:51:49Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"M-Shop"}],"file_date_updated":"2023-01-30T09:49:55Z","article_number":"e10490","citation":{"apa":"Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., &#38; Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative antibiotic response. <i>Molecular Systems Biology</i>. Embo Press. <a href=\"https://doi.org/10.15252/msb.202110490\">https://doi.org/10.15252/msb.202110490</a>","ieee":"A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M. T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic response,” <i>Molecular Systems Biology</i>, vol. 18, no. 9. Embo Press, 2022.","chicago":"Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” <i>Molecular Systems Biology</i>. Embo Press, 2022. <a href=\"https://doi.org/10.15252/msb.202110490\">https://doi.org/10.15252/msb.202110490</a>.","short":"A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach, Molecular Systems Biology 18 (2022).","mla":"Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” <i>Molecular Systems Biology</i>, vol. 18, no. 9, e10490, Embo Press, 2022, doi:<a href=\"https://doi.org/10.15252/msb.202110490\">10.15252/msb.202110490</a>.","ista":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022. Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. 18(9), e10490.","ama":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated negative feedback shapes quantitative antibiotic response. <i>Molecular Systems Biology</i>. 2022;18(9). doi:<a href=\"https://doi.org/10.15252/msb.202110490\">10.15252/msb.202110490</a>"},"publication_identifier":{"eissn":["1744-4292"]},"acknowledgement":"This work was in part supported by Human Frontier Science Program GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund (FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352. We wouldlike to thank the Bollenbach group for regular fruitful discussions. We areparticularly thankful for the technical assistance of Booshini Fernando andfor discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba Machine Shop for their support inbuilding a housing for the stacker of the plate reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open Accessfunding enabled and organized by Projekt DEAL.","status":"public","oa":1,"issue":"9","external_id":{"isi":["000856482800001"]},"article_type":"original","_id":"12261","year":"2022","has_accepted_license":"1","volume":18,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","abstract":[{"text":"Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole-cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth-mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance.","lang":"eng"}],"date_created":"2023-01-16T09:58:34Z","oa_version":"Published Version","publication":"Molecular Systems Biology","title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","department":[{"_id":"ToBo"}],"publisher":"Embo Press"},{"abstract":[{"text":"The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.","lang":"eng"}],"oa_version":"Published Version","date_created":"2023-01-16T09:59:06Z","department":[{"_id":"EM-Fac"}],"title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","publication":"Nature Structural & Molecular Biology","publisher":"Springer Nature","citation":{"ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. <i>Nature Structural &#38; Molecular Biology</i>. 2022;29(9):942-953. doi:<a href=\"https://doi.org/10.1038/s41594-022-00832-5\">10.1038/s41594-022-00832-5</a>","mla":"Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:<a href=\"https://doi.org/10.1038/s41594-022-00832-5\">10.1038/s41594-022-00832-5</a>.","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser, C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel, D. Haselbach, H. Bergler, Nature Structural &#38; Molecular Biology 29 (2022) 942–953.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural &#38; Molecular Biology. 29(9), 942–953.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41594-022-00832-5\">https://doi.org/10.1038/s41594-022-00832-5</a>.","ieee":"M. Prattes <i>et al.</i>, “Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser, G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-022-00832-5\">https://doi.org/10.1038/s41594-022-00832-5</a>"},"publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"status":"public","acknowledgement":"We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert, J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants 32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A. J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1 and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM during early phases of this\r\nproject. This research was supported by the Scientific Service Units of IST Austria through\r\nresources provided by the Electron Microscopy Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics), University Graz for support with the quantification of\r\nthe SPR