[{"language":[{"iso":"eng"}],"keyword":["Cell Biology","Molecular Biology"],"publication":"Molecular Cell","has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","month":"11","file":[{"checksum":"999e443b54e4fdaa2542ca5a97619731","file_size":7368534,"date_created":"2023-01-24T09:29:02Z","content_type":"application/pdf","file_name":"2022_MolecularCell_Zapletal.pdf","date_updated":"2023-01-24T09:29:02Z","success":1,"relation":"main_file","access_level":"open_access","creator":"dernst","file_id":"12354"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-11-03T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["1097-2765"]},"oa":1,"page":"4064-4079.e13","quality_controlled":"1","file_date_updated":"2023-01-24T09:29:02Z","publisher":"Elsevier","article_type":"original","_id":"12143","pmid":1,"scopus_import":"1","author":[{"full_name":"Zapletal, David","last_name":"Zapletal","first_name":"David"},{"first_name":"Eliska","last_name":"Taborska","full_name":"Taborska, Eliska"},{"last_name":"Pasulka","first_name":"Josef","full_name":"Pasulka, Josef"},{"last_name":"Malik","first_name":"Radek","full_name":"Malik, Radek"},{"first_name":"Karel","last_name":"Kubicek","full_name":"Kubicek, Karel"},{"full_name":"Zanova, Martina","first_name":"Martina","last_name":"Zanova"},{"full_name":"Much, Christian","first_name":"Christian","last_name":"Much"},{"last_name":"Sebesta","first_name":"Marek","full_name":"Sebesta, Marek"},{"last_name":"Buccheri","first_name":"Valeria","full_name":"Buccheri, Valeria"},{"full_name":"Horvat, Filip","last_name":"Horvat","first_name":"Filip"},{"full_name":"Jenickova, Irena","first_name":"Irena","last_name":"Jenickova"},{"full_name":"Prochazkova, Michaela","first_name":"Michaela","last_name":"Prochazkova"},{"first_name":"Jan","last_name":"Prochazka","full_name":"Prochazka, Jan"},{"first_name":"Matyas","last_name":"Pinkas","full_name":"Pinkas, Matyas"},{"full_name":"Novacek, Jiri","last_name":"Novacek","first_name":"Jiri"},{"full_name":"Joseph, Diego F.","first_name":"Diego F.","last_name":"Joseph"},{"full_name":"Sedlacek, Radislav","first_name":"Radislav","last_name":"Sedlacek"},{"orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"O’Carroll, Dónal","last_name":"O’Carroll","first_name":"Dónal"},{"full_name":"Stefl, Richard","first_name":"Richard","last_name":"Stefl"},{"full_name":"Svoboda, Petr","first_name":"Petr","last_name":"Svoboda"}],"issue":"21","publication_status":"published","department":[{"_id":"CaBe"}],"date_created":"2023-01-12T12:05:36Z","article_processing_charge":"No","title":"Structural and functional basis of mammalian microRNA biogenesis by Dicer","intvolume":"        82","volume":82,"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.","ddc":["570"],"date_updated":"2023-08-04T08:57:17Z","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.","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>.","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.","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.","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>.","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>"},"year":"2022","isi":1,"external_id":{"pmid":["36332606"],"isi":["000898565300011"]},"doi":"10.1016/j.molcel.2022.10.010","day":"03","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"}]},{"file_date_updated":"2023-01-24T10:10:43Z","ec_funded":1,"quality_controlled":"1","article_type":"letter_note","publisher":"Frontiers Media","author":[{"full_name":"Gambino, Giuditta","last_name":"Gambino","first_name":"Giuditta"},{"full_name":"Bhik-Ghanie, Rebecca","first_name":"Rebecca","last_name":"Bhik-Ghanie"},{"full_name":"Giglia, Giuseppe","first_name":"Giuseppe","last_name":"Giglia"},{"first_name":"M. Victoria","last_name":"Puig","full_name":"Puig, M. Victoria"},{"id":"44B06F76-F248-11E8-B48F-1D18A9856A87","last_name":"Ramirez Villegas","first_name":"Juan F","full_name":"Ramirez Villegas, Juan F"},{"last_name":"Zaldivar","first_name":"Daniel","full_name":"Zaldivar, Daniel"}],"_id":"12149","scopus_import":"1","title":"Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels","intvolume":"        16","publication_status":"published","article_processing_charge":"No","department":[{"_id":"JoCs"}],"date_created":"2023-01-12T12:07:39Z","ddc":["570"],"acknowledgement":"This work was supported by a DFG grant ZA990/1 to DZ. This work was supported by the MSCA EU proposal 841301 - DREAM, European Commission; Horizon 2020 - Research and Innovation Framework Programme to JFRV.","volume":16,"isi":1,"external_id":{"isi":["000886671400001"]},"date_updated":"2023-08-04T09:01:06Z","citation":{"apa":"Gambino, G., Bhik-Ghanie, R., Giglia, G., Puig, M. V., Ramirez Villegas, J. F., &#38; Zaldivar, D. (2022). Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. <i>Frontiers in Neural Circuits</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fncir.2022.1028154\">https://doi.org/10.3389/fncir.2022.1028154</a>","ama":"Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar D. Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. <i>Frontiers in Neural Circuits</i>. 2022;16. doi:<a href=\"https://doi.org/10.3389/fncir.2022.1028154\">10.3389/fncir.2022.1028154</a>","chicago":"Gambino, Giuditta, Rebecca Bhik-Ghanie, Giuseppe Giglia, M. Victoria Puig, Juan F Ramirez Villegas, and Daniel Zaldivar. “Editorial: Neuromodulatory Ascending Systems: Their Influence at the Microscopic and Macroscopic Levels.” <i>Frontiers in Neural Circuits</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fncir.2022.1028154\">https://doi.org/10.3389/fncir.2022.1028154</a>.","ieee":"G. Gambino, R. Bhik-Ghanie, G. Giglia, M. V. Puig, J. F. Ramirez Villegas, and D. Zaldivar, “Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels,” <i>Frontiers in Neural Circuits</i>, vol. 16. Frontiers Media, 2022.","mla":"Gambino, Giuditta, et al. “Editorial: Neuromodulatory Ascending Systems: Their Influence at the Microscopic and Macroscopic Levels.” <i>Frontiers in Neural Circuits</i>, vol. 16, 1028154, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fncir.2022.1028154\">10.3389/fncir.2022.1028154</a>.","short":"G. Gambino, R. Bhik-Ghanie, G. Giglia, M.V. Puig, J.F. Ramirez Villegas, D. Zaldivar, Frontiers in Neural Circuits 16 (2022).","ista":"Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar D. 2022. Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. Frontiers in Neural Circuits. 16, 1028154."},"year":"2022","abstract":[{"text":"Editorial on the Research Topic","lang":"eng"}],"doi":"10.3389/fncir.2022.1028154","day":"26","language":[{"iso":"eng"}],"keyword":["Cellular and Molecular Neuroscience","Cognitive Neuroscience","Sensory Systems","Neuroscience (miscellaneous)"],"publication":"Frontiers in Neural Circuits","has_accepted_license":"1","month":"10","article_number":"1028154","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"26BAE2E4-B435-11E9-9278-68D0E5697425","grant_number":"841301","name":"The Brainstem-Hippocampus Network Uncovered: Dynamics, Reactivation and Memory Consolidation"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"12357","creator":"dernst","success":1,"relation":"main_file","access_level":"open_access","date_updated":"2023-01-24T10:10:43Z","content_type":"application/pdf","file_name":"2022_FrontiersNeuralCircuits_Gambino.pdf","date_created":"2023-01-24T10:10:43Z","file_size":110031,"checksum":"457aa00e1800847abb340853058531de"}],"date_published":"2022-10-26T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["1662-5110"]}},{"abstract":[{"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.","lang":"eng"}],"day":"17","doi":"10.1371/journal.pcbi.1010586","external_id":{"isi":["000924885500005"]},"isi":1,"year":"2022","citation":{"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).","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.","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>","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>","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>.","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."