[{"publication":"Nature Communications","ec_funded":1,"date_updated":"2023-08-04T09:25:23Z","department":[{"_id":"EdHa"}],"intvolume":"        13","oa":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13068"}]},"volume":13,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Randriamanantsoa, S.","first_name":"S.","last_name":"Randriamanantsoa"},{"last_name":"Papargyriou","first_name":"A.","full_name":"Papargyriou, A."},{"full_name":"Maurer, H. C.","first_name":"H. C.","last_name":"Maurer"},{"full_name":"Peschke, K.","first_name":"K.","last_name":"Peschke"},{"first_name":"M.","last_name":"Schuster","full_name":"Schuster, M."},{"first_name":"G.","last_name":"Zecchin","full_name":"Zecchin, G."},{"first_name":"K.","last_name":"Steiger","full_name":"Steiger, K."},{"last_name":"Öllinger","first_name":"R.","full_name":"Öllinger, R."},{"full_name":"Saur, D.","last_name":"Saur","first_name":"D."},{"last_name":"Scheel","first_name":"C.","full_name":"Scheel, C."},{"last_name":"Rad","first_name":"R.","full_name":"Rad, R."},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B"},{"full_name":"Reichert, M.","first_name":"M.","last_name":"Reichert"},{"first_name":"A. R.","last_name":"Bausch","full_name":"Bausch, A. R."}],"_id":"12217","file":[{"relation":"main_file","file_size":22645149,"date_created":"2023-01-27T08:14:48Z","date_updated":"2023-01-27T08:14:48Z","access_level":"open_access","success":1,"file_name":"2022_NatureCommunications_Randriamanantsoa.pdf","checksum":"295261b5172274fd5b8f85a6a6058828","creator":"dernst","file_id":"12416","content_type":"application/pdf"}],"date_created":"2023-01-16T09:46:53Z","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."}],"year":"2022","article_number":"5219","citation":{"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).","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>.","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>.","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.","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.","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>"},"file_date_updated":"2023-01-27T08:14:48Z","oa_version":"Published Version","article_processing_charge":"No","title":"Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids","publication_status":"published","article_type":"original","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.","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-022-32806-y","scopus_import":"1","status":"public","month":"09","isi":1,"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"language":[{"iso":"eng"}],"ddc":["570"],"external_id":{"isi":["000850348400025"]},"date_published":"2022-09-05T00:00:00Z","type":"journal_article","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"license":"https://creativecommons.org/licenses/by/4.0/","project":[{"grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis"}],"has_accepted_license":"1","quality_controlled":"1","day":"05"},{"volume":5,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Mary W","last_name":"Muhia","id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d","full_name":"Muhia, Mary W"},{"full_name":"YuanXiang, PingAn","last_name":"YuanXiang","first_name":"PingAn"},{"full_name":"Sedlacik, Jan","first_name":"Jan","last_name":"Sedlacik"},{"first_name":"Jürgen R.","last_name":"Schwarz","full_name":"Schwarz, Jürgen R."},{"last_name":"Heisler","first_name":"Frank F.","full_name":"Heisler, Frank F."},{"first_name":"Kira V.","last_name":"Gromova","full_name":"Gromova, Kira V."},{"last_name":"Thies","first_name":"Edda","full_name":"Thies, Edda"},{"full_name":"Breiden, Petra","last_name":"Breiden","first_name":"Petra"},{"last_name":"Pechmann","first_name":"Yvonne","full_name":"Pechmann, Yvonne"},{"full_name":"Kreutz, Michael R.","first_name":"Michael R.","last_name":"Kreutz"},{"full_name":"Kneussel, Matthias","first_name":"Matthias","last_name":"Kneussel"}],"date_updated":"2023-08-04T09:25:59Z","publication":"Communications Biology","department":[{"_id":"PreCl"}],"intvolume":"         5","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2023-01-27T08:23:46Z","publication_status":"published","title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","publication_identifier":{"issn":["2399-3642"]},"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.","article_type":"original","scopus_import":"1","doi":"10.1038/s42003-022-03446-1","date_created":"2023-01-16T09:48:19Z","file":[{"success":1,"access_level":"open_access","file_name":"2022_CommBiology_Muhia.pdf","date_created":"2023-01-27T08:23:46Z","file_size":3968356,"date_updated":"2023-01-27T08:23:46Z","relation":"main_file","file_id":"12417","creator":"dernst","content_type":"application/pdf","checksum":"bd95be1e77090208b79bc45ea8785d0b"}],"_id":"12224","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"}],"citation":{"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>","ieee":"M. W. Muhia <i>et al.</i>, “Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes,” <i>Communications Biology</i>, vol. 5. Springer Nature, 2022.","ista":"Muhia MW, YuanXiang P, Sedlacik J, Schwarz JR, Heisler FF, Gromova KV, Thies E, Breiden P, Pechmann Y, Kreutz MR, Kneussel M. 2022. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. 5, 589.","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>.","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).","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>","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","article_number":"589","type":"journal_article","external_id":{"isi":["000811777900003"]},"date_published":"2022-06-15T00:00:00Z","publisher":"Springer Nature","status":"public","isi":1,"month":"06","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"ddc":["570"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"15","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"}},{"article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2023-01-27T10:36:50Z","publication_status":"published","title":"Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"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.","article_type":"original","scopus_import":"1","doi":"10.1242/dev.200215","date_created":"2023-01-16T09:50:12Z","file":[{"success":1,"access_level":"open_access","file_name":"2022_Development_Kogure.pdf","relation":"main_file","file_size":9160451,"date_updated":"2023-01-27T10:36:50Z","date_created":"2023-01-27T10:36:50Z","content_type":"application/pdf","creator":"dernst","file_id":"12423","checksum":"871b9c58eb79b9e60752de25a46938d6"}],"_id":"12231","abstract":[{"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.","lang":"eng"}],"citation":{"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>","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).","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>.","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>.","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.","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.","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>"},"year":"2022","article_number":"dev200215","volume":149,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Kogure, Yuki S.","last_name":"Kogure","first_name":"Yuki S."