[{"date_published":"2021-12-01T00:00:00Z","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","external_id":{"pmid":["34850679"],"isi":["000754832000001"]},"ddc":["570"],"author":[{"last_name":"Choi","first_name":"Jaemyung","full_name":"Choi, Jaemyung"},{"last_name":"Lyons","first_name":"David B","full_name":"Lyons, David B"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman"}],"publication":"eLife","publisher":"eLife Sciences Publications","doi":"10.7554/elife.72676","file_date_updated":"2022-05-16T10:42:22Z","type":"journal_article","language":[{"iso":"eng"}],"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","pmid":1,"publication_identifier":{"issn":["2050-084X"]},"date_updated":"2023-08-17T06:21:08Z","project":[{"name":"Quantitative analysis of DNA methylation maintenance with chromatin","grant_number":"725746","_id":"62935a00-2b32-11ec-9570-eff30fa39068","call_identifier":"H2020"}],"quality_controlled":"1","date_created":"2021-12-10T13:12:08Z","year":"2021","volume":10,"isi":1,"file":[{"creator":"dernst","file_size":2715200,"checksum":"22ed4c55fb550f6da02ae55c359be651","relation":"main_file","access_level":"open_access","date_updated":"2022-05-16T10:42:22Z","success":1,"file_id":"11384","content_type":"application/pdf","date_created":"2022-05-16T10:42:22Z","file_name":"2021_eLife_Choi.pdf"}],"department":[{"_id":"DaZi"}],"acknowledgement":"We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"12","_id":"10533","article_type":"original","title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin","oa":1,"publication_status":"published","has_accepted_license":"1","day":"01","citation":{"ama":"Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>","short":"J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).","mla":"Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>, vol. 10, e72676, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>.","ieee":"J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.","chicago":"Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>.","apa":"Choi, J., Lyons, D. B., &#38; Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>"},"intvolume":"        10","keyword":["genetics and molecular biology"],"ec_funded":1,"abstract":[{"text":"Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.","lang":"eng"}],"article_number":"e72676","status":"public"},{"acknowledged_ssus":[{"_id":"PreCl"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"},{"grant_number":"F07807","name":"Neural stem cells in autism and epilepsy","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"},{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","call_identifier":"FWF"}],"date_updated":"2024-09-10T12:04:26Z","date_created":"2021-05-28T11:49:46Z","year":"2021","quality_controlled":"1","file":[{"file_size":9358599,"creator":"kschuh","relation":"main_file","checksum":"337e0f7959c35ec959984cacdcb472ba","content_type":"application/pdf","date_created":"2021-05-28T12:39:43Z","file_id":"9430","access_level":"open_access","success":1,"date_updated":"2021-05-28T12:39:43Z","file_name":"2021_NatureCommunications_Morandell.pdf"}],"isi":1,"volume":12,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","publication_identifier":{"eissn":["2041-1723"]},"publisher":"Springer Nature","doi":"10.1038/s41467-021-23123-x","type":"journal_article","file_date_updated":"2021-05-28T12:39:43Z","language":[{"iso":"eng"}],"date_published":"2021-05-24T00:00:00Z","external_id":{"isi":["000658769900010"]},"oa_version":"Published Version","author":[{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin","full_name":"Morandell, Jasmin"},{"id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A","full_name":"Schwarz, Lena A","last_name":"Schwarz"},{"last_name":"Basilico","first_name":"Bernadette","full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173"},{"last_name":"Tasciyan","first_name":"Saren","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","last_name":"Dimchev","full_name":"Dimchev, Georgi A","first_name":"Georgi A"},{"first_name":"Armel","full_name":"Nicolas, Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sommer","full_name":"Sommer, Christoph M","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"full_name":"Kreuzinger, Caroline","first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dotter","full_name":"Dotter, Christoph","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus","first_name":"Lisa","full_name":"Knaus, Lisa"},{"id":"D23090A2-9057-11EA-883A-A8396FC7A38F","last_name":"Dobler","first_name":"Zoe","full_name":"Dobler, Zoe"},{"last_name":"Cacci","first_name":"Emanuele","full_name":"Cacci, Emanuele"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","full_name":"Schur, Florian KM","last_name":"Schur"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"ddc":["572"],"issue":"1","publication":"Nature Communications","ec_funded":1,"abstract":[{"lang":"eng","text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs."}],"status":"public","article_number":"3058","has_accepted_license":"1","day":"24","citation":{"mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>.","ieee":"J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>.","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021)."},"intvolume":"        12","keyword":["General Biochemistry","Genetics and Molecular Biology"],"month":"05","_id":"9429","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","publication_status":"published","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}],"record":[{"id":"7800","status":"public","relation":"earlier_version"},{"status":"public","relation":"dissertation_contains","id":"12401"}]},"oa":1,"acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}]},{"has_accepted_license":"1","day":"28","citation":{"ieee":"M. Obr <i>et al.</i>, “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” <i>Nature Communications</i>, vol. 12, no. 1. Nature Research, 2021.","mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>, vol. 12, no. 1, 3226, Nature Research, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>.","chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” <i>Nature Communications</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>.","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226.","apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-021-23506-0\">https://doi.org/10.1038/s41467-021-23506-0</a>","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23506-0\">10.1038/s41467-021-23506-0</a>","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021)."},"intvolume":"        12","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"abstract":[{"lang":"eng","text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles."}],"status":"public","article_number":"3226","acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF).","department":[{"_id":"FlSc"}],"month":"05","_id":"9431","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","publication_status":"published","title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/","description":"News on IST Homepage","relation":"press_release"}]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","scopus_import":"1","publication_identifier":{"eissn":["2041-1723"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"date_updated":"2023-08-08T13:53:53Z","year":"2021","date_created":"2021-05-28T14:25:50Z","quality_controlled":"1","file":[{"success":1,"date_updated":"2021-06-09T15:21:14Z","access_level":"open_access","date_created":"2021-06-09T15:21:14Z","file_id":"9538","content_type":"application/pdf","file_name":"2021_NatureCommunications_Obr.pdf","creator":"kschuh","file_size":6166295,"checksum":"53ccc53d09a9111143839dbe7784e663","relation":"main_file"}],"isi":1,"volume":12,"date_published":"2021-05-28T00:00:00Z","external_id":{"isi":["000659145000011"]},"oa_version":"Published Version","author":[{"last_name":"Obr","full_name":"Obr, Martin","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ricana","first_name":"Clifton L.","full_name":"Ricana, Clifton L."