},"date_updated":"2023-08-04T09:03:21Z","ddc":["570"],"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.","volume":18,"intvolume":"        18","title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","date_created":"2023-01-12T12:08:10Z","department":[{"_id":"AnSa"}],"article_processing_charge":"No","publication_status":"published","issue":"10","author":[{"full_name":"Jiang, Xiuyun","first_name":"Xiuyun","last_name":"Jiang"},{"first_name":"Lena","last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena"},{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo","first_name":"Christian Eduardo","last_name":"Vanhille-Campos"},{"full_name":"Pfitzner, Anna-Katharina","last_name":"Pfitzner","first_name":"Anna-Katharina"},{"last_name":"Lominadze","first_name":"Elene","full_name":"Lominadze, Elene"},{"first_name":"Aurélien","last_name":"Roux","full_name":"Roux, Aurélien"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"}],"scopus_import":"1","_id":"12152","article_type":"original","publisher":"Public Library of Science","file_date_updated":"2023-01-24T10:45:01Z","ec_funded":1,"quality_controlled":"1","oa":1,"publication_identifier":{"issn":["1553-7358"]},"type":"journal_article","date_published":"2022-10-17T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"relation":"software","url":"https://github.com/sharonJXY/3-filament-model"}]},"file":[{"date_updated":"2023-01-24T10:45:01Z","file_name":"2022_PLoSCompBio_Jiang.pdf","content_type":"application/pdf","date_created":"2023-01-24T10:45:01Z","checksum":"bada6a7865e470cf42bbdfa67dd471d2","file_size":2641067,"file_id":"12359","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file"}],"article_number":"e1010586","month":"10","project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"},{"name":"The evolution of trafficking: from archaea to eukaryotes","grant_number":"96752","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"PLOS Computational Biology","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}]},{"volume":31,"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. ","ddc":["570"],"year":"2022","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>.","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.","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>","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>","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.","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>."},"date_updated":"2023-02-13T09:20:34Z","day":"01","doi":"10.1016/j.coisb.2022.100435","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"}],"quality_controlled":"1","file_date_updated":"2023-01-24T12:14:10Z","publisher":"Elsevier","article_type":"original","scopus_import":"1","_id":"12156","issue":"9","author":[{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"1","last_name":"Tkačik","first_name":"Gašper"}],"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"GaTk"}],"date_created":"2023-01-12T12:08:51Z","publication_status":"published","intvolume":"        31","title":"Eukaryotic gene regulation at equilibrium, or non?","file":[{"creator":"dernst","file_id":"12362","relation":"main_file","access_level":"open_access","success":1,"file_name":"2022_CurrentBiology_Zoller.pdf","content_type":"application/pdf","date_updated":"2023-01-24T12:14:10Z","file_size":2214944,"checksum":"97ef01e0cc60cdc84f45640a0f248fb0","date_created":"2023-01-24T12:14:10Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-09-01T00:00:00Z","publication_identifier":{"issn":["2452-3100"]},"oa":1,"keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Current Opinion in Systems Biology","project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","article_number":"100435","month":"09"},{"file":[{"creator":"dernst","file_id":"12363","access_level":"open_access","success":1,"relation":"main_file","content_type":"application/pdf","file_name":"2022_eLife_Hayward.pdf","date_updated":"2023-01-24T12:21:32Z","file_size":18935612,"checksum":"28de155b231ac1c8d4501c98b2fb359a","date_created":"2023-01-24T12:21:32Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"eissn":["2050-084X"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-09-26T00:00:00Z","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"language":[{"iso":"eng"}],"oa_version":"Published Version","article_number":"66697","month":"09","has_accepted_license":"1","publication":"eLife","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","volume":11,"ddc":["570"],"day":"26","doi":"10.7554/elife.66697","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"}],"year":"2022","citation":{"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).","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>.","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>.","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>","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>"},"date_updated":"2023-08-04T09:04:58Z","external_id":{"isi":["000890735600001"]},"isi":1,"publisher":"eLife Sciences Publications","article_type":"original","quality_controlled":"1","file_date_updated":"2023-01-24T12:21:32Z","article_processing_charge":"No","date_created":"2023-01-12T12:09:00Z","department":[{"_id":"NiBa"}],"publication_status":"published","intvolume":"        11","title":"Polygenic adaptation after a sudden change in environment","scopus_import":"1","_id":"12157","author":[{"id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","full_name":"Hayward, Laura","last_name":"Hayward","first_name":"Laura"},{"full_name":"Sella, Guy","last_name":"Sella","first_name":"Guy"}]},{"year":"2022","citation":{"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.","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>.","apa":"Prehal, C., von Mentlen, J.-M., Drvarič Talian, S., Vizintin, A., Dominko, R., Amenitsch, H., … Wood, V. (2022). On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-33931-4\">https://doi.org/10.1038/s41467-022-33931-4</a>","ama":"Prehal C, von Mentlen J-M, Drvarič Talian S, et al. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-33931-4\">10.1038/s41467-022-33931-4</a>","ista":"Prehal C, von Mentlen J-M, Drvarič Talian S, Vizintin A, Dominko R, Amenitsch H, Porcar L, Freunberger SA, Wood V. 2022. On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering. Nature Communications. 13, 6326.","short":"C. Prehal, J.-M. von Mentlen, S. Drvarič Talian, A. Vizintin, R. Dominko, H. Amenitsch, L. Porcar, S.A. Freunberger, V. Wood, Nature Communications 13 (2022).","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>."},"date_updated":"2023-08-04T09:15:31Z","external_id":{"isi":["000871563700006"],"pmid":["36280671"]},"isi":1,"day":"24","doi":"10.1038/s41467-022-33931-4","abstract":[{"lang":"eng","text":"The inadequate understanding of the mechanisms that reversibly convert molecular sulfur (S) into lithium sulfide (Li<jats:sub>2</jats:sub>S) via soluble polysulfides (PSs) formation impedes the development of high-performance lithium-sulfur (Li-S) batteries with non-aqueous electrolyte solutions. Here, we use operando small and wide angle X-ray scattering and operando small angle neutron scattering (SANS) measurements to track the nucleation, growth and dissolution of solid deposits from atomic to sub-micron scales during real-time Li-S cell operation. In particular, stochastic modelling based on the SANS data allows quantifying the nanoscale phase evolution during battery cycling. We show that next to nano-crystalline Li<jats:sub>2</jats:sub>S the deposit comprises solid short-chain PSs particles. The analysis of the experimental data suggests that initially, Li<jats:sub>2</jats:sub>S<jats:sub>2</jats:sub> precipitates from the solution and then is partially converted via solid-state electroreduction to Li<jats:sub>2</jats:sub>S. We further demonstrate that mass transport, rather than electron transport through a thin passivating film, limits the discharge capacity and rate performance in Li-S cells."