},{"full_name":"Muraoka, Hiromochi","last_name":"Muraoka","first_name":"Hiromochi"},{"full_name":"Koizumi, Wataru C.","first_name":"Wataru C.","last_name":"Koizumi"},{"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"},{"last_name":"Oka","first_name":"Kotaro","full_name":"Oka, Kotaro"},{"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"},{"full_name":"Hotta, Kohji","first_name":"Kohji","last_name":"Hotta"}],"date_updated":"2023-08-04T09:33:24Z","publication":"Development","department":[{"_id":"CaHe"}],"intvolume":"       149","quality_controlled":"1","day":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","issue":"21","type":"journal_article","date_published":"2022-11-01T00:00:00Z","external_id":{"pmid":["36227591"],"isi":["000903991700002"]},"pmid":1,"publisher":"The Company of Biologists","status":"public","isi":1,"month":"11","keyword":["Developmental Biology","Molecular Biology"],"ddc":["570"],"language":[{"iso":"eng"}]},{"external_id":{"pmid":["36174555"],"isi":["000898428700006"]},"date_published":"2022-10-01T00:00:00Z","type":"journal_article","publisher":"Elsevier","pmid":1,"status":"public","month":"10","isi":1,"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"01","page":"2290-2304.e7","issue":"19","volume":57,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Hino, Naoya","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307","last_name":"Hino","first_name":"Naoya"},{"first_name":"Kimiya","last_name":"Matsuda","full_name":"Matsuda, Kimiya"},{"full_name":"Jikko, Yuya","first_name":"Yuya","last_name":"Jikko"},{"full_name":"Maryu, Gembu","last_name":"Maryu","first_name":"Gembu"},{"full_name":"Sakai, Katsuya","first_name":"Katsuya","last_name":"Sakai"},{"full_name":"Imamura, Ryu","first_name":"Ryu","last_name":"Imamura"},{"last_name":"Tsukiji","first_name":"Shinya","full_name":"Tsukiji, Shinya"},{"last_name":"Aoki","first_name":"Kazuhiro","full_name":"Aoki, Kazuhiro"},{"first_name":"Kenta","last_name":"Terai","full_name":"Terai, Kenta"},{"full_name":"Hirashima, Tsuyoshi","first_name":"Tsuyoshi","last_name":"Hirashima"},{"last_name":"Trepat","first_name":"Xavier","full_name":"Trepat, Xavier"},{"first_name":"Michiyuki","last_name":"Matsuda","full_name":"Matsuda, Michiyuki"}],"publication":"Developmental Cell","date_updated":"2023-08-04T09:38:53Z","department":[{"_id":"CaHe"}],"intvolume":"        57","article_processing_charge":"No","oa_version":"None","title":"A feedback loop between lamellipodial extension and HGF-ERK signaling specifies leader cells during collective cell migration","publication_status":"published","article_type":"original","publication_identifier":{"issn":["1534-5807"]},"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.","doi":"10.1016/j.devcel.2022.09.003","scopus_import":"1","_id":"12238","date_created":"2023-01-16T09:51:39Z","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."}],"year":"2022","citation":{"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>","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.","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.","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>.","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>","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.","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>."}},{"day":"03","page":"1533-1542","quality_controlled":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"issue":"10","publisher":"Elsevier","pmid":1,"external_id":{"pmid":["36081349"],"isi":["000882769800009"]},"date_published":"2022-10-03T00:00:00Z","type":"journal_article","keyword":["Plant Science","Molecular Biology"],"language":[{"iso":"eng"}],"ddc":["580"],"status":"public","month":"10","isi":1,"article_type":"original","publication_identifier":{"issn":["1674-2052"]},"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.","doi":"10.1016/j.molp.2022.09.003","scopus_import":"1","file_date_updated":"2023-01-30T07:46:51Z","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","publication_status":"published","abstract":[{"lang":"eng","text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs."}],"year":"2022","citation":{"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.","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>","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>.","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.","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.","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>"},"_id":"12239","file":[{"creator":"dernst","file_id":"12435","content_type":"application/pdf","checksum":"04d5c12490052d03e4dc4412338a43dd","access_level":"open_access","success":1,"file_name":"2022_MolecularPlant_Johnson.pdf","date_updated":"2023-01-30T07:46:51Z","relation":"main_file","date_created":"2023-01-30T07:46:51Z","file_size":2307251}],"date_created":"2023-01-16T09:51:49Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","last_name":"Costanzo","first_name":"Tommaso"},{"full_name":"Dahhan, Dana A.","first_name":"Dana A.","last_name":"Dahhan"},{"full_name":"Bednarek, Sebastian Y.","last_name":"Bednarek","first_name":"Sebastian Y."},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"oa":1,"volume":15,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"intvolume":"        15","publication":"Molecular Plant","date_updated":"2023-08-04T09:39:24Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}]},{"issue":"19","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"01","quality_controlled":"1","ddc":["570"],"language":[{"iso":"eng"}],"keyword":["Developmental Biology","Molecular Biology"],"isi":1,"month":"10","status":"public","pmid":1,"publisher":"The Company of Biologists","type":"journal_article","external_id":{"pmid":["36189829"],"isi":["000918161000003"]},"date_published":"2022-10-01T00:00:00Z","citation":{"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>","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.","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.","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>","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>.","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>."