},{"last_name":"Nikulin","first_name":"Nadia","full_name":"Nikulin, Nadia"},{"full_name":"Feathers, Jon-Philip R.","first_name":"Jon-Philip R.","last_name":"Feathers"},{"last_name":"Klanschnig","first_name":"Marco","full_name":"Klanschnig, Marco"},{"id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","last_name":"Thader","full_name":"Thader, Andreas","first_name":"Andreas"},{"last_name":"Johnson","full_name":"Johnson, Marc C.","first_name":"Marc C."},{"last_name":"Vogt","full_name":"Vogt, Volker M.","first_name":"Volker M."},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur"},{"last_name":"Dick","first_name":"Robert A.","full_name":"Dick, Robert A."}],"ddc":["570"],"issue":"1","publication":"Nature Communications","publisher":"Nature Research","doi":"10.1038/s41467-021-23506-0","type":"journal_article","file_date_updated":"2021-06-09T15:21:14Z","language":[{"iso":"eng"}]},{"publication":"Nature Communications","issue":"1","ddc":["570"],"author":[{"last_name":"Prattes","first_name":"Michael","full_name":"Prattes, Michael"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rössler, Ingrid","first_name":"Ingrid","last_name":"Rössler"},{"last_name":"Klein","full_name":"Klein, Isabella","first_name":"Isabella"},{"last_name":"Hetzmannseder","first_name":"Christina","full_name":"Hetzmannseder, Christina"},{"full_name":"Zisser, Gertrude","first_name":"Gertrude","last_name":"Zisser"},{"last_name":"Gruber","full_name":"Gruber, Christian C.","first_name":"Christian C."},{"full_name":"Gruber, Karl","first_name":"Karl","last_name":"Gruber"},{"last_name":"Haselbach","first_name":"David","full_name":"Haselbach, David"},{"last_name":"Bergler","full_name":"Bergler, Helmut","first_name":"Helmut"}],"external_id":{"isi":["000664874700014"],"pmid":["34108481"]},"oa_version":"Published Version","date_published":"2021-06-09T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2021-06-15T18:55:59Z","type":"journal_article","doi":"10.1038/s41467-021-23854-x","publisher":"Springer Nature","publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","volume":12,"isi":1,"file":[{"checksum":"40fc24c1310930990b52a8ad1142ee97","relation":"main_file","creator":"cziletti","file_size":3397292,"file_name":"2021_NatureComm_Prattes.pdf","date_updated":"2021-06-15T18:55:59Z","access_level":"open_access","success":1,"file_id":"9556","date_created":"2021-06-15T18:55:59Z","content_type":"application/pdf"}],"quality_controlled":"1","year":"2021","date_created":"2021-06-10T14:57:45Z","date_updated":"2023-08-08T14:05:26Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"department":[{"_id":"EM-Fac"}],"acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","oa":1,"publication_status":"published","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"06","_id":"9540","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"intvolume":"        12","citation":{"short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021).","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483.","ieee":"M. Prattes <i>et al.</i>, “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>."},"day":"09","has_accepted_license":"1","article_number":"3483","status":"public","abstract":[{"lang":"eng","text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases."}]},{"scopus_import":"1","publication_identifier":{"issn":["2041-1723"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","volume":12,"file":[{"checksum":"6036a8cdae95e1707c2a04d54e325ff4","relation":"main_file","creator":"kschuh","file_size":3108845,"file_name":"2021_NatureCommunications_Vandael.pdf","date_updated":"2021-12-17T11:34:50Z","success":1,"access_level":"open_access","content_type":"application/pdf","file_id":"10563","date_created":"2021-12-17T11:34:50Z"}],"isi":1,"date_updated":"2023-08-10T14:16:16Z","acknowledged_ssus":[{"_id":"SSU"}],"project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"}],"quality_controlled":"1","year":"2021","date_created":"2021-08-06T07:22:55Z","ddc":["570"],"author":[{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","first_name":"David H","full_name":"Vandael, David H","last_name":"Vandael"},{"first_name":"Yuji","full_name":"Okamoto, Yuji","last_name":"Okamoto","id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas"}],"publication":"Nature Communications","issue":"1","date_published":"2021-05-18T00:00:00Z","external_id":{"isi":["000655481800014"]},"oa_version":"Published Version","file_date_updated":"2021-12-17T11:34:50Z","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Springer","doi":"10.1038/s41467-021-23153-5","citation":{"chicago":"Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>. Springer, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>.","apa":"Vandael, D. H., Okamoto, Y., &#38; Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. Springer. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>","ista":"Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912.","ieee":"D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” <i>Nature Communications</i>, vol. 12, no. 1. Springer, 2021.","mla":"Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>, vol. 12, no. 1, 2912, Springer, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>.","short":"D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).","ama":"Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>"},"intvolume":"        12","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"has_accepted_license":"1","day":"18","abstract":[{"text":"The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses.","lang":"eng"}],"article_number":"2912","status":"public","ec_funded":1,"department":[{"_id":"PeJo"}],"acknowledgement":"We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J.","article_type":"original","related_material":{"link":[{"url":"https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/","description":"News on IST Homepage","relation":"press_release"}]},"oa":1,"title":"Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9778","month":"05"},{"publisher":"Elsevier","doi":"10.1016/j.cub.2021.02.043","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2021-05-24T00:00:00Z","external_id":{"isi":["000654652200002"],"pmid":["33711252"]},"oa_version":"Preprint","author":[{"last_name":"Stahnke","full_name":"Stahnke, Stephanie","first_name":"Stephanie"},{"first_name":"Hermann","full_name":"Döring, Hermann","last_name":"Döring"},{"first_name":"Charly","full_name":"Kusch, Charly","last_name":"Kusch"},{"full_name":"de Gorter, David J.J.","first_name":"David J.J.","last_name":"de Gorter"},{"last_name":"Dütting","full_name":"Dütting, Sebastian","first_name":"Sebastian"},{"last_name":"Guledani","full_name":"Guledani, Aleks","first_name":"Aleks"},{"last_name":"Pleines","first_name":"Irina","full_name":"Pleines, Irina"},{"last_name":"Schnoor","full_name":"Schnoor, Michael","first_name":"Michael"},{"first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"first_name":"Robert","full_name":"Geffers, Robert","last_name":"Geffers"},{"full_name":"Rohde, Manfred","first_name":"Manfred","last_name":"Rohde"},{"last_name":"Müsken","full_name":"Müsken, Mathias","first_name":"Mathias"},{"last_name":"Kage","first_name":"Frieda","full_name":"Kage, Frieda"},{"full_name":"Steffen, Anika","first_name":"Anika","last_name":"Steffen"},{"last_name":"Faix","full_name":"Faix, Jan","first_name":"Jan"},{"last_name":"Nieswandt","first_name":"Bernhard","full_name":"Nieswandt, Bernhard"},{"last_name":"Rottner","full_name":"Rottner, Klemens","first_name":"Klemens"},{"last_name":"Stradal","first_name":"Theresia E.B.","full_name":"Stradal, Theresia E.B."