}],"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. ","volume":13,"ddc":["540"],"scopus_import":"1","_id":"12208","pmid":1,"author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"full_name":"von Mentlen, Jean-Marc","last_name":"von Mentlen","first_name":"Jean-Marc"},{"full_name":"Drvarič Talian, Sara","last_name":"Drvarič Talian","first_name":"Sara"},{"full_name":"Vizintin, Alen","first_name":"Alen","last_name":"Vizintin"},{"full_name":"Dominko, Robert","first_name":"Robert","last_name":"Dominko"},{"first_name":"Heinz","last_name":"Amenitsch","full_name":"Amenitsch, Heinz"},{"last_name":"Porcar","first_name":"Lionel","full_name":"Porcar, Lionel"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Wood, Vanessa","last_name":"Wood","first_name":"Vanessa"}],"date_created":"2023-01-16T09:45:09Z","department":[{"_id":"StFr"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        13","title":"On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering","quality_controlled":"1","file_date_updated":"2023-01-27T07:19:11Z","publisher":"Springer Nature","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-10-24T00:00:00Z","publication_identifier":{"issn":["2041-1723"]},"oa":1,"file":[{"relation":"main_file","success":1,"access_level":"open_access","creator":"dernst","file_id":"12411","checksum":"5034336dbf0f860030ef745c08df9e0e","file_size":4216931,"date_created":"2023-01-27T07:19:11Z","file_name":"2022_NatureCommunications_Prehal.pdf","content_type":"application/pdf","date_updated":"2023-01-27T07:19:11Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","publication":"Nature Communications","oa_version":"Published Version","article_number":"6326","month":"10","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"language":[{"iso":"eng"}]},{"oa":1,"publication_identifier":{"issn":["2041-1723"]},"date_published":"2022-09-05T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","related_material":{"record":[{"id":"13068","relation":"research_data","status":"public"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","relation":"main_file","success":1,"file_id":"12416","creator":"dernst","date_created":"2023-01-27T08:14:48Z","checksum":"295261b5172274fd5b8f85a6a6058828","file_size":22645149,"date_updated":"2023-01-27T08:14:48Z","file_name":"2022_NatureCommunications_Randriamanantsoa.pdf","content_type":"application/pdf"}],"month":"09","article_number":"5219","oa_version":"Published Version","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"}],"publication":"Nature Communications","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"abstract":[{"lang":"eng","text":"The development dynamics and self-organization of glandular branched epithelia is of utmost importance for our understanding of diverse processes ranging from normal tissue growth to the growth of cancerous tissues. Using single primary murine pancreatic ductal adenocarcinoma (PDAC) cells embedded in a collagen matrix and adapted media supplementation, we generate organoids that self-organize into highly branched structures displaying a seamless lumen connecting terminal end buds, replicating in vivo PDAC architecture. We identify distinct morphogenesis phases, each characterized by a unique pattern of cell invasion, matrix deformation, protein expression, and respective molecular dependencies. We propose a minimal theoretical model of a branching and proliferating tissue, capturing the dynamics of the first phases. Observing the interaction of morphogenesis, mechanical environment and gene expression in vitro sets a benchmark for the understanding of self-organization processes governing complex organoid structure formation processes and branching morphogenesis."}],"doi":"10.1038/s41467-022-32806-y","day":"05","isi":1,"external_id":{"isi":["000850348400025"]},"date_updated":"2023-08-04T09:25:23Z","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>","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>","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>.","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.","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).","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."},"year":"2022","ddc":["570"],"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.","volume":13,"title":"Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids","intvolume":"        13","publication_status":"published","article_processing_charge":"No","department":[{"_id":"EdHa"}],"date_created":"2023-01-16T09:46:53Z","author":[{"last_name":"Randriamanantsoa","first_name":"S.","full_name":"Randriamanantsoa, S."},{"first_name":"A.","last_name":"Papargyriou","full_name":"Papargyriou, A."},{"full_name":"Maurer, H. C.","last_name":"Maurer","first_name":"H. C."},{"first_name":"K.","last_name":"Peschke","full_name":"Peschke, K."},{"last_name":"Schuster","first_name":"M.","full_name":"Schuster, M."},{"full_name":"Zecchin, G.","last_name":"Zecchin","first_name":"G."},{"first_name":"K.","last_name":"Steiger","full_name":"Steiger, K."},{"full_name":"Öllinger, R.","first_name":"R.","last_name":"Öllinger"},{"first_name":"D.","last_name":"Saur","full_name":"Saur, D."},{"first_name":"C.","last_name":"Scheel","full_name":"Scheel, C."},{"full_name":"Rad, R.","first_name":"R.","last_name":"Rad"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Reichert","first_name":"M.","full_name":"Reichert, M."},{"full_name":"Bausch, A. R.","first_name":"A. R.","last_name":"Bausch"}],"_id":"12217","scopus_import":"1","article_type":"original","publisher":"Springer Nature","file_date_updated":"2023-01-27T08:14:48Z","quality_controlled":"1","ec_funded":1},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"relation":"main_file","access_level":"open_access","success":1,"file_id":"12417","creator":"dernst","date_created":"2023-01-27T08:23:46Z","checksum":"bd95be1e77090208b79bc45ea8785d0b","file_size":3968356,"date_updated":"2023-01-27T08:23:46Z","content_type":"application/pdf","file_name":"2022_CommBiology_Muhia.pdf"}],"date_published":"2022-06-15T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["2399-3642"]},"language":[{"iso":"eng"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"publication":"Communications Biology","has_accepted_license":"1","month":"06","article_number":"589","oa_version":"Published Version","ddc":["570"],"volume":5,"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.","isi":1,"external_id":{"isi":["000811777900003"]},"date_updated":"2023-08-04T09:25:59Z","citation":{"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.","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>.","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>","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>","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>."},"year":"2022","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"}],"doi":"10.1038/s42003-022-03446-1","day":"15","file_date_updated":"2023-01-27T08:23:46Z","quality_controlled":"1","article_type":"original","publisher":"Springer Nature","author":[{"full_name":"Muhia, Mary W","first_name":"Mary W","last_name":"Muhia","id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d"},{"full_name":"YuanXiang, PingAn","first_name":"PingAn","last_name":"YuanXiang"},{"full_name":"Sedlacik, Jan","first_name":"Jan","last_name":"Sedlacik"},{"full_name":"Schwarz, Jürgen R.","first_name":"Jürgen R.","last_name":"Schwarz"},{"full_name":"Heisler, Frank F.","last_name":"Heisler","first_name":"Frank F."