},"article_number":"dev200474","year":"2022","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"}],"date_created":"2023-01-16T09:53:17Z","file":[{"success":1,"access_level":"open_access","file_name":"2022_Development_Soto.pdf","date_updated":"2023-01-30T08:35:44Z","relation":"main_file","date_created":"2023-01-30T08:35:44Z","file_size":9348839,"creator":"dernst","file_id":"12438","content_type":"application/pdf","checksum":"d7c29b74e9e4032308228cc704a30e88"}],"_id":"12245","scopus_import":"1","doi":"10.1242/dev.200474","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"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.","article_type":"original","title":"Sequential and additive expression of miR-9 precursors control timing of neurogenesis","publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2023-01-30T08:35:44Z","intvolume":"       149","department":[{"_id":"AnKi"}],"date_updated":"2023-08-04T09:41:08Z","publication":"Development","author":[{"first_name":"Ximena","last_name":"Soto","full_name":"Soto, Ximena"},{"full_name":"Burton, Joshua","first_name":"Joshua","last_name":"Burton"},{"full_name":"Manning, Cerys S.","last_name":"Manning","first_name":"Cerys S."},{"id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","first_name":"Thomas","last_name":"Minchington"},{"full_name":"Lea, Robert","last_name":"Lea","first_name":"Robert"},{"full_name":"Lee, Jessica","last_name":"Lee","first_name":"Jessica"},{"first_name":"Jochen","last_name":"Kursawe","full_name":"Kursawe, Jochen"},{"last_name":"Rattray","first_name":"Magnus","full_name":"Rattray, Magnus"},{"first_name":"Nancy","last_name":"Papalopulu","full_name":"Papalopulu, Nancy"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":149,"oa":1,"related_material":{"link":[{"url":" https://github.com/burtonjosh/StepwiseMir9","relation":"software"}]}},{"language":[{"iso":"eng"}],"ddc":["570"],"keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"month":"09","isi":1,"status":"public","publisher":"Embo Press","date_published":"2022-09-01T00:00:00Z","external_id":{"isi":["000856482800001"]},"type":"journal_article","issue":"9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","day":"01","quality_controlled":"1","intvolume":"        18","department":[{"_id":"ToBo"}],"publication":"Molecular Systems Biology","date_updated":"2023-08-04T09:51:49Z","author":[{"full_name":"Angermayr, Andreas","orcid":"0000-0001-8619-2223","id":"4677C796-F248-11E8-B48F-1D18A9856A87","last_name":"Angermayr","first_name":"Andreas"},{"first_name":"Tin Yau","last_name":"Pang","full_name":"Pang, Tin Yau"},{"last_name":"Chevereau","first_name":"Guillaume","full_name":"Chevereau, Guillaume"},{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","full_name":"Mitosch, Karin","first_name":"Karin","last_name":"Mitosch"},{"first_name":"Martin J","last_name":"Lercher","full_name":"Lercher, Martin J"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"M-Shop"}],"oa":1,"volume":18,"year":"2022","article_number":"e10490","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>","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.","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.","short":"A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach, Molecular Systems Biology 18 (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>.","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>","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>."},"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"}],"_id":"12261","date_created":"2023-01-16T09:58:34Z","file":[{"file_id":"12446","creator":"dernst","content_type":"application/pdf","checksum":"8b1d8f5ea20c8408acf466435fb6ae01","file_name":"2022_MolecularSystemsBio_Angermayr.pdf","success":1,"access_level":"open_access","relation":"main_file","file_size":1098812,"date_updated":"2023-01-30T09:49:55Z","date_created":"2023-01-30T09:49:55Z"}],"doi":"10.15252/msb.202110490","scopus_import":"1","article_type":"original","publication_identifier":{"eissn":["1744-4292"]},"acknowledgement":"This work was in part supported by Human Frontier Science Program GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund (FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352. We wouldlike to thank the Bollenbach group for regular fruitful discussions. We areparticularly thankful for the technical assistance of Booshini Fernando andfor discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba Machine Shop for their support inbuilding a housing for the stacker of the plate reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open Accessfunding enabled and organized by Projekt DEAL.","title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","publication_status":"published","file_date_updated":"2023-01-30T09:49:55Z","article_processing_charge":"No","oa_version":"Published Version"},{"day":"12","page":"942-953","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","issue":"9","publisher":"Springer Nature","pmid":1,"external_id":{"isi":["000852942100004"],"pmid":["36097293"]},"date_published":"2022-09-12T00:00:00Z","type":"journal_article","keyword":["Molecular Biology","Structural Biology"],"language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"09","isi":1,"article_type":"original","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"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.","doi":"10.1038/s41594-022-00832-5","scopus_import":"1","file_date_updated":"2023-01-30T10:00:04Z","article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","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"}],"year":"2022","citation":{"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>.","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>.","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>","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.","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>","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.","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."