}],"publication":"Current Biology","issue":"10","date_updated":"2023-08-17T07:01:14Z","page":"2051-2064.e8","quality_controlled":"1","year":"2021","date_created":"2022-03-08T07:51:04Z","volume":31,"isi":1,"article_processing_charge":"No","scopus_import":"1","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.03.24.005835"}],"publication_identifier":{"issn":["0960-9822"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"05","_id":"10834","article_type":"original","oa":1,"title":"Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion","publication_status":"published","acknowledgement":"We are grateful to Silvia Prettin, Ina Schleicher, and Petra Hagendorff for expert technical assistance; David Dettbarn for animal keeping and breeding; and Lothar Gröbe and Maria Höxter for cell sorting. We also thank Werner Tegge for peptides and Giorgio Scita for antibodies. This work was supported, in part, by the Deutsche Forschungsgemeinschaft (DFG), Priority Programm SPP1150 (to T.E.B.S., K.R., and M. Sixt), and by DFG grant GRK2223/1 (to K.R.). T.E.B.S. acknowledges support by the Helmholtz Society through HGF impulse fund W2/W3-066 and M. Schnoor by the Mexican Council for Science and Technology (CONACyT, 284292 ), Fund SEP-Cinvestav ( 108 ), and the Royal Society, UK (Newton Advanced Fellowship, NAF/R1/180017 ).","department":[{"_id":"MiSi"}],"abstract":[{"text":"Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation and the protrusion of branched actin filament networks. Moreover, Hem1 loss of function in immune cells causes autoimmune diseases in humans. Here, we show that genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis as well as phagocytic cup formation in addition to defects in lamellipodial protrusion and migration. Moreover, Hem1-null macrophages displayed strong defects in cell adhesion despite unaltered podosome formation and concomitant extracellular matrix degradation. Specifically, dynamics of both adhesion and de-adhesion as well as concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly compromised. Accordingly, disruption of WRC function in non-hematopoietic cells coincided with both defects in adhesion turnover and altered FAK and paxillin phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes, but not lamellipodia formation, were partially rescued by small molecule activation of FAK. A full rescue of the phenotype, including lamellipodia formation, required not only the presence of WRCs but also their binding to and activation by Rac. Collectively, our results uncover that WRC impacts on integrin-dependent processes in a FAK-dependent manner, controlling formation and dismantling of adhesions, relevant for properly grabbing onto extracellular surfaces and particles during cell edge expansion, like in migration or phagocytosis.","lang":"eng"}],"status":"public","day":"24","intvolume":"        31","citation":{"short":"S. Stahnke, H. Döring, C. Kusch, D.J.J. de Gorter, S. Dütting, A. Guledani, I. Pleines, M. Schnoor, M.K. Sixt, R. Geffers, M. Rohde, M. Müsken, F. Kage, A. Steffen, J. Faix, B. Nieswandt, K. Rottner, T.E.B. Stradal, Current Biology 31 (2021) 2051–2064.e8.","ama":"Stahnke S, Döring H, Kusch C, et al. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. 2021;31(10):2051-2064.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>","chicago":"Stahnke, Stephanie, Hermann Döring, Charly Kusch, David J.J. de Gorter, Sebastian Dütting, Aleks Guledani, Irina Pleines, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>.","ista":"Stahnke S, Döring H, Kusch C, de Gorter DJJ, Dütting S, Guledani A, Pleines I, Schnoor M, Sixt MK, Geffers R, Rohde M, Müsken M, Kage F, Steffen A, Faix J, Nieswandt B, Rottner K, Stradal TEB. 2021. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 31(10), 2051–2064.e8.","apa":"Stahnke, S., Döring, H., Kusch, C., de Gorter, D. J. J., Dütting, S., Guledani, A., … Stradal, T. E. B. (2021). Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>","ieee":"S. Stahnke <i>et al.</i>, “Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion,” <i>Current Biology</i>, vol. 31, no. 10. Elsevier, p. 2051–2064.e8, 2021.","mla":"Stahnke, Stephanie, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>, vol. 31, no. 10, Elsevier, 2021, p. 2051–2064.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>."},"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"]},{"doi":"10.1111/mec.15861","publisher":"Wiley","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2022-03-08T11:31:30Z","oa_version":"Published Version","external_id":{"isi":["000669439700001"],"pmid":["33638231"]},"date_published":"2021-08-01T00:00:00Z","issue":"15","publication":"Molecular Ecology","author":[{"first_name":"Anja M","full_name":"Westram, Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"}],"ddc":["570"],"date_created":"2022-03-08T11:28:32Z","year":"2021","page":"3797-3814","quality_controlled":"1","date_updated":"2023-09-05T16:02:19Z","isi":1,"file":[{"creator":"dernst","file_size":1726548,"checksum":"d5611f243ceb63a0e091d6662ebd9cda","relation":"main_file","success":1,"date_updated":"2022-03-08T11:31:30Z","access_level":"open_access","file_id":"10839","date_created":"2022-03-08T11:31:30Z","content_type":"application/pdf","file_name":"2021_MolecularEcology_Westram.pdf"}],"volume":30,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"pmid":1,"scopus_import":"1","month":"08","_id":"10838","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","oa":1,"title":"Using replicate hybrid zones to understand the genomic basis of adaptive divergence","article_type":"original","department":[{"_id":"BeVi"}],"acknowledgement":"We thank everyone who helped with fieldwork, snail processing and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Mark Ravinet, Irena Senčić and Zuzanna Zagrodzka. We are also grateful to Edinburgh Genomics for library preparation and sequencing, to Stuart Baird and Mark Ravinet for helpful discussions, and to three anonymous reviewers for their constructive comments. This work was supported by the Natural Environment Research Council (NE/K014021/1), the European Research Council (AdG-693030-BARRIERS), Swedish Research Councils Formas and Vetenskapsrådet through a Linnaeus grant to the Centre for Marine Evolutionary Biology (217-2008-1719), the European Regional Development Fund (POCI-01-0145-FEDER-030628), and the Fundação para a iência e a Tecnologia,\r\nPortugal (PTDC/BIA-EVL/\r\n30628/2017). A.M.W. and R.F. were\r\nfunded by the European Union’s Horizon 2020 research and innovation\r\nprogramme under Marie Skłodowska-Curie\r\ngrant agreements\r\nno. 754411/797747 and no. 706376, respectively.","status":"public","abstract":[{"text":"Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder–rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones.","lang":"eng"}],"day":"01","has_accepted_license":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"citation":{"ama":"Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. <i>Molecular Ecology</i>. 2021;30(15):3797-3814. doi:<a href=\"https://doi.org/10.1111/mec.15861\">10.1111/mec.15861</a>","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, Molecular Ecology 30 (2021) 3797–3814.","mla":"Westram, Anja M., et al. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” <i>Molecular Ecology</i>, vol. 30, no. 15, Wiley, 2021, pp. 3797–814, doi:<a href=\"https://doi.org/10.1111/mec.15861\">10.1111/mec.15861</a>.","ieee":"A. M. Westram, R. Faria, K. Johannesson, and R. Butlin, “Using replicate hybrid zones to understand the genomic basis of adaptive divergence,” <i>Molecular Ecology</i>, vol. 30, no. 15. Wiley, pp. 3797–3814, 2021.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, and Roger Butlin. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” <i>Molecular Ecology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/mec.15861\">https://doi.org/10.1111/mec.15861</a>.","ista":"Westram AM, Faria R, Johannesson K, Butlin R. 2021. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology. 30(15), 3797–3814.","apa":"Westram, A. M., Faria, R., Johannesson, K., &#38; Butlin, R. (2021). Using replicate hybrid zones to understand the genomic basis of adaptive divergence. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15861\">https://doi.org/10.1111/mec.15861</a>"},"intvolume":"        30"},{"extern":"1","abstract":[{"lang":"eng","text":"In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function."