},{"first_name":"Kira V.","last_name":"Gromova","full_name":"Gromova, Kira V."},{"full_name":"Thies, Edda","last_name":"Thies","first_name":"Edda"},{"first_name":"Petra","last_name":"Breiden","full_name":"Breiden, Petra"},{"first_name":"Yvonne","last_name":"Pechmann","full_name":"Pechmann, Yvonne"},{"full_name":"Kreutz, Michael R.","first_name":"Michael R.","last_name":"Kreutz"},{"first_name":"Matthias","last_name":"Kneussel","full_name":"Kneussel, Matthias"}],"_id":"12224","scopus_import":"1","title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","intvolume":"         5","publication_status":"published","department":[{"_id":"PreCl"}],"article_processing_charge":"No","date_created":"2023-01-16T09:48:19Z"},{"keyword":["Developmental Biology","Molecular Biology"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Development","oa_version":"Published Version","article_number":"dev200215","month":"11","file":[{"creator":"dernst","file_id":"12423","success":1,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_Development_Kogure.pdf","date_updated":"2023-01-27T10:36:50Z","checksum":"871b9c58eb79b9e60752de25a46938d6","file_size":9160451,"date_created":"2023-01-27T10:36:50Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-11-01T00:00:00Z","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"oa":1,"quality_controlled":"1","file_date_updated":"2023-01-27T10:36:50Z","publisher":"The Company of Biologists","article_type":"original","scopus_import":"1","_id":"12231","pmid":1,"issue":"21","author":[{"last_name":"Kogure","first_name":"Yuki S.","full_name":"Kogure, Yuki S."},{"full_name":"Muraoka, Hiromochi","last_name":"Muraoka","first_name":"Hiromochi"},{"last_name":"Koizumi","first_name":"Wataru C.","full_name":"Koizumi, Wataru C."},{"last_name":"Gelin-alessi","first_name":"Raphaël","full_name":"Gelin-alessi, Raphaël"},{"id":"3263621A-F248-11E8-B48F-1D18A9856A87","full_name":"Godard, Benoit G","first_name":"Benoit G","last_name":"Godard"},{"full_name":"Oka, Kotaro","first_name":"Kotaro","last_name":"Oka"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"},{"first_name":"Kohji","last_name":"Hotta","full_name":"Hotta, Kohji"}],"department":[{"_id":"CaHe"}],"article_processing_charge":"No","date_created":"2023-01-16T09:50:12Z","publication_status":"published","intvolume":"       149","title":"Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona","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.","volume":149,"ddc":["570"],"year":"2022","citation":{"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>.","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.","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>","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>","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>."},"date_updated":"2023-08-04T09:33:24Z","external_id":{"isi":["000903991700002"],"pmid":["36227591"]},"isi":1,"day":"01","doi":"10.1242/dev.200215","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_published":"2022-10-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["1534-5807"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication":"Developmental Cell","oa_version":"None","month":"10","language":[{"iso":"eng"}],"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"date_updated":"2023-08-04T09:38:53Z","year":"2022","citation":{"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.","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>.","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>","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.","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>.","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."},"isi":1,"external_id":{"isi":["000898428700006"],"pmid":["36174555"]},"doi":"10.1016/j.devcel.2022.09.003","day":"01","abstract":[{"lang":"eng","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."}],"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.","volume":57,"_id":"12238","pmid":1,"scopus_import":"1","author":[{"first_name":"Naoya","last_name":"Hino","full_name":"Hino, Naoya","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307"},{"full_name":"Matsuda, Kimiya","first_name":"Kimiya","last_name":"Matsuda"},{"first_name":"Yuya","last_name":"Jikko","full_name":"Jikko, Yuya"},{"full_name":"Maryu, Gembu","last_name":"Maryu","first_name":"Gembu"},{"full_name":"Sakai, Katsuya","last_name":"Sakai","first_name":"Katsuya"},{"full_name":"Imamura, Ryu","first_name":"Ryu","last_name":"Imamura"},{"full_name":"Tsukiji, Shinya","first_name":"Shinya","last_name":"Tsukiji"},{"last_name":"Aoki","first_name":"Kazuhiro","full_name":"Aoki, Kazuhiro"},{"last_name":"Terai","first_name":"Kenta","full_name":"Terai, Kenta"},{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"first_name":"Xavier","last_name":"Trepat","full_name":"Trepat, Xavier"},{"first_name":"Michiyuki","last_name":"Matsuda","full_name":"Matsuda, Michiyuki"}],"issue":"19","publication_status":"published","article_processing_charge":"No","department":[{"_id":"CaHe"}],"date_created":"2023-01-16T09:51:39Z","title":"A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration","intvolume":"        57","page":"2290-2304.e7","quality_controlled":"1","publisher":"Elsevier","article_type":"original"},{"has_accepted_license":"1","publication":"Molecular Plant","month":"10","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"oa_version":"Published Version","keyword":["Plant Science","Molecular Biology"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2022-10-03T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["1674-2052"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"access_level":"open_access","relation":"main_file","success":1,"file_id":"12435","creator":"dernst","date_created":"2023-01-30T07:46:51Z","file_size":2307251,"checksum":"04d5c12490052d03e4dc4412338a43dd","date_updated":"2023-01-30T07:46:51Z","content_type":"application/pdf","file_name":"2022_MolecularPlant_Johnson.pdf"}],"issue":"10","author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","first_name":"Tommaso","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815"},{"full_name":"Dahhan, Dana A.","first_name":"Dana A.","last_name":"Dahhan"},{"full_name":"Bednarek, Sebastian Y.","first_name":"Sebastian Y.","last_name":"Bednarek"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","pmid":1,"_id":"12239","intvolume":"        15","title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"date_created":"2023-01-16T09:51:49Z","article_processing_charge":"Yes (via OA deal)","publication_status":"published","file_date_updated":"2023-01-30T07:46:51Z","quality_controlled":"1","page":"1533-1542","article_type":"original","publisher":"Elsevier","external_id":{"isi":["000882769800009"],"pmid":["36081349"]},"isi":1,"citation":{"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>.","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>","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. 2022;15(10):1533-1542. doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","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.","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>."},"year":"2022","date_updated":"2023-08-04T09:39:24Z","abstract":[{"text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.","lang":"eng"}],"day":"03","doi":"10.1016/j.molp.2022.09.003","ddc":["580"],"volume":15,"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."