particle release assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences, Vienna for her help in early stages of the SPR experiments.","oa":1,"external_id":{"pmid":["36097293"],"isi":["000852942100004"]},"article_type":"original","issue":"9","_id":"12262","has_accepted_license":"1","year":"2022","page":"942-953","volume":29,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","keyword":["Molecular Biology","Structural Biology"],"quality_controlled":"1","date_published":"2022-09-12T00:00:00Z","author":[{"full_name":"Prattes, Michael","first_name":"Michael","last_name":"Prattes"},{"last_name":"Grishkovskaya","first_name":"Irina","full_name":"Grishkovskaya, Irina"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hetzmannseder, Christina","last_name":"Hetzmannseder","first_name":"Christina"},{"full_name":"Zisser, Gertrude","first_name":"Gertrude","last_name":"Zisser"},{"first_name":"Carolin","last_name":"Sailer","full_name":"Sailer, Carolin"},{"full_name":"Kargas, Vasileios","last_name":"Kargas","first_name":"Vasileios"},{"first_name":"Mathias","last_name":"Loibl","full_name":"Loibl, Mathias"},{"last_name":"Gerhalter","first_name":"Magdalena","full_name":"Gerhalter, Magdalena"},{"full_name":"Kofler, Lisa","first_name":"Lisa","last_name":"Kofler"},{"last_name":"Warren","first_name":"Alan J.","full_name":"Warren, Alan J."},{"first_name":"Florian","last_name":"Stengel","full_name":"Stengel, Florian"},{"last_name":"Haselbach","first_name":"David","full_name":"Haselbach, David"},{"full_name":"Bergler, Helmut","first_name":"Helmut","last_name":"Bergler"}],"doi":"10.1038/s41594-022-00832-5","date_updated":"2023-08-04T09:52:20Z","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"EM-Fac"}],"file_date_updated":"2023-01-30T10:00:04Z","language":[{"iso":"eng"}],"month":"09","isi":1,"pmid":1,"day":"12","ddc":["570"],"intvolume":"        29","publication_status":"published","file":[{"file_id":"12447","date_updated":"2023-01-30T10:00:04Z","checksum":"2d5c3ec01718fefd7553052b0b8a0793","file_name":"2022_NatureStrucMolecBio_Prattes.pdf","file_size":9935057,"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2023-01-30T10:00:04Z","success":1,"content_type":"application/pdf"}]},{"volume":221,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"12272","has_accepted_license":"1","year":"2022","status":"public","oa":1,"issue":"8","external_id":{"pmid":["35856919"],"isi":["000874717200001"]},"article_type":"original","citation":{"apa":"Stopp, J. A., &#38; Sixt, M. K. (2022). Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>","ieee":"J. A. Stopp and M. K. Sixt, “Plan your trip before you leave: The neutrophils’ search-and-run journey,” <i>Journal of Cell Biology</i>, vol. 221, no. 8. Rockefeller University Press, 2022.","chicago":"Stopp, Julian A, and Michael K Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>.","mla":"Stopp, Julian A., and Michael K. Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>, vol. 221, no. 8, e202206127, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>.","short":"J.A. Stopp, M.K. Sixt, Journal of Cell Biology 221 (2022).","ista":"Stopp JA, Sixt MK. 2022. Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. 221(8), e202206127.","ama":"Stopp JA, Sixt MK. Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. 2022;221(8). doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>"},"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"publication":"Journal of Cell Biology","department":[{"_id":"MiSi"}],"title":"Plan your trip before you leave: The neutrophils’ search-and-run journey","publisher":"Rockefeller University Press","date_created":"2023-01-16T10:01:08Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Reading, interpreting and crawling along gradients of chemotactic cues is one of the most complex questions in cell biology. In this issue, Georgantzoglou et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo models to map the temporal sequence of how neutrophils respond to an acutely arising gradient of chemoattractant."}],"intvolume":"       221","file":[{"file_id":"12451","date_updated":"2023-01-30T10:39:34Z","file_size":969969,"file_name":"2022_JourCellBiology_Stopp.pdf","checksum":"6b1620743669679b48b9389bb40f5a11","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2023-01-30T10:39:34Z"}],"publication_status":"published","pmid":1,"ddc":["570"],"day":"20","month":"07","isi":1,"language":[{"iso":"eng"}],"file_date_updated":"2023-01-30T10:39:34Z","article_number":"e202206127","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"author":[{"first_name":"Julian A","last_name":"Stopp","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"}],"date_published":"2022-07-20T00:00:00Z","article_processing_charge":"No","date_updated":"2023-12-21T14:30:01Z","doi":"10.1083/jcb.202206127","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14697"}]},"keyword":["Cell Biology"],"scopus_import":"1","quality_controlled":"1"}]