}],"status":"public","day":"08","citation":{"short":"S. Krishna, R. Arrojo e Drigo, J.S. Capitanio, R. Ramachandra, M. Ellisman, M. Hetzer, Developmental Cell 56 (2021) P2952–2965.e9.","ama":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. 2021;56(21):P2952-2965.e9. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>","ista":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. 2021. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. Developmental Cell. 56(21), P2952–2965.e9.","apa":"Krishna, S., Arrojo e Drigo, R., Capitanio, J. S., Ramachandra, R., Ellisman, M., &#38; Hetzer, M. (2021). Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>","chicago":"Krishna, Shefali, Rafael Arrojo e Drigo, Juliana S. Capitanio, Ranjan Ramachandra, Mark Ellisman, and Martin Hetzer. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>.","mla":"Krishna, Shefali, et al. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>, vol. 56, no. 21, Elsevier, 2021, p. P2952–2965.e9, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>.","ieee":"S. Krishna, R. Arrojo e Drigo, J. S. Capitanio, R. Ramachandra, M. Ellisman, and M. Hetzer, “Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain,” <i>Developmental Cell</i>, vol. 56, no. 21. Elsevier, p. P2952–2965.e9, 2021."},"intvolume":"        56","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"_id":"11052","month":"11","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","article_type":"original","publication_status":"published","title":"Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain","date_updated":"2022-07-18T08:26:38Z","date_created":"2022-04-07T07:43:14Z","year":"2021","page":"P2952-2965.e9","quality_controlled":"1","volume":56,"article_processing_charge":"No","pmid":1,"scopus_import":"1","publication_identifier":{"issn":["1534-5807"]},"publisher":"Elsevier","doi":"10.1016/j.devcel.2021.10.008","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2021-11-08T00:00:00Z","external_id":{"pmid":["34715012"]},"oa_version":"None","author":[{"last_name":"Krishna","first_name":"Shefali","full_name":"Krishna, Shefali"},{"last_name":"Arrojo e Drigo","full_name":"Arrojo e Drigo, Rafael","first_name":"Rafael"},{"first_name":"Juliana S.","full_name":"Capitanio, Juliana S.","last_name":"Capitanio"},{"full_name":"Ramachandra, Ranjan","first_name":"Ranjan","last_name":"Ramachandra"},{"last_name":"Ellisman","full_name":"Ellisman, Mark","first_name":"Mark"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"HETZER","full_name":"HETZER, Martin W","first_name":"Martin W"}],"issue":"21","publication":"Developmental Cell"},{"scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/","open_access":"1"}],"pmid":1,"publication_identifier":{"issn":["1553-7404"]},"article_processing_charge":"No","volume":16,"date_updated":"2023-05-08T10:54:39Z","quality_controlled":"1","year":"2020","date_created":"2023-01-16T09:16:10Z","author":[{"full_name":"Christophorou, Nicolas","first_name":"Nicolas","last_name":"Christophorou"},{"full_name":"She, Wenjing","first_name":"Wenjing","last_name":"She"},{"first_name":"Jincheng","full_name":"Long, Jincheng","last_name":"Long"},{"first_name":"Aurélie","full_name":"Hurel, Aurélie","last_name":"Hurel"},{"full_name":"Beaubiat, Sébastien","first_name":"Sébastien","last_name":"Beaubiat"},{"first_name":"Yassir","full_name":"Idir, Yassir","last_name":"Idir"},{"full_name":"Tagliaro-Jahns, Marina","first_name":"Marina","last_name":"Tagliaro-Jahns"},{"last_name":"Chambon","full_name":"Chambon, Aurélie","first_name":"Aurélie"},{"full_name":"Solier, Victor","first_name":"Victor","last_name":"Solier"},{"full_name":"Vezon, Daniel","first_name":"Daniel","last_name":"Vezon"},{"last_name":"Grelon","first_name":"Mathilde","full_name":"Grelon, Mathilde"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","last_name":"Feng","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi"},{"last_name":"Bouché","full_name":"Bouché, Nicolas","first_name":"Nicolas"},{"first_name":"Christine","full_name":"Mézard, Christine","last_name":"Mézard"}],"publication":"PLOS Genetics","issue":"6","date_published":"2020-06-29T00:00:00Z","oa_version":"Published Version","external_id":{"pmid":["32598340"]},"type":"journal_article","language":[{"iso":"eng"}],"publisher":"Public Library of Science (PLoS)","doi":"10.1371/journal.pgen.1008894","intvolume":"        16","citation":{"ieee":"N. Christophorou <i>et al.</i>, “AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization,” <i>PLOS Genetics</i>, vol. 16, no. 6. Public Library of Science (PLoS), 2020.","mla":"Christophorou, Nicolas, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” <i>PLOS Genetics</i>, vol. 16, no. 6, e1008894, Public Library of Science (PLoS), 2020, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008894\">10.1371/journal.pgen.1008894</a>.","apa":"Christophorou, N., She, W., Long, J., Hurel, A., Beaubiat, S., Idir, Y., … Mézard, C. (2020). AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. <i>PLOS Genetics</i>. Public Library of Science (PLoS). <a href=\"https://doi.org/10.1371/journal.pgen.1008894\">https://doi.org/10.1371/journal.pgen.1008894</a>","chicago":"Christophorou, Nicolas, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” <i>PLOS Genetics</i>. Public Library of Science (PLoS), 2020. <a href=\"https://doi.org/10.1371/journal.pgen.1008894\">https://doi.org/10.1371/journal.pgen.1008894</a>.","ista":"Christophorou N, She W, Long J, Hurel A, Beaubiat S, Idir Y, Tagliaro-Jahns M, Chambon A, Solier V, Vezon D, Grelon M, Feng X, Bouché N, Mézard C. 2020. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 16(6), e1008894.","ama":"Christophorou N, She W, Long J, et al. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. <i>PLOS Genetics</i>. 2020;16(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008894\">10.1371/journal.pgen.1008894</a>","short":"N. Christophorou, W. She, J. Long, A. Hurel, S. Beaubiat, Y. Idir, M. Tagliaro-Jahns, A. Chambon, V. Solier, D. Vezon, M. Grelon, X. Feng, N. Bouché, C. Mézard, PLOS Genetics 16 (2020)."},"keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"day":"29","abstract":[{"text":"Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells.","lang":"eng"}],"extern":"1","article_number":"e1008894","status":"public","acknowledgement":"The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.","department":[{"_id":"XiFe"}],"article_type":"original","oa":1,"title":"AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","_id":"12189"},{"oa":1,"title":"The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments","publication_status":"published","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","_id":"8402","article_number":"2","status":"public","abstract":[{"lang":"eng","text":"Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.\r\nResults: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.\r\nConclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins."}],"extern":"1","keyword":["Biotechnology","Plant Science","General Biochemistry","Genetics and Molecular Biology","Developmental Biology","Cell Biology","Physiology","Ecology","Evolution","Behavior and Systematics","Structural Biology","General Agricultural and Biological Sciences"],"intvolume":"        18","citation":{"short":"H. Rampelt, I. Sucec, B. Bersch, P. Horten, I. Perschil, J.-C. Martinou, M. van der Laan, N. Wiedemann, P. Schanda, N. Pfanner, BMC Biology 18 (2020).","ama":"Rampelt H, Sucec I, Bersch B, et al. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. <i>BMC Biology</i>. 2020;18. doi:<a href=\"https://doi.org/10.1186/s12915-019-0733-6\">10.1186/s12915-019-0733-6</a>","ista":"Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der Laan M, Wiedemann N, Schanda P, Pfanner N. 2020. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. 18, 2.","chicago":"Rampelt, Heike, Iva Sucec, Beate Bersch, Patrick Horten, Inge Perschil, Jean-Claude Martinou, Martin van der Laan, Nils Wiedemann, Paul Schanda, and Nikolaus Pfanner. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” <i>BMC Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1186/s12915-019-0733-6\">https://doi.org/10.1186/s12915-019-0733-6</a>.","apa":"Rampelt, H., Sucec, I., Bersch, B., Horten, P., Perschil, I., Martinou, J.-C., … Pfanner, N. (2020). The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. <i>BMC Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12915-019-0733-6\">https://doi.org/10.1186/s12915-019-0733-6</a>","mla":"Rampelt, Heike, et al. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” <i>BMC Biology</i>, vol. 18, 2, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1186/s12915-019-0733-6\">10.1186/s12915-019-0733-6</a>.","ieee":"H. Rampelt <i>et al.</i>, “The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments,” <i>BMC Biology</i>, vol. 18. Springer Nature, 2020."},"day":"06","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1186/s12915-019-0733-6","publisher":"Springer Nature","publication":"BMC Biology","author":[{"first_name":"Heike","full_name":"Rampelt, Heike","last_name":"Rampelt"},{"first_name":"Iva","full_name":"Sucec, Iva","last_name":"Sucec"},{"first_name":"Beate","full_name":"Bersch, Beate","last_name":"Bersch"},{"full_name":"Horten, Patrick","first_name":"Patrick","last_name":"Horten"},{"last_name":"Perschil","first_name":"Inge","full_name":"Perschil, Inge"},{"first_name":"Jean-Claude","full_name":"Martinou, Jean-Claude","last_name":"Martinou"},{"last_name":"van der Laan","full_name":"van der Laan, Martin","first_name":"Martin"},{"first_name":"Nils","full_name":"Wiedemann, Nils","last_name":"Wiedemann"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul"},{"last_name":"Pfanner","first_name":"Nikolaus","full_name":"Pfanner, Nikolaus"}],"external_id":{"pmid":["31907035"]},"oa_version":"Published Version","date_published":"2020-01-06T00:00:00Z","volume":18,"quality_controlled":"1","date_created":"2020-09-17T10:26:53Z","year":"2020","date_updated":"2021-01-12T08:19:02Z","publication_identifier":{"issn":["1741-7007"]},"pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12915-019-0733-6"}],"article_processing_charge":"No"},{"publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"isi":1,"file":[{"file_name":"2020_NatureComm_Arnold.pdf","date_created":"2020-09-18T13:02:37Z","content_type":"application/pdf","file_id":"8530","access_level":"open_access","date_updated":"2020-09-18T13:02:37Z","success":1,"relation":"main_file","checksum":"88f92544889eb18bb38e25629a422a86","file_size":1002818,"creator":"dernst"}],"volume":11,"year":"2020","date_created":"2020-09-18T10:56:20Z","quality_controlled":"1","acknowledged_ssus":[{"_id":"NanoFab"}],"project":[{"_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","grant_number":"732894","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","grant_number":"862644","call_identifier":"H2020"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"date_updated":"2024-08-07T07:11:51Z","publication":"Nature Communications","author":[{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M","first_name":"Georg M","last_name":"Arnold"},{"id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378","last_name":"Wulf","full_name":"Wulf, Matthias","first_name":"Matthias"},{"orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir","full_name":"Barzanjeh, Shabir"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","full_name":"Redchenko, Elena","last_name":"Redchenko"},{"last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","full_name":"Hease, William J","first_name":"William J","last_name":"Hease"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","last_name":"Hassani","full_name":"Hassani, Farid","first_name":"Farid"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink"}],"ddc":["530"],"oa_version":"Published Version","external_id":{"isi":["000577280200001"]},"date_published":"2020-09-08T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2020-09-18T13:02:37Z","doi":"10.1038/s41467-020-18269-z","publisher":"Springer Nature","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"intvolume":"        11","citation":{"ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>.","mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>, vol. 11, 4460, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>.","ieee":"G. M. Arnold <i>et al.</i>, “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>"},"day":"08","has_accepted_license":"1","status":"public","article_number":"4460","abstract":[{"lang":"eng","text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a <jats:italic>V</jats:italic><jats:sub><jats:italic>π</jats:italic></jats:sub> as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform."}],"ec_funded":1,"department":[{"_id":"JoFi"}],"acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET).","publication_status":"published","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","oa":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-18912-9","relation":"erratum"},{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","relation":"press_release"}],"record":[{"id":"13056","status":"public","relation":"research_data"}]},"article_type":"original","month":"09","_id":"8529","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"year":"2020","date_created":"2020-09-25T07:23:13Z","quality_controlled":"1","date_updated":"2023-08-22T09:37:24Z","file":[{"file_size":1822469,"creator":"dernst","relation":"main_file","checksum":"eada7bc8dd16a49390137cff882ef328","content_type":"application/pdf","date_created":"2020-09-28T13:16:15Z","file_id":"8585","date_updated":"2020-09-28T13:16:15Z","access_level":"open_access","success":1,"file_name":"2020_NatureComm_Prehal.pdf"}],"isi":1,"volume":11,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-020-18610-6","publisher":"Springer Nature","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2020-09-28T13:16:15Z","external_id":{"isi":["000573756600004"]},"oa_version":"Published Version","date_published":"2020-09-24T00:00:00Z","publication":"Nature Communications","author":[{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"first_name":"Harald","full_name":"Fitzek, Harald","last_name":"Fitzek"},{"first_name":"Gerald","full_name":"Kothleitner, Gerald","last_name":"Kothleitner"},{"full_name":"Presser, Volker","first_name":"Volker","last_name":"Presser"},{"first_name":"Bernhard","full_name":"Gollas, Bernhard","last_name":"Gollas"},{"first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319"},{"first_name":"Qamar","full_name":"Abbas, Qamar","last_name":"Abbas"}],"ddc":["530"],"status":"public","article_number":"4838","abstract":[{"lang":"eng","text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries."}],"day":"24","has_accepted_license":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"intvolume":"        11","citation":{"ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","ieee":"C. Prehal <i>et al.</i>, “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>, vol. 11, 4838, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>.","ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>.","apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., &#38; Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>"},"month":"09","_id":"8568","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","oa":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-19720-x"}]},"title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","article_type":"original","department":[{"_id":"StFr"}]},{"date_published":"2020-11-04T00:00:00Z","oa_version":"Published