},{"file":[{"date_updated":"2023-01-30T08:35:44Z","content_type":"application/pdf","file_name":"2022_Development_Soto.pdf","date_created":"2023-01-30T08:35:44Z","checksum":"d7c29b74e9e4032308228cc704a30e88","file_size":9348839,"file_id":"12438","creator":"dernst","relation":"main_file","success":1,"access_level":"open_access"}],"status":"public","related_material":{"link":[{"url":" https://github.com/burtonjosh/StepwiseMir9","relation":"software"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-10-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"oa":1,"language":[{"iso":"eng"}],"keyword":["Developmental Biology","Molecular Biology"],"publication":"Development","has_accepted_license":"1","oa_version":"Published Version","month":"10","article_number":"dev200474","volume":149,"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.","ddc":["570"],"date_updated":"2023-08-04T09:41:08Z","citation":{"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>.","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.","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>","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>","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.","short":"X. Soto, J. Burton, C.S. Manning, T. Minchington, R. Lea, J. Lee, J. Kursawe, M. Rattray, N. Papalopulu, Development 149 (2022).","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>."},"year":"2022","isi":1,"external_id":{"pmid":["36189829"],"isi":["000918161000003"]},"doi":"10.1242/dev.200474","day":"01","abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","file_date_updated":"2023-01-30T08:35:44Z","publisher":"The Company of Biologists","article_type":"original","_id":"12245","pmid":1,"scopus_import":"1","author":[{"last_name":"Soto","first_name":"Ximena","full_name":"Soto, Ximena"},{"full_name":"Burton, Joshua","last_name":"Burton","first_name":"Joshua"},{"first_name":"Cerys S.","last_name":"Manning","full_name":"Manning, Cerys S."},{"id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","last_name":"Minchington","first_name":"Thomas"},{"last_name":"Lea","first_name":"Robert","full_name":"Lea, Robert"},{"full_name":"Lee, Jessica","first_name":"Jessica","last_name":"Lee"},{"first_name":"Jochen","last_name":"Kursawe","full_name":"Kursawe, Jochen"},{"first_name":"Magnus","last_name":"Rattray","full_name":"Rattray, Magnus"},{"first_name":"Nancy","last_name":"Papalopulu","full_name":"Papalopulu, Nancy"}],"issue":"19","publication_status":"published","date_created":"2023-01-16T09:53:17Z","department":[{"_id":"AnKi"}],"article_processing_charge":"No","title":"Sequential and additive expression of miR-9 precursors control timing of neurogenesis","intvolume":"       149"},{"intvolume":"        18","title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","department":[{"_id":"ToBo"}],"article_processing_charge":"No","date_created":"2023-01-16T09:58:34Z","publication_status":"published","issue":"9","author":[{"id":"4677C796-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Angermayr","orcid":"0000-0001-8619-2223","full_name":"Angermayr, Andreas"},{"full_name":"Pang, Tin Yau","last_name":"Pang","first_name":"Tin Yau"},{"first_name":"Guillaume","last_name":"Chevereau","full_name":"Chevereau, Guillaume"},{"full_name":"Mitosch, Karin","last_name":"Mitosch","first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lercher, Martin J","last_name":"Lercher","first_name":"Martin J"},{"last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"12261","article_type":"original","publisher":"Embo Press","file_date_updated":"2023-01-30T09:49:55Z","quality_controlled":"1","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"}],"day":"01","doi":"10.15252/msb.202110490","external_id":{"isi":["000856482800001"]},"isi":1,"year":"2022","citation":{"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>","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>.","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>.","short":"A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach, Molecular Systems Biology 18 (2022).","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."},"date_updated":"2023-08-04T09:51:49Z","ddc":["570"],"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.","volume":18,"article_number":"e10490","month":"09","oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"}],"has_accepted_license":"1","publication":"Molecular Systems Biology","keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"eissn":["1744-4292"]},"type":"journal_article","date_published":"2022-09-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"8b1d8f5ea20c8408acf466435fb6ae01","file_size":1098812,"date_created":"2023-01-30T09:49:55Z","content_type":"application/pdf","file_name":"2022_MolecularSystemsBio_Angermayr.pdf","date_updated":"2023-01-30T09:49:55Z","access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"12446"}]},{"scopus_import":"1","pmid":1,"_id":"12262","issue":"9","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"},{"first_name":"Gertrude","last_name":"Zisser","full_name":"Zisser, Gertrude"},{"last_name":"Sailer","first_name":"Carolin","full_name":"Sailer, Carolin"},{"full_name":"Kargas, Vasileios","first_name":"Vasileios","last_name":"Kargas"},{"last_name":"Loibl","first_name":"Mathias","full_name":"Loibl, Mathias"},{"last_name":"Gerhalter","first_name":"Magdalena","full_name":"Gerhalter, Magdalena"},{"full_name":"Kofler, Lisa","first_name":"Lisa","last_name":"Kofler"},{"full_name":"Warren, Alan J.","first_name":"Alan J.","last_name":"Warren"},{"full_name":"Stengel, Florian","first_name":"Florian","last_name":"Stengel"},{"full_name":"Haselbach, David","last_name":"Haselbach","first_name":"David"},{"full_name":"Bergler, Helmut","last_name":"Bergler","first_name":"Helmut"}],"department":[{"_id":"EM-Fac"}],"date_created":"2023-01-16T09:59:06Z","article_processing_charge":"No","publication_status":"published","intvolume":"        29","title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","quality_controlled":"1","page":"942-953","file_date_updated":"2023-01-30T10:00:04Z","publisher":"Springer Nature","article_type":"original","year":"2022","citation":{"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.","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>.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural &#38; Molecular Biology. 29(9), 942–953.","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. <i>Nature Structural &#38; Molecular Biology</i>. 2022;29(9):942-953. doi:<a href=\"https://doi.org/10.1038/s41594-022-00832-5\">10.1038/s41594-022-00832-5</a>","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>","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."},"date_updated":"2023-08-04T09:52:20Z","external_id":{"pmid":["36097293"],"isi":["000852942100004"]},"isi":1,"day":"12","doi":"10.1038/s41594-022-00832-5","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"}],"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.","volume":29,"ddc":["570"],"has_accepted_license":"1","publication":"Nature Structural & Molecular Biology","acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","month":"09","keyword":["Molecular Biology","Structural Biology"],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-09-12T00:00:00Z","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"oa":1,"file":[{"success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"12447","file_size":9935057,"checksum":"2d5c3ec01718fefd7553052b0b8a0793","date_created":"2023-01-30T10:00:04Z","file_name":"2022_NatureStrucMolecBio_Prattes.pdf","content_type":"application/pdf","date_updated":"2023-01-30T10:00:04Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"volume":23,"acknowledgement":"We thank Scott Garforth, Sarah Garrett, Peri Kurshan, Yehuda Salzberg, PamelaStanley, Robert Townley, and members of the B€ulow laboratory for commentson the manuscript or helpful discussions during the course of this work. Wethank David Miller, Shohei Mitani, Kang Shen, and Iain Wilson for reagents,and Yuji Kohara for theyk11g705cDNA clone. We are grateful to MeeraTrivedi for sharing thedzIs117strain prior to publication. Some strains wereprovided by the Caenorhabditis Genome Center (funded by the NIH Office ofResearch Infrastructure Programs P40OD010440). This work was supportedby grants from the National Institute of Health (NIH): R01NS096672andR21NS111145to HEB; F31NS100370to MR; T32GM007288and F31HD066967to CADB; P30HD071593to Albert Einstein College of Medicine. We acknowl-edge support to MR by the Department of Neuroscience. NJRS was the recipi-ent of a Colciencias-Fulbright Fellowship and HEB of an Irma T. Hirschl/Monique Weill-Caulier research fellowship","year":"2022","citation":{"chicago":"Rahman, Maisha, Nelson Ramirez, Carlos A Diaz‐Balzac, and Hannes E Bülow. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” <i>EMBO Reports</i>. Embo Press, 2022. <a href=\"https://doi.org/10.15252/embr.202154163\">https://doi.org/10.15252/embr.202154163</a>.","ieee":"M. Rahman, N. Ramirez, C. A. Diaz‐Balzac, and H. E. Bülow, “Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning,” <i>EMBO Reports</i>, vol. 23, no. 7. Embo Press, 2022.","ama":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. <i>EMBO Reports</i>. 2022;23(7). doi:<a href=\"https://doi.org/10.15252/embr.202154163\">10.15252/embr.202154163</a>","apa":"Rahman, M., Ramirez, N., Diaz‐Balzac, C. A., &#38; Bülow, H. E. (2022). Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. <i>EMBO Reports</i>. Embo Press. <a href=\"https://doi.org/10.15252/embr.202154163\">https://doi.org/10.15252/embr.202154163</a>","ista":"Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. 2022. Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning. EMBO Reports. 23(7), e54163.","mla":"Rahman, Maisha, et al. “Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory Dendrite Patterning.” <i>EMBO Reports</i>, vol. 23, no. 7, e54163, Embo Press, 2022, doi:<a href=\"https://doi.org/10.15252/embr.202154163\">10.15252/embr.202154163</a>.","short":"M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022)."},"date_updated":"2023-10-03T11:25:54Z","external_id":{"isi":["000797302700001"],"pmid":["35586945"]},"isi":1,"day":"05","doi":"10.15252/embr.202154163","abstract":[{"text":"N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting the secretory pathway and have been implicated in protein folding, stability, and localization. Mutations in genes important for N-glycosylation result in congenital disorders of glycosylation that are often associated with intellectual disability. Here, we show that structurally distinct N-glycans regulate an extracellular protein complex involved in the patterning of somatosensory dendrites in Caenorhabditis elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme in the biosynthesis of specific N-glycans, regulates the activity of the Menorin adhesion complex without obviously affecting the protein stability and localization of its components. AMAN-2 functions cell-autonomously to allow for decoration of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures regulate dendrite patterning by coordinating the activity of an extracellular adhesion complex, suggesting that the molecular diversity of N-glycans can contribute to developmental specificity in the nervous system.","lang":"eng"}],"quality_controlled":"1","publisher":"Embo Press","article_type":"original","scopus_import":"1","_id":"12275","pmid":1,"issue":"7","author":[{"last_name":"Rahman","first_name":"Maisha","full_name":"Rahman, Maisha"},{"full_name":"Ramirez, Nelson","last_name":"Ramirez","first_name":"Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425"},{"first_name":"Carlos A","last_name":"Diaz‐Balzac","full_name":"Diaz‐Balzac, Carlos A"},{"last_name":"Bülow","first_name":"Hannes E","full_name":"Bülow, Hannes E"}],"date_created":"2023-01-16T10:01:44Z","department":[{"_id":"MaDe"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        23","title":"Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning","main_file_link":[{"url":"https://doi.org/10.15252/embr.202154163","open_access":"1"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_published":"2022-07-05T00:00:00Z","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"oa":1,"keyword":["Genetics","Molecular Biology","Biochemistry"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"EMBO Reports","oa_version":"Published Version","article_number":"e54163","month":"07"},{"file":[{"date_updated":"2023-01-30T11:28:13Z","file_name":"2022_PlosCompBio_Schmid.pdf","content_type":"application/pdf","date_created":"2023-01-30T11:28:13Z","checksum":"31b6b311b6731f1658277a9dfff6632c","file_size":3143222,"file_id":"12460","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1553-7358"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-06-14T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"oa_version":"Published Version","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"month":"06","article_number":"e1010149","publication":"PLOS Computational Biology","has_accepted_license":"1","volume":18,"acknowledgement":"This work was supported by the European Research Council (https://erc.europa.eu/)\r\nCoG 863818 (ForM-SMArt) (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","ddc":["000","570"],"doi":"10.1371/journal.pcbi.1010149","day":"14","abstract":[{"text":"In repeated interactions, players can use strategies that respond to the outcome of previous rounds. Much of the existing literature on direct reciprocity assumes that all competing individuals use the same strategy space. Here, we study both learning and evolutionary dynamics of players that differ in the strategy space they explore. We focus on the infinitely repeated donation game and compare three natural strategy spaces: memory-1 strategies, which consider the last moves of both players, reactive strategies, which respond to the last move of the co-player, and unconditional strategies. These three strategy spaces differ in the memory capacity that is needed. We compute the long term average payoff that is achieved in a pairwise learning process. We find that smaller strategy spaces can dominate larger ones. For weak selection, unconditional players dominate both reactive and memory-1 players. For intermediate selection, reactive players dominate memory-1 players. Only for strong selection and low cost-to-benefit ratio, memory-1 players dominate the others. We observe that the supergame between strategy spaces can be a social dilemma: maximum payoff is achieved if both players explore a larger strategy space, but smaller strategy spaces dominate.","lang":"eng"}],"date_updated":"2025-07-14T09:09:49Z","year":"2022","citation":{"apa":"Schmid, L., Hilbe, C., Chatterjee, K., &#38; Nowak, M. (2022). Direct reciprocity between individuals that use different strategy spaces. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">https://doi.org/10.1371/journal.pcbi.1010149</a>","ama":"Schmid L, Hilbe C, Chatterjee K, Nowak M. Direct reciprocity between individuals that use different strategy spaces. <i>PLOS Computational Biology</i>. 2022;18(6). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">10.1371/journal.pcbi.1010149</a>","chicago":"Schmid, Laura, Christian Hilbe, Krishnendu Chatterjee, and Martin Nowak. “Direct Reciprocity between Individuals That Use Different Strategy Spaces.” <i>PLOS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">https://doi.org/10.1371/journal.pcbi.1010149</a>.","ieee":"L. Schmid, C. Hilbe, K. Chatterjee, and M. Nowak, “Direct reciprocity between individuals that use different strategy spaces,” <i>PLOS Computational Biology</i>, vol. 18, no. 6. Public Library of Science, 2022.","mla":"Schmid, Laura, et al. “Direct Reciprocity between Individuals That Use Different Strategy Spaces.” <i>PLOS Computational Biology</i>, vol. 18, no. 6, e1010149, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">10.1371/journal.pcbi.1010149</a>.","short":"L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology 18 (2022).","ista":"Schmid L, Hilbe C, Chatterjee K, Nowak M. 2022. Direct reciprocity between individuals that use different strategy spaces. PLOS Computational Biology. 