},"_id":"12262","date_created":"2023-01-16T09:59:06Z","file":[{"checksum":"2d5c3ec01718fefd7553052b0b8a0793","creator":"dernst","file_id":"12447","content_type":"application/pdf","relation":"main_file","file_size":9935057,"date_created":"2023-01-30T10:00:04Z","date_updated":"2023-01-30T10:00:04Z","file_name":"2022_NatureStrucMolecBio_Prattes.pdf","access_level":"open_access","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Prattes, Michael","last_name":"Prattes","first_name":"Michael"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"last_name":"Hetzmannseder","first_name":"Christina","full_name":"Hetzmannseder, Christina"},{"first_name":"Gertrude","last_name":"Zisser","full_name":"Zisser, Gertrude"},{"first_name":"Carolin","last_name":"Sailer","full_name":"Sailer, Carolin"},{"full_name":"Kargas, Vasileios","first_name":"Vasileios","last_name":"Kargas"},{"full_name":"Loibl, Mathias","last_name":"Loibl","first_name":"Mathias"},{"first_name":"Magdalena","last_name":"Gerhalter","full_name":"Gerhalter, Magdalena"},{"full_name":"Kofler, Lisa","first_name":"Lisa","last_name":"Kofler"},{"first_name":"Alan J.","last_name":"Warren","full_name":"Warren, Alan J."},{"full_name":"Stengel, Florian","first_name":"Florian","last_name":"Stengel"},{"full_name":"Haselbach, David","last_name":"Haselbach","first_name":"David"},{"full_name":"Bergler, Helmut","first_name":"Helmut","last_name":"Bergler"}],"oa":1,"volume":29,"acknowledged_ssus":[{"_id":"EM-Fac"}],"intvolume":"        29","publication":"Nature Structural & Molecular Biology","date_updated":"2023-08-04T09:52:20Z","department":[{"_id":"EM-Fac"}]},{"day":"05","quality_controlled":"1","issue":"7","has_accepted_license":"1","pmid":1,"publisher":"Embo Press","type":"journal_article","external_id":{"isi":["000797302700001"],"pmid":["35586945"]},"date_published":"2022-07-05T00:00:00Z","language":[{"iso":"eng"}],"keyword":["Genetics","Molecular Biology","Biochemistry"],"isi":1,"month":"07","status":"public","scopus_import":"1","doi":"10.15252/embr.202154163","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15252/embr.202154163"}],"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","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"article_type":"original","publication_status":"published","title":"Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning","oa_version":"Published Version","article_processing_charge":"No","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>.","short":"M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022).","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>","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>.","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>","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.","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."},"article_number":"e54163","year":"2022","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"}],"date_created":"2023-01-16T10:01:44Z","_id":"12275","author":[{"full_name":"Rahman, Maisha","last_name":"Rahman","first_name":"Maisha"},{"last_name":"Ramirez","first_name":"Nelson","full_name":"Ramirez, Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425"},{"first_name":"Carlos A","last_name":"Diaz‐Balzac","full_name":"Diaz‐Balzac, Carlos A"},{"full_name":"Bülow, Hannes E","first_name":"Hannes E","last_name":"Bülow"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":23,"oa":1,"intvolume":"        23","department":[{"_id":"MaDe"}],"date_updated":"2023-10-03T11:25:54Z","publication":"EMBO Reports"},{"intvolume":"        18","publication":"PLOS Computational Biology","date_updated":"2025-07-14T09:09:49Z","ec_funded":1,"department":[{"_id":"KrCh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Schmid","first_name":"Laura","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"oa":1,"volume":18,"abstract":[{"lang":"eng","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."}],"article_number":"e1010149","year":"2022","citation":{"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>","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.","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.","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>.","short":"L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology 18 (2022).","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>","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>."},"_id":"12280","date_created":"2023-01-16T10:02:51Z","file":[{"success":1,"access_level":"open_access","file_name":"2022_PlosCompBio_Schmid.pdf","date_created":"2023-01-30T11:28:13Z","relation":"main_file","file_size":3143222,"date_updated":"2023-01-30T11:28:13Z","content_type":"application/pdf","creator":"dernst","file_id":"12460","checksum":"31b6b311b6731f1658277a9dfff6632c"}],"article_type":"original","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.","publication_identifier":{"eissn":["1553-7358"]},"doi":"10.1371/journal.pcbi.1010149","scopus_import":"1","file_date_updated":"2023-01-30T11:28:13Z","oa_version":"Published Version","article_processing_charge":"No","title":"Direct reciprocity between individuals that use different strategy spaces","publication_status":"published","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}],"ddc":["000","570"],"status":"public","month":"06","isi":1,"publisher":"Public Library of Science","pmid":1,"date_published":"2022-06-14T00:00:00Z","external_id":{"pmid":["35700167"],"isi":["000843626800031"]},"type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"has_accepted_license":"1","issue":"6","day":"14","quality_controlled":"1"},{"quality_controlled":"1","day":"15","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","grant_number":"692692"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention","call_identifier":"H2020","grant_number":"756502"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00312","call_identifier":"FWF"},{"grant_number":"LT000256","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017"}],"type":"journal_article","external_id":{"pmid":["36040301"],"isi":["000892204300001"]},"date_published":"2022-09-15T00:00:00Z","pmid":1,"publisher":"eLife Sciences