Version","external_id":{"isi":["000573860700001"]},"ddc":["570"],"author":[{"last_name":"Tian","full_name":"Tian, Anhao","first_name":"Anhao"},{"last_name":"Kang","first_name":"Bo","full_name":"Kang, Bo"},{"last_name":"Li","full_name":"Li, Baizhou","first_name":"Baizhou"},{"full_name":"Qiu, Biying","first_name":"Biying","last_name":"Qiu"},{"last_name":"Jiang","full_name":"Jiang, Wenhong","first_name":"Wenhong"},{"last_name":"Shao","first_name":"Fangjie","full_name":"Shao, Fangjie"},{"first_name":"Qingqing","full_name":"Gao, Qingqing","last_name":"Gao"},{"last_name":"Liu","full_name":"Liu, Rui","first_name":"Rui"},{"last_name":"Cai","first_name":"Chengwei","full_name":"Cai, Chengwei"},{"first_name":"Rui","full_name":"Jing, Rui","last_name":"Jing"},{"first_name":"Wei","full_name":"Wang, Wei","last_name":"Wang"},{"last_name":"Chen","first_name":"Pengxiang","full_name":"Chen, Pengxiang"},{"full_name":"Liang, Qinghui","first_name":"Qinghui","last_name":"Liang"},{"first_name":"Lili","full_name":"Bao, Lili","last_name":"Bao"},{"full_name":"Man, Jianghong","first_name":"Jianghong","last_name":"Man"},{"full_name":"Wang, Yan","first_name":"Yan","last_name":"Wang"},{"first_name":"Yu","full_name":"Shi, Yu","last_name":"Shi"},{"full_name":"Li, Jin","first_name":"Jin","last_name":"Li"},{"first_name":"Minmin","full_name":"Yang, Minmin","last_name":"Yang"},{"last_name":"Wang","first_name":"Lisha","full_name":"Wang, Lisha"},{"last_name":"Zhang","first_name":"Jianmin","full_name":"Zhang, Jianmin"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhu","full_name":"Zhu, Junming","first_name":"Junming"},{"last_name":"Bian","first_name":"Xiuwu","full_name":"Bian, Xiuwu"},{"full_name":"Wang, Ying‐Jie","first_name":"Ying‐Jie","last_name":"Wang"},{"first_name":"Chong","full_name":"Liu, Chong","last_name":"Liu"}],"issue":"21","publication":"Advanced Science","publisher":"Wiley","doi":"10.1002/advs.202001724","file_date_updated":"2020-12-10T14:07:24Z","type":"journal_article","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","publication_identifier":{"issn":["2198-3844"]},"date_updated":"2023-08-22T09:53:01Z","project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","year":"2020","date_created":"2020-10-01T09:44:13Z","volume":7,"isi":1,"file":[{"checksum":"92818c23ecc70e35acfa671f3cfb9909","relation":"main_file","creator":"dernst","file_size":7835833,"file_name":"2020_AdvScience_Tian.pdf","date_updated":"2020-12-10T14:07:24Z","access_level":"open_access","success":1,"file_id":"8938","content_type":"application/pdf","date_created":"2020-12-10T14:07:24Z"}],"acknowledgement":"The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo, and Q. Wu for their critical comments on the manuscript. They also thank Dr. H. Zong for providing the CKO_NG2‐CreER model. This work is supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001 to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and 2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists, China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.","department":[{"_id":"SiHi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8592","month":"11","article_type":"original","title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","oa":1,"publication_status":"published","has_accepted_license":"1","day":"04","intvolume":"         7","citation":{"apa":"Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020). Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. <i>Advanced Science</i>. Wiley. <a href=\"https://doi.org/10.1002/advs.202001724\">https://doi.org/10.1002/advs.202001724</a>","ista":"Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R, Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724.","chicago":"Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” <i>Advanced Science</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/advs.202001724\">https://doi.org/10.1002/advs.202001724</a>.","ieee":"A. Tian <i>et al.</i>, “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” <i>Advanced Science</i>, vol. 7, no. 21. Wiley, 2020.","mla":"Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” <i>Advanced Science</i>, vol. 7, no. 21, 2001724, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/advs.202001724\">10.1002/advs.202001724</a>.","short":"A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai, R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M. Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced Science 7 (2020).","ama":"Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. <i>Advanced Science</i>. 2020;7(21). doi:<a href=\"https://doi.org/10.1002/advs.202001724\">10.1002/advs.202001724</a>"},"keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"ec_funded":1,"abstract":[{"text":"Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.","lang":"eng"}],"article_number":"2001724","status":"public"},{"quality_controlled":"1","date_created":"2020-11-09T07:49:36Z","year":"2020","date_updated":"2023-08-22T12:36:07Z","volume":11,"file":[{"date_created":"2020-11-09T07:56:24Z","file_id":"8745","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-11-09T07:56:24Z","success":1,"file_name":"2020_NatureComm_Schulte.pdf","file_size":1670898,"creator":"dernst","relation":"main_file","checksum":"b2688f0347e69e6629bba582077278c5"}],"isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","publication_identifier":{"issn":["2041-1723"]},"scopus_import":"1","doi":"10.1038/s41467-020-19372-x","publisher":"Springer Nature","language":[{"iso":"eng"}],"file_date_updated":"2020-11-09T07:56:24Z","type":"journal_article","oa_version":"Published Version","external_id":{"isi":["000592028600001"]},"date_published":"2020-11-04T00:00:00Z","publication":"Nature Communications","ddc":["570"],"author":[{"full_name":"Schulte, Linda","first_name":"Linda","last_name":"Schulte"},{"first_name":"Jiafei","full_name":"Mao, Jiafei","last_name":"Mao"},{"last_name":"Reitz","first_name":"Julian","full_name":"Reitz, Julian"},{"first_name":"Sridhar","full_name":"Sreeramulu, Sridhar","last_name":"Sreeramulu"},{"last_name":"Kudlinzki","first_name":"Denis","full_name":"Kudlinzki, Denis"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"last_name":"Meier-Credo","first_name":"Jakob","full_name":"Meier-Credo, Jakob"},{"full_name":"Saxena, Krishna","first_name":"Krishna","last_name":"Saxena"},{"full_name":"Buhr, Florian","first_name":"Florian","last_name":"Buhr"},{"last_name":"Langer","first_name":"Julian D.","full_name":"Langer, Julian D."},{"full_name":"Blackledge, Martin","first_name":"Martin","last_name":"Blackledge"},{"last_name":"Frangakis","first_name":"Achilleas S.","full_name":"Frangakis, Achilleas S."},{"full_name":"Glaubitz, Clemens","first_name":"Clemens","last_name":"Glaubitz"},{"full_name":"Schwalbe, Harald","first_name":"Harald","last_name":"Schwalbe"}],"article_number":"5569","status":"public","abstract":[{"lang":"eng","text":"Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding."}],"day":"04","has_accepted_license":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"citation":{"chicago":"Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>.","ista":"Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569.","apa":"Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>","mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>, vol. 11, 5569, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>.","ieee":"L. Schulte <i>et al.</i>, “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","short":"L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).","ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>"},"intvolume":"        11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"11","_id":"8744","oa":1,"title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","publication_status":"published","article_type":"original","department":[{"_id":"EM-Fac"}],"acknowledgement":"We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC."},{"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"scopus_import":"1","date_created":"2020-11-18T07:20:23Z","year":"2020","quality_controlled":"1","date_updated":"2023-08-22T12:49:18Z","isi":1,"file":[{"relation":"main_file","checksum":"555456dd0e47bcf9e0994bcb95577e88","file_size":2498594,"creator":"dernst","file_name":"2020_PlosCompBio_Kaveh.pdf","date_created":"2020-11-18T07:26:10Z","file_id":"8768","content_type":"application/pdf","date_updated":"2020-11-18T07:26:10Z","success":1,"access_level":"open_access"}],"volume":16,"external_id":{"isi":["000591317200004"]},"oa_version":"Published Version","date_published":"2020-11-05T00:00:00Z","publication":"PLOS Computational Biology","issue":"11","author":[{"full_name":"Kaveh, Kamran","first_name":"Kamran","last_name":"Kaveh"},{"last_name":"McAvoy","full_name":"McAvoy, Alex","first_name":"Alex"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"ddc":["000"],"doi":"10.1371/journal.pcbi.1008402","publisher":"Public Library of Science","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2020-11-18T07:26:10Z","day":"05","has_accepted_license":"1","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"intvolume":"        16","citation":{"ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” <i>PLOS Computational Biology</i>, vol. 16, no. 11. Public Library of Science, 2020.","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>.","chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>.","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., &#38; Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. 2020;16(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020)."},"status":"public","article_number":"e1008402","abstract":[{"lang":"eng","text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring."}],"acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","department":[{"_id":"KrCh"}],"month":"11","_id":"8767","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","title":"The Moran process on 2-chromatic graphs","oa":1,"article_type":"original"},{"intvolume":"        11","citation":{"ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>, vol. 11, 6437, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>.","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., &#38; Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020)."},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"has_accepted_license":"1","day":"22","abstract":[{"lang":"eng","text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation."}],"status":"public","article_number":"6437","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"article_type":"original","publication_status":"published","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","description":"News on IST Homepage"}]},"title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","oa":1,"month":"12","_id":"8971","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file":[{"date_created":"2020-12-28T08:16:10Z","content_type":"application/pdf","file_id":"8975","access_level":"open_access","date_updated":"2020-12-28T08:16:10Z","success":1,"file_name":"2020_NatureComm_Faessler.pdf","file_size":3958727,"creator":"dernst","relation":"main_file","checksum":"55d43ea0061cc4027ba45e966e1db8cc"}],"isi":1,"volume":11,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"},{"call_identifier":"FWF","grant_number":"M02495","name":"Protein structure and function in filopodia across scales","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"date_updated":"2023-08-24T11:01:50Z","date_created":"2020-12-23T08:25:45Z","year":"2020","quality_controlled":"1","author":[{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian","full_name":"Fäßler, Florian"},{"orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","full_name":"Dimchev, Georgi A","first_name":"Georgi A"},{"full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wan, William","first_name":"William","last_name":"Wan"},{"last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"publication":"Nature Communications","date_published":"2020-12-22T00:00:00Z","oa_version":"Published Version","external_id":{"isi":["000603078000003"]},"type":"journal_article","file_date_updated":"2020-12-28T08:16:10Z","language":[{"iso":"eng"}],"publisher":"Springer Nature","doi":"10.1038/s41467-020-20286-x"},{"quality_controlled":"1","page":"1140-1155.e18","date_created":"2021-11-26T08:02:27Z","year":"2020","date_updated":"2021-11-26T08:58:37Z","volume":182,"article_processing_charge":"No","publication_identifier":{"issn":["0092-8674"]},"scopus_import":"1","pmid":1,"main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S0092867420309296","open_access":"1"}],"doi":"10.1016/j.cell.2020.07.021","publisher":"Elsevier","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"Published Version","external_id":{"pmid":["32814015"]},"date_published":"2020-08-18T00:00:00Z","issue":"5","publication":"Cell","author":[{"full_name":"Pfitzner, Anna-Katharina","first_name":"Anna-Katharina","last_name":"Pfitzner"},{"first_name":"Vincent","full_name":"Mercier, Vincent","last_name":"Mercier"},{"last_name":"Jiang","full_name":"Jiang, Xiuyun","first_name":"Xiuyun"},{"last_name":"Moser von Filseck","first_name":"Joachim","full_name":"Moser von Filseck, Joachim"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Roux","first_name":"Aurélien","full_name":"Roux, Aurélien"}],"status":"public","abstract":[{"lang":"eng","text":"The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity."}],"extern":"1","day":"18","keyword":["general biochemistry","genetics and molecular biology"],"citation":{"ieee":"A.-K. Pfitzner <i>et al.</i>, “An ESCRT-III polymerization sequence drives membrane deformation and fission,” <i>Cell</i>, vol. 182, no. 5. Elsevier, p. 1140–1155.e18, 2020.","mla":"Pfitzner, Anna-Katharina, et al. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” <i>Cell</i>, vol. 182, no. 5, Elsevier, 2020, p. 1140–1155.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">10.1016/j.cell.2020.07.021</a>.","apa":"Pfitzner, A.-K., Mercier, V., Jiang, X., Moser von Filseck, J., Baum, B., Šarić, A., &#38; Roux, A. (2020). An ESCRT-III polymerization sequence drives membrane deformation and fission. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">https://doi.org/10.1016/j.cell.2020.07.021</a>","chicago":"Pfitzner, Anna-Katharina, Vincent Mercier, Xiuyun Jiang, Joachim Moser von Filseck, Buzz Baum, Anđela Šarić, and Aurélien Roux. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” <i>Cell</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">https://doi.org/10.1016/j.cell.2020.07.021</a>.","ista":"Pfitzner A-K, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux A. 2020. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 182(5), 1140–1155.e18.","ama":"Pfitzner A-K, Mercier V, Jiang X, et al. An ESCRT-III polymerization sequence drives membrane deformation and fission. <i>Cell</i>. 2020;182(5):1140-1155.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">10.1016/j.cell.2020.07.021</a>","short":"A.-K. Pfitzner, V. Mercier, X. Jiang, J. Moser von Filseck, B. Baum, A. Šarić, A. Roux, Cell 182 (2020) 1140–1155.e18."},"intvolume":"       182","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10348","month":"08","title":"An ESCRT-III polymerization sequence drives membrane deformation and fission","oa":1,"publication_status":"published","article_type":"original","acknowledgement":"The authors thank Nicolas Chiaruttini, Jean Gruenberg, and Lena Harker-Kirschneck for careful correction of this manuscript and helpful discussions. The authors want to thank the NCCR Chemical Biology for constant support during this project. A.R. acknowledges funding from the Swiss National Fund for Research (31003A_130520, 31003A_149975, and 31003A_173087) and the European Research Council Consolidator (311536). A.Š. acknowledges the European Research Council (802960). B.B. thanks the BBSRC (BB/K009001/1) and Wellcome Trust (203276/Z/16/Z) for support. J.M.v.F. acknowledges funding through an EMBO Long-Term Fellowship (ALTF 1065-2015), the European Commission FP7 (Marie Curie Actions, LTFCOFUND2013, and GA-2013-609409), and a Transitional Postdoc fellowship (2015/345) from the Swiss SystemsX.ch initiative, evaluated by the Swiss National Science Foundation and Swiss National Science Foundation Research (SNSF SINERGIA 160728/1 [leader, Sophie Martin])."