18(6), e1010149."},"isi":1,"external_id":{"isi":["000843626800031"],"pmid":["35700167"]},"publisher":"Public Library of Science","article_type":"original","ec_funded":1,"quality_controlled":"1","file_date_updated":"2023-01-30T11:28:13Z","publication_status":"published","date_created":"2023-01-16T10:02:51Z","article_processing_charge":"No","department":[{"_id":"KrCh"}],"title":"Direct reciprocity between individuals that use different strategy spaces","intvolume":"        18","pmid":1,"_id":"12280","scopus_import":"1","author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","first_name":"Laura","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329"},{"first_name":"Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"issue":"6"},{"quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-01-30T11:50:53Z","publisher":"eLife Sciences Publications","article_type":"original","scopus_import":"1","_id":"12288","pmid":1,"author":[{"orcid":"0000-0002-4792-1881","full_name":"Sumser, Anton L","first_name":"Anton L","last_name":"Sumser","id":"3320A096-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas"},{"last_name":"Ben Simon","first_name":"Yoav","full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"MaJö"},{"_id":"PeJo"}],"article_processing_charge":"No","date_created":"2023-01-16T10:04:15Z","publication_status":"published","intvolume":"        11","title":"Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling","volume":11,"acknowledgement":"We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical Facility (PCF). This project was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC advanced grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).","ddc":["570"],"citation":{"ieee":"A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","chicago":"Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>.","apa":"Sumser, A. L., Jösch, M. A., Jonas, P. M., &#38; Ben Simon, Y. (2022). Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>","ama":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>","ista":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. eLife. 11, 79848.","mla":"Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>, vol. 11, 79848, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>.","short":"A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022)."},"year":"2022","date_updated":"2023-08-04T10:29:48Z","external_id":{"pmid":["36040301"],"isi":["000892204300001"]},"isi":1,"day":"15","doi":"10.7554/elife.79848","abstract":[{"text":"To understand the function of neuronal circuits, it is crucial to disentangle the connectivity patterns within the network. However, most tools currently used to explore connectivity have low throughput, low selectivity, or limited accessibility. Here, we report the development of an improved packaging system for the production of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers orders of magnitude higher with no background contamination, at a fraction of the production time, while preserving the efficiency of transsynaptic labeling. Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal populations, tailored for diverse experimental requirements. We demonstrate the power and flexibility of the new system by uncovering hidden local and distal inhibitory connections in the mouse hippocampal formation and by imaging the functional properties of a cortical microcircuit across weeks. Our novel production pipeline provides a convenient approach to generate new rabies vectors, while our toolkit flexibly and efficiently expands the current capacity to label, manipulate and image the neuronal activity of interconnected neuronal circuits in vitro and in vivo.","lang":"eng"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"eLife","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"name":"Circuits of Visual Attention","grant_number":"756502","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"oa_version":"Published Version","article_number":"79848","month":"09","file":[{"file_name":"2022_eLife_Sumser.pdf","content_type":"application/pdf","date_updated":"2023-01-30T11:50:53Z","file_size":8506811,"checksum":"5a2a65e3e7225090c3d8199f3bbd7b7b","date_created":"2023-01-30T11:50:53Z","creator":"dernst","file_id":"12463","access_level":"open_access","success":1,"relation":"main_file"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-09-15T00:00:00Z","publication_identifier":{"eissn":["2050-084X"]},"oa":1},{"article_type":"review","publisher":"Wiley","quality_controlled":"1","page":"2240-2251","intvolume":"        64","title":"DNA methylation dynamics during germline development","date_created":"2023-02-23T09:15:57Z","article_processing_charge":"No","department":[{"_id":"XiFe"}],"publication_status":"published","issue":"12","author":[{"first_name":"Shengbo","last_name":"He","full_name":"He, Shengbo"},{"last_name":"Feng","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"}],"scopus_import":"1","_id":"12670","pmid":1,"extern":"1","volume":64,"abstract":[{"lang":"eng","text":"DNA methylation plays essential homeostatic functions in eukaryotic genomes. In animals, DNA methylation is also developmentally regulated and, in turn, regulates development. In the past two decades, huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development, especially during sexual reproduction. The power of whole-genome sequencing and cell isolation techniques, as well as bioinformatics tools, have enabled recent studies to reveal dynamic changes in DNA methylation during germline development. Furthermore, the combination of these technological advances with genetics, developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines. In this review, we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants."}],"day":"07","doi":"10.1111/jipb.13422","external_id":{"pmid":["36478632"]},"year":"2022","citation":{"ama":"He S, Feng X. DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. 2022;64(12):2240-2251. doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>","apa":"He, S., &#38; Feng, X. (2022). DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>","chicago":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>.","ieee":"S. He and X. Feng, “DNA methylation dynamics during germline development,” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12. Wiley, pp. 2240–2251, 2022.","short":"S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.","mla":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12, Wiley, 2022, pp. 2240–51, doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>.","ista":"He S, Feng X. 2022. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. 64(12), 2240–2251."