Publications","isi":1,"month":"09","status":"public","ddc":["570"],"language":[{"iso":"eng"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"title":"Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling","publication_status":"published","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2023-01-30T11:50:53Z","scopus_import":"1","doi":"10.7554/elife.79848","publication_identifier":{"eissn":["2050-084X"]},"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).","article_type":"original","date_created":"2023-01-16T10:04:15Z","file":[{"checksum":"5a2a65e3e7225090c3d8199f3bbd7b7b","content_type":"application/pdf","creator":"dernst","file_id":"12463","date_created":"2023-01-30T11:50:53Z","relation":"main_file","file_size":8506811,"date_updated":"2023-01-30T11:50:53Z","file_name":"2022_eLife_Sumser.pdf","access_level":"open_access","success":1}],"_id":"12288","citation":{"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).","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>","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>.","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.","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.","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>"},"article_number":"79848","year":"2022","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"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"volume":11,"oa":1,"author":[{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4792-1881","full_name":"Sumser, Anton L","first_name":"Anton L","last_name":"Sumser"},{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","last_name":"Jösch","first_name":"Maximilian A"},{"last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ben Simon","first_name":"Yoav","full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaJö"},{"_id":"PeJo"}],"date_updated":"2023-08-04T10:29:48Z","ec_funded":1,"publication":"eLife","intvolume":"        11"},{"issue":"12","quality_controlled":"1","day":"07","page":"2240-2251","status":"public","month":"12","extern":"1","keyword":["Plant Science","General Biochemistry","Genetics and Molecular Biology","Biochemistry"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2022-12-07T00:00:00Z","external_id":{"pmid":["36478632"]},"pmid":1,"publisher":"Wiley","date_created":"2023-02-23T09:15:57Z","_id":"12670","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."}],"citation":{"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>.","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>","short":"S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.","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>.","ista":"He S, Feng X. 2022. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. 64(12), 2240–2251.","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.","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>"},"year":"2022","oa_version":"Published Version","article_processing_charge":"No","title":"DNA methylation dynamics during germline development","publication_status":"published","publication_identifier":{"eissn":["1744-7909"],"issn":["1672-9072"]},"article_type":"review","scopus_import":"1","doi":"10.1111/jipb.13422","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.13422"}],"date_updated":"2023-05-08T10:59:00Z","publication":"Journal of Integrative Plant Biology","department":[{"_id":"XiFe"}],"intvolume":"        64","volume":64,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"He","first_name":"Shengbo","full_name":"He, Shengbo"},{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","first_name":"Xiaoqi"}]},{"year":"2022","citation":{"ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848).","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848. The Royal Society, 2022.","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1848). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","apa":"Barton, N. H., &#38; Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>.","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>."},"abstract":[{"text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.","lang":"eng"}],"_id":"10787","date_created":"2022-02-21T16:08:10Z","file":[{"file_id":"11719","creator":"dernst","content_type":"application/pdf","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","access_level":"open_access","success":1,"date_created":"2022-08-02T06:14:32Z","file_size":1349672,"date_updated":"2022-08-02T06:14:32Z","relation":"main_file"}],"doi":"10.1098/rstb.2021.0009","scopus_import":"1","article_type":"original","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"publication_status":"published","title":"The response of a metapopulation to a changing environment","file_date_updated":"2022-08-02T06:14:32Z","article_processing_charge":"No","oa_version":"Published Version","intvolume":"       377","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","date_updated":"2025-05-26T09:05:09Z","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","full_name":"Olusanya, Oluwafunmilola O","first_name":"Oluwafunmilola O","last_name":"Olusanya"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"related_material":{"record":[{"id":"14711","status":"public","relation":"dissertation_contains"}]},"volume":377,"issue":"1848","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896"}],"day":"11","quality_controlled":"1","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"month":"04","isi":1,"status":"public","publisher":"The Royal Society","pmid":1,"external_id":{"pmid":["35184588"],"isi":["000758140300001"]},"date_published":"2022-04-11T00:00:00Z","type":"journal_article"},{"publication":"Cell Reports","date_updated":"2024-03-25T23:30:25Z","ec_funded":1,"department":[{"_id":"JoDa"},{"_id":"GaNo"}],"intvolume":"        39","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12364"}]},"oa":1,"volume":39,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Villa, Carlo Emanuele","last_name":"Villa","first_name":"Carlo Emanuele"},{"last_name":"Cheroni","first_name":"Cristina","full_name":"Cheroni, Cristina"},{"last_name":"Dotter","first_name":"Christoph","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096"},{"last_name":"López-Tóbon","first_name":"Alejandro","full_name":"López-Tóbon, Alejandro"},{"full_name":"Oliveira, Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","last_name":"Oliveira","first_name":"Bárbara"},{"id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","full_name":"Sacco, Roberto","first_name":"Roberto","last_name":"Sacco"},{"first_name":"Aysan Çerağ","last_name":"Yahya","id":"365A65F8-F248-11E8-B48F-1D18A9856A87","full_name":"Yahya, Aysan Çerağ"},{"last_name":"Morandell","first_name":"Jasmin","full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michele","last_name":"Gabriele","full_name":"Gabriele, Michele"},{"orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","last_name":"Tavakoli"},{"last_name":"Lyudchik","first_name":"Julia","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"last_name":"Gabitto","first_name":"Mariano","full_name":"Gabitto, Mariano"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"},{"full_name":"Testa, Giuseppe","last_name":"Testa","first_name":"Giuseppe"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino"}],"_id":"11160","file":[{"content_type":"application/pdf","creator":"dernst","file_id":"11164","checksum":"b4e8d68f0268dec499af333e6fd5d8e1","access_level":"open_access","success":1,"file_name":"2022_CellReports_Villa.pdf","file_size":"7808644","date_updated":"2022-04-15T09:06:25Z","date_created":"2022-04-15T09:06:25Z","relation":"main_file"}],"date_created":"2022-04-15T09:03:10Z","abstract":[{"text":"Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling.","lang":"eng"}],"year":"2022","article_number":"110615","citation":{"short":"C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco, A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer, M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).","chicago":"Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon, Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>.","apa":"Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco, R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>","mla":"Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>, vol. 39, no. 1, 110615, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>.","ama":"Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. 2022;39(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>","ista":"Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG, Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.","ieee":"C. E. Villa <i>et al.</i>, “CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories,” <i>Cell Reports</i>, vol. 39, no. 1. Elsevier, 2022."},"file_date_updated":"2022-04-15T09:06:25Z","article_processing_charge":"Yes","oa_version":"Published Version","title":"CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories","publication_status":"published","article_type":"original","acknowledgement":"We thank Farnaz Freeman for technical assistance. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This work supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs); the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele; and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures were created using BioRender.com.","publication_identifier":{"issn":["2211-1247"]},"doi":"10.1016/j.celrep.2022.110615","status":"public","month":"04","isi":1,"keyword":["General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"ddc":["570"],"date_published":"2022-04-05T00:00:00Z","external_id":{"pmid":["35385734"],"isi":["000785983900003"]},"type":"journal_article","publisher":"Elsevier","pmid":1,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","grant_number":"715508"},{"_id":"2690FEAC-B435-11E9-9278-68D0E5697425","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","grant_number":"I04205","call_identifier":"FWF"}],"issue":"1","quality_controlled":"1","day":"05"},{"intvolume":"        74","date_updated":"2023-08-03T06:31:06Z","publication":"Current Opinion in Structural Biology","department":[{"_id":"LeSa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"37233050-F248-11E8-B48F-1D18A9856A87","full_name":"Kampjut, Domen","first_name":"Domen","last_name":"Kampjut"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A"}],"volume":74,"oa":1,"abstract":[{"lang":"eng","text":"Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I."}],"citation":{"ista":"Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350.","ieee":"D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging blueprint for the mechanism,” <i>Current Opinion in Structural Biology</i>, vol. 74. Elsevier, 2022.","ama":"Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. 2022;74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>","short":"D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022).","apa":"Kampjut, D., &#38; Sazanov, L. A. (2022). Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>.","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>, vol. 74, 102350, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>."},"article_number":"102350","year":"2022","date_created":"2022-04-15T09:32:35Z","file":[{"file_size":815607,"date_updated":"2022-08-05T05:56:03Z","date_created":"2022-08-05T05:56:03Z","relation":"main_file","access_level":"open_access","success":1,"file_name":"2022_CurrentOpStructBiology_Kampjut.pdf","checksum":"72bdde48853643a32d42b75f54965c44","content_type":"application/pdf","file_id":"11725","creator":"dernst"}],"_id":"11167","publication_identifier":{"issn":["0959-440X"]},"article_type":"original","scopus_import":"1","doi":"10.1016/j.sbi.2022.102350","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2022-08-05T05:56:03Z","title":"Structure of respiratory complex I – An emerging blueprint for the mechanism","publication_status":"published","keyword":["Molecular Biology","Structural Biology"],"ddc":["570"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"06","pmid":1,"publisher":"Elsevier","type":"journal_article","date_published":"2022-06-01T00:00:00Z","external_id":{"pmid":["35316665"],"isi":["000829029500020"]},"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"01","quality_controlled":"1"},{"page":"P2375-2389","day":"06","quality_controlled":"1","issue":"11","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"}],"pmid":1,"publisher":"Elsevier","type":"journal_article","date_published":"2022-06-06T00:00:00Z","external_id":{"pmid":["35508170"],"isi":["000822399200019"]},"ddc":["570"],"language":[{"iso":"eng"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"isi":1,"month":"06","status":"public","scopus_import":"1","doi":"10.1016/j.cub.2022.04.024","publication_identifier":{"issn":["0960-9822"]},"acknowledgement":"This work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank Noé Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.","article_type":"original","title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2022-08-05T06:29:18Z","citation":{"mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>.","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., &#38; Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>","chicago":"Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur, Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>.","ama":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. 2022;32(11):P2375-2389. doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>","ista":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.","ieee":"W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz, “Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks,” <i>Current Biology</i>, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022."