},"date_updated":"2023-05-08T10:59:00Z","keyword":["Plant Science","General Biochemistry","Genetics and Molecular Biology","Biochemistry"],"language":[{"iso":"eng"}],"month":"12","oa_version":"Published Version","publication":"Journal of Integrative Plant Biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.13422"}],"oa":1,"publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"type":"journal_article","date_published":"2022-12-07T00:00:00Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.03.24.005835"}],"oa":1,"publication_identifier":{"issn":["0960-9822"]},"date_published":"2021-05-24T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"month":"05","oa_version":"Preprint","publication":"Current Biology","volume":31,"acknowledgement":"We are grateful to Silvia Prettin, Ina Schleicher, and Petra Hagendorff for expert technical assistance; David Dettbarn for animal keeping and breeding; and Lothar Gröbe and Maria Höxter for cell sorting. We also thank Werner Tegge for peptides and Giorgio Scita for antibodies. This work was supported, in part, by the Deutsche Forschungsgemeinschaft (DFG), Priority Programm SPP1150 (to T.E.B.S., K.R., and M. Sixt), and by DFG grant GRK2223/1 (to K.R.). T.E.B.S. acknowledges support by the Helmholtz Society through HGF impulse fund W2/W3-066 and M. Schnoor by the Mexican Council for Science and Technology (CONACyT, 284292 ), Fund SEP-Cinvestav ( 108 ), and the Royal Society, UK (Newton Advanced Fellowship, NAF/R1/180017 ).","abstract":[{"text":"Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation and the protrusion of branched actin filament networks. Moreover, Hem1 loss of function in immune cells causes autoimmune diseases in humans. Here, we show that genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis as well as phagocytic cup formation in addition to defects in lamellipodial protrusion and migration. Moreover, Hem1-null macrophages displayed strong defects in cell adhesion despite unaltered podosome formation and concomitant extracellular matrix degradation. Specifically, dynamics of both adhesion and de-adhesion as well as concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly compromised. Accordingly, disruption of WRC function in non-hematopoietic cells coincided with both defects in adhesion turnover and altered FAK and paxillin phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes, but not lamellipodia formation, were partially rescued by small molecule activation of FAK. A full rescue of the phenotype, including lamellipodia formation, required not only the presence of WRCs but also their binding to and activation by Rac. Collectively, our results uncover that WRC impacts on integrin-dependent processes in a FAK-dependent manner, controlling formation and dismantling of adhesions, relevant for properly grabbing onto extracellular surfaces and particles during cell edge expansion, like in migration or phagocytosis.","lang":"eng"}],"doi":"10.1016/j.cub.2021.02.043","day":"24","isi":1,"external_id":{"pmid":["33711252"],"isi":["000654652200002"]},"date_updated":"2023-08-17T07:01:14Z","citation":{"ieee":"S. Stahnke <i>et al.</i>, “Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion,” <i>Current Biology</i>, vol. 31, no. 10. Elsevier, p. 2051–2064.e8, 2021.","chicago":"Stahnke, Stephanie, Hermann Döring, Charly Kusch, David J.J. de Gorter, Sebastian Dütting, Aleks Guledani, Irina Pleines, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>.","ama":"Stahnke S, Döring H, Kusch C, et al. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. 2021;31(10):2051-2064.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>","apa":"Stahnke, S., Döring, H., Kusch, C., de Gorter, D. J. J., Dütting, S., Guledani, A., … Stradal, T. E. B. (2021). Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>","ista":"Stahnke S, Döring H, Kusch C, de Gorter DJJ, Dütting S, Guledani A, Pleines I, Schnoor M, Sixt MK, Geffers R, Rohde M, Müsken M, Kage F, Steffen A, Faix J, Nieswandt B, Rottner K, Stradal TEB. 2021. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 31(10), 2051–2064.e8.","mla":"Stahnke, Stephanie, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>, vol. 31, no. 10, Elsevier, 2021, p. 2051–2064.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>.","short":"S. Stahnke, H. Döring, C. Kusch, D.J.J. de Gorter, S. Dütting, A. Guledani, I. Pleines, M. Schnoor, M.K. Sixt, R. Geffers, M. Rohde, M. Müsken, F. Kage, A. Steffen, J. Faix, B. Nieswandt, K. Rottner, T.E.B. Stradal, Current Biology 31 (2021) 2051–2064.e8."},"year":"2021","article_type":"original","publisher":"Elsevier","page":"2051-2064.e8","quality_controlled":"1","title":"Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion","intvolume":"        31","publication_status":"published","date_created":"2022-03-08T07:51:04Z","department":[{"_id":"MiSi"}],"article_processing_charge":"No","author":[{"full_name":"Stahnke, Stephanie","last_name":"Stahnke","first_name":"Stephanie"},{"last_name":"Döring","first_name":"Hermann","full_name":"Döring, Hermann"},{"full_name":"Kusch, Charly","first_name":"Charly","last_name":"Kusch"},{"full_name":"de Gorter, David J.J.","first_name":"David J.J.","last_name":"de Gorter"},{"full_name":"Dütting, Sebastian","last_name":"Dütting","first_name":"Sebastian"},{"first_name":"Aleks","last_name":"Guledani","full_name":"Guledani, Aleks"},{"full_name":"Pleines, Irina","last_name":"Pleines","first_name":"Irina"},{"full_name":"Schnoor, Michael","first_name":"Michael","last_name":"Schnoor"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Geffers, Robert","last_name":"Geffers","first_name":"Robert"},{"last_name":"Rohde","first_name":"Manfred","full_name":"Rohde, Manfred"},{"full_name":"Müsken, Mathias","first_name":"Mathias","last_name":"Müsken"},{"last_name":"Kage","first_name":"Frieda","full_name":"Kage, Frieda"},{"first_name":"Anika","last_name":"Steffen","full_name":"Steffen, Anika"},{"full_name":"Faix, Jan","first_name":"Jan","last_name":"Faix"},{"full_name":"Nieswandt, Bernhard","first_name":"Bernhard","last_name":"Nieswandt"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"},{"first_name":"Theresia E.B.","last_name":"Stradal","full_name":"Stradal, Theresia E.B."}],"issue":"10","_id":"10834","pmid":1,"scopus_import":"1"},{"scopus_import":"1","_id":"11052","pmid":1,"issue":"21","author":[{"full_name":"Krishna, Shefali","last_name":"Krishna","first_name":"Shefali"},{"last_name":"Arrojo e Drigo","first_name":"Rafael","full_name":"Arrojo e Drigo, Rafael"},{"last_name":"Capitanio","first_name":"Juliana S.","full_name":"Capitanio, Juliana S."},{"first_name":"Ranjan","last_name":"Ramachandra","full_name":"Ramachandra, Ranjan"},{"full_name":"Ellisman, Mark","first_name":"Mark","last_name":"Ellisman"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"date_created":"2022-04-07T07:43:14Z","article_processing_charge":"No","publication_status":"published","intvolume":"        56","title":"Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain","quality_controlled":"1","page":"P2952-2965.e9","publisher":"Elsevier","article_type":"original","year":"2021","citation":{"chicago":"Krishna, Shefali, Rafael Arrojo e Drigo, Juliana S. Capitanio, Ranjan Ramachandra, Mark Ellisman, and Martin Hetzer. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>.","ieee":"S. Krishna, R. Arrojo e Drigo, J. S. Capitanio, R. Ramachandra, M. Ellisman, and M. Hetzer, “Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain,” <i>Developmental Cell</i>, vol. 56, no. 21. Elsevier, p. P2952–2965.e9, 2021.","apa":"Krishna, S., Arrojo e Drigo, R., Capitanio, J. S., Ramachandra, R., Ellisman, M., &#38; Hetzer, M. (2021). Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>","ama":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. 2021;56(21):P2952-2965.e9. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>","ista":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. 2021. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. Developmental Cell. 56(21), P2952–2965.e9.","short":"S. Krishna, R. Arrojo e Drigo, J.S. Capitanio, R. Ramachandra, M. Ellisman, M. Hetzer, Developmental Cell 56 (2021) P2952–2965.e9.","mla":"Krishna, Shefali, et al. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>, vol. 56, no. 21, Elsevier, 2021, p. P2952–2965.e9, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>."},"date_updated":"2022-07-18T08:26:38Z","external_id":{"pmid":["34715012"]},"day":"08","doi":"10.1016/j.devcel.2021.10.008","abstract":[{"lang":"eng","text":"In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function."}],"volume":56,"extern":"1","publication":"Developmental Cell","oa_version":"None","month":"11","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2021-11-08T00:00:00Z","publication_identifier":{"issn":["1534-5807"]},"status":"public","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd"}]