},"year":"2022","abstract":[{"text":"One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.","lang":"eng"}],"file":[{"content_type":"application/pdf","file_id":"11730","creator":"dernst","checksum":"af3f24d97c016d844df237abef987639","success":1,"access_level":"open_access","file_name":"2022_CurrentBiology_Nicolas.pdf","date_created":"2022-08-05T06:29:18Z","relation":"main_file","date_updated":"2022-08-05T06:29:18Z","file_size":12827717}],"date_created":"2022-05-04T06:22:06Z","_id":"11351","author":[{"last_name":"Nicolas","first_name":"William J.","full_name":"Nicolas, William J."},{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian"},{"last_name":"Dutka","first_name":"Przemysław","full_name":"Dutka, Przemysław"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"},{"first_name":"Grant","last_name":"Jensen","full_name":"Jensen, Grant"},{"full_name":"Meyerowitz, Elliot","first_name":"Elliot","last_name":"Meyerowitz"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":32,"oa":1,"intvolume":"        32","department":[{"_id":"FlSc"}],"date_updated":"2023-08-03T07:05:36Z","publication":"Current Biology"},{"abstract":[{"text":"The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ.","lang":"eng"}],"year":"2022","article_number":"2635","citation":{"ista":"Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635.","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>","short":"P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).","chicago":"Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>.","apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., &#38; Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>","mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>, vol. 13, 2635, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>."},"_id":"11373","date_created":"2022-05-13T09:06:28Z","file":[{"checksum":"5af863ee1b95a0710f6ee864d68dc7a6","content_type":"application/pdf","file_id":"11374","creator":"dernst","date_updated":"2022-05-13T09:10:51Z","date_created":"2022-05-13T09:10:51Z","file_size":6945191,"relation":"main_file","access_level":"open_access","success":1,"file_name":"2022_NatureCommunications_Radler.pdf"}],"article_type":"original","acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-022-30301-y","scopus_import":"1","file_date_updated":"2022-05-13T09:10:51Z","article_processing_charge":"No","oa_version":"Published Version","title":"In vitro reconstitution of Escherichia coli divisome activation","publication_status":"published","intvolume":"        13","publication":"Nature Communications","ec_funded":1,"date_updated":"2024-02-21T12:35:18Z","department":[{"_id":"MaLo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Radler","first_name":"Philipp","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 "},{"first_name":"Natalia S.","last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S."},{"full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","first_name":"Paulo R"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Lopez Pelegrin, Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Pelegrin","first_name":"Maria D"},{"id":"B9577E20-AA38-11E9-AC9A-0930E6697425","full_name":"Michalik, David","first_name":"David","last_name":"Michalik"},{"last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-34485-1","relation":"erratum"}],"record":[{"status":"public","relation":"dissertation_contains","id":"14280"},{"id":"10934","status":"public","relation":"research_data"}]},"oa":1,"volume":13,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020"},{"grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"}],"has_accepted_license":"1","day":"12","quality_controlled":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"05","isi":1,"publisher":"Springer Nature","date_published":"2022-05-12T00:00:00Z","external_id":{"isi":["000795171100037"]},"type":"journal_article"},{"intvolume":"        84","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"date_updated":"2023-08-03T07:20:53Z","ec_funded":1,"publication":"Bulletin of Mathematical Biology","author":[{"first_name":"Raimundo J","last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"},{"full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","last_name":"Khudiakova","first_name":"Kseniia"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":84,"oa":1,"related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"citation":{"chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","apa":"Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>.","ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022.","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. 2022;84(8). doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>"},"article_number":"74","year":"2022","abstract":[{"lang":"eng","text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks."}],"date_created":"2022-06-17T16:16:15Z","file":[{"checksum":"05a1fe7d10914a00c2bca9b447993a65","content_type":"application/pdf","file_id":"11455","creator":"dernst","relation":"main_file","file_size":463025,"date_updated":"2022-06-20T07:51:32Z","date_created":"2022-06-20T07:51:32Z","access_level":"open_access","success":1,"file_name":"2022_BulletinMathBiology_Saona.pdf"}],"_id":"11447","scopus_import":"1","doi":"10.1007/s11538-022-01029-z","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","article_type":"original","publication_status":"published","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","file_date_updated":"2022-06-20T07:51:32Z","ddc":["510","570"],"language":[{"iso":"eng"}],"keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"isi":1,"month":"06","status":"public","publisher":"Springer Nature","type":"journal_article","date_published":"2022-06-17T00:00:00Z","external_id":{"isi":["000812509800001"]},"issue":"8","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"call_identifier":"H2020","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales"},{"grant_number":"I05127","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","name":"Evolutionary analysis of gene regulation"}],"day":"17","quality_controlled":"1"},{"_id":"11448","date_created":"2022-06-18T09:06:59Z","file":[{"relation":"main_file","date_updated":"2022-06-20T07:44:19Z","file_size":5297213,"date_created":"2022-06-20T07:44:19Z","file_name":"2022_eLife_Somermeyer.pdf","success":1,"access_level":"open_access","checksum":"7573c28f44028ab0cc81faef30039e44","creator":"dernst","file_id":"11454","content_type":"application/pdf"}],"article_number":"75842","year":"2022","citation":{"mla":"Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>, vol. 11, 75842, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>.","short":"L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022).","chicago":"Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>.","apa":"Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>","ama":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>","ista":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.","ieee":"L. Gonzalez Somermeyer <i>et al.</i>, “Heterogeneity of the GFP fitness landscape and data-driven protein design,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022."},"abstract":[{"lang":"eng","text":"Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering."}],"title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","publication_status":"published","file_date_updated":"2022-06-20T07:44:19Z","oa_version":"Published Version","article_processing_charge":"No","doi":"10.7554/elife.75842","scopus_import":"1","article_type":"original","publication_identifier":{"issn":["2050-084X"]},"acknowledgement":"We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova for technical assistance and data interpretation. Core facility Biomolecular Interactions and Crystallization of CEITEC Masaryk University is gratefully acknowledged for the obtaining of the scientific data presented in this paper. This research was supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF). MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility in the Vanderbilt University Center for Structural Biology. We are grateful to Joel M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4, the Imperial College Research Fellowship and the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\"). Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH). This work was supported by a Russian Science Foundation grant 19-74-10102.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385.","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"publication":"eLife","ec_funded":1,"date_updated":"2023-08-03T07:20:15Z","intvolume":"        11","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"oa":1,"volume":11,"author":[{"first_name":"Louisa","last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","full_name":"Gonzalez Somermeyer, Louisa"},{"full_name":"Fleiss, Aubin","last_name":"Fleiss","first_name":"Aubin"},{"first_name":"Alexander S","last_name":"Mishin","full_name":"Mishin, Alexander S"},{"last_name":"Bozhanova","first_name":"Nina G","full_name":"Bozhanova, Nina G"},{"first_name":"Anna A","last_name":"Igolkina","full_name":"Igolkina, Anna A"},{"full_name":"Meiler, Jens","first_name":"Jens","last_name":"Meiler"},{"full_name":"Alaball Pujol, Maria-Elisenda","last_name":"Alaball Pujol","first_name":"Maria-Elisenda"},{"full_name":"Putintseva, Ekaterina V","first_name":"Ekaterina V","last_name":"Putintseva"},{"first_name":"Karen S","last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","call_identifier":"H2020"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","quality_controlled":"1","day":"05","month":"05","isi":1,"status":"public","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"date_published":"2022-05-05T00:00:00Z","external_id":{"isi":["000799197200001"]},"type":"journal_article","publisher":"eLife Sciences Publications"},{"title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2022-06-24T08:22:59Z","doi":"10.1186/s13229-022-00508-3","publication_identifier":{"issn":["2040-2392"]},"acknowledgement":"This study was funded by NIMH R21MH115347 to KSZ. KSZ is further supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan de Crescenzo for early contributions to this project.","article_type":"original","date_created":"2022-06-23T14:28:55Z","file":[{"success":1,"access_level":"open_access","file_name":"2022_MolecularAutism_Schaaf.pdf","date_created":"2022-06-24T08:22:59Z","date_updated":"2022-06-24T08:22:59Z","file_size":7552298,"relation":"main_file","content_type":"application/pdf","file_id":"11461","creator":"dernst","checksum":"525d2618e855139089bbfc3e3d49d1b2"}],"_id":"11460","citation":{"ama":"Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. 2022;13. doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>","ieee":"Z. A. Schaaf <i>et al.</i>, “WDFY3 mutation alters laminar position and morphology of cortical neurons,” <i>Molecular Autism</i>, vol. 13. Springer Nature, 2022.","ista":"Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons. Molecular Autism. 13, 27.","mla":"Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>, vol. 13, 27, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>.","apa":"Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>","chicago":"Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>.","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022)."},"article_number":"27","year":"2022","abstract":[{"text":"Background: Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild-type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients or some of the other neurodevelopmental conditions associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed several cell autonomous requirements of WDFY3 in neuronal development that could underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity in postnatal life.","lang":"eng"}],"volume":13,"related_material":{"link":[{"url":"https://doi.org/10.1186/s13229-023-00539-4","relation":"erratum"}]},"oa":1,"author":[{"full_name":"Schaaf, Zachary A.","last_name":"Schaaf","first_name":"Zachary A."},{"last_name":"Tat","first_name":"Lyvin","full_name":"Tat, Lyvin"},{"first_name":"Noemi","last_name":"Cannizzaro","full_name":"Cannizzaro, Noemi"},{"first_name":"Ralph","last_name":"Green","full_name":"Green, Ralph"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zarbalis","first_name":"Konstantinos S.","full_name":"Zarbalis, Konstantinos S."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SiHi"}],"date_updated":"2023-08-03T07:21:32Z","publication":"Molecular Autism","intvolume":"        13","quality_controlled":"1","day":"22","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","external_id":{"isi":["000814641400001"]},"date_published":"2022-06-22T00:00:00Z","publisher":"Springer Nature","isi":1,"month":"06","status":"public","ddc":["570"],"language":[{"iso":"eng"}],"keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"]}]