},{"language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2022-04-08T06:53:10Z","doi":"10.7554/elife.54383","publisher":"eLife Sciences Publications","publication":"eLife","author":[{"first_name":"Simone","full_name":"Bersini, Simone","last_name":"Bersini"},{"first_name":"Roberta","full_name":"Schulte, Roberta","last_name":"Schulte"},{"last_name":"Huang","full_name":"Huang, Ling","first_name":"Ling"},{"full_name":"Tsai, Hannah","first_name":"Hannah","last_name":"Tsai"},{"first_name":"Martin W","full_name":"HETZER, Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X"}],"ddc":["570"],"oa_version":"Published Version","external_id":{"pmid":["32896271"]},"date_published":"2020-09-08T00:00:00Z","file":[{"file_name":"2020_eLife_Bersini.pdf","date_created":"2022-04-08T06:53:10Z","content_type":"application/pdf","file_id":"11132","date_updated":"2022-04-08T06:53:10Z","access_level":"open_access","success":1,"relation":"main_file","checksum":"f8b3821349a194050be02570d8fe7d4b","file_size":4399825,"creator":"dernst"}],"volume":9,"date_created":"2022-04-07T07:43:48Z","year":"2020","quality_controlled":"1","date_updated":"2022-07-18T08:30:37Z","publication_identifier":{"issn":["2050-084X"]},"pmid":1,"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","publication_status":"published","title":"Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome","oa":1,"article_type":"original","_id":"11055","month":"09","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","article_number":"e54383","extern":"1","abstract":[{"lang":"eng","text":"Vascular dysfunctions are a common feature of multiple age-related diseases. However, modeling healthy and pathological aging of the human vasculature represents an unresolved experimental challenge. Here, we generated induced vascular endothelial cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial junction stability, as vascular aging markers. A functional assay performed on PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which plays a key role in both vascular calcification and endothelial barrier damage observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered the functionality of the vascular barrier in vitro, hence representing a potential future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These results show that iVECs and iSMCs retain disease-related signatures, allowing modeling of vascular aging and HGPS in vitro."}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"citation":{"ieee":"S. Bersini, R. Schulte, L. Huang, H. Tsai, and M. Hetzer, “Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","mla":"Bersini, Simone, et al. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>, vol. 9, e54383, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>.","apa":"Bersini, S., Schulte, R., Huang, L., Tsai, H., &#38; Hetzer, M. (2020). Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>","ista":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. 2020. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. eLife. 9, e54383.","chicago":"Bersini, Simone, Roberta Schulte, Ling Huang, Hannah Tsai, and Martin Hetzer. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>.","ama":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>","short":"S. Bersini, R. Schulte, L. Huang, H. Tsai, M. Hetzer, ELife 9 (2020)."},"intvolume":"         9","day":"08","has_accepted_license":"1"},{"publication_identifier":{"issn":["2366-7478","2366-7478"]},"scopus_import":"1","pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"article_processing_charge":"No","volume":4,"file":[{"file_name":"2020_AdvancedBiosystems_Bersini.pdf","file_id":"11134","date_created":"2022-04-08T07:06:05Z","content_type":"application/pdf","date_updated":"2022-04-08T07:06:05Z","success":1,"access_level":"open_access","relation":"main_file","checksum":"5584d9a1609812dc75c02ce1e35d2ec0","file_size":2490829,"creator":"dernst"}],"quality_controlled":"1","year":"2020","date_created":"2022-04-07T07:43:57Z","date_updated":"2022-07-18T08:30:48Z","publication":"Advanced Biosystems","issue":"5","ddc":["570"],"author":[{"last_name":"Bersini","first_name":"Simone","full_name":"Bersini, Simone"},{"full_name":"Arrojo e Drigo, Rafael","first_name":"Rafael","last_name":"Arrojo e Drigo"},{"first_name":"Ling","full_name":"Huang, Ling","last_name":"Huang"},{"first_name":"Maxim N.","full_name":"Shokhirev, Maxim N.","last_name":"Shokhirev"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","first_name":"Martin W","full_name":"HETZER, Martin W","last_name":"HETZER"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","external_id":{"pmid":["32402127"]},"oa_version":"Published Version","date_published":"2020-05-01T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2022-04-08T07:06:05Z","type":"journal_article","doi":"10.1002/adbi.202000044","publisher":"Wiley","keyword":["General Biochemistry","Genetics and Molecular Biology","Biomedical Engineering","Biomaterials"],"citation":{"chicago":"Bersini, Simone, Rafael Arrojo e Drigo, Ling Huang, Maxim N. Shokhirev, and Martin Hetzer. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” <i>Advanced Biosystems</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/adbi.202000044\">https://doi.org/10.1002/adbi.202000044</a>.","apa":"Bersini, S., Arrojo e Drigo, R., Huang, L., Shokhirev, M. N., &#38; Hetzer, M. (2020). Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. <i>Advanced Biosystems</i>. Wiley. <a href=\"https://doi.org/10.1002/adbi.202000044\">https://doi.org/10.1002/adbi.202000044</a>","ista":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. 2020. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. Advanced Biosystems. 4(5), 2000044.","mla":"Bersini, Simone, et al. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” <i>Advanced Biosystems</i>, vol. 4, no. 5, 2000044, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/adbi.202000044\">10.1002/adbi.202000044</a>.","ieee":"S. Bersini, R. Arrojo e Drigo, L. Huang, M. N. Shokhirev, and M. Hetzer, “Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease,” <i>Advanced Biosystems</i>, vol. 4, no. 5. Wiley, 2020.","short":"S. Bersini, R. Arrojo e Drigo, L. Huang, M.N. Shokhirev, M. Hetzer, Advanced Biosystems 4 (2020).","ama":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. <i>Advanced Biosystems</i>. 2020;4(5). doi:<a href=\"https://doi.org/10.1002/adbi.202000044\">10.1002/adbi.202000044</a>"},"intvolume":"         4","day":"01","has_accepted_license":"1","article_number":"2000044","status":"public","abstract":[{"lang":"eng","text":"Aging of the circulatory system correlates with the pathogenesis of a large spectrum of diseases. However, it is largely unknown which factors drive the age-dependent or pathological decline of the vasculature and how vascular defects relate to tissue aging. The goal of the study is to design a multianalytical approach to identify how the cellular microenvironment (i.e., fibroblasts) and serum from healthy donors of different ages or Alzheimer disease (AD) patients can modulate the functionality of organ-specific vascular endothelial cells (VECs). Long-living human microvascular networks embedding VECs and fibroblasts from skin biopsies are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate that fibroblasts from young donors restore the functionality of aged endothelial cells, an effect also achieved by serum from young donors. New biomarkers of vascular aging are validated in human biopsies and it is shown that young serum induces angiopoietin-like-4, which can restore compromised vascular barriers. This strategy is then employed to characterize transcriptional/functional changes induced on the blood–brain barrier by AD serum, demonstrating the importance of PTP4A3 in the regulation of permeability. Features of vascular degeneration during aging and AD are recapitulated, and a tool to identify novel biomarkers that can be exploited to develop future therapeutics modulating vascular function is established."}],"extern":"1","oa":1,"title":"Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease","publication_status":"published","article_type":"original","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11056","month":"05"},{"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"issn":["0890-9369","1549-5477"]},"scopus_import":"1","pmid":1,"quality_controlled":"1","page":"913-930","date_created":"2022-04-07T07:44:09Z","year":"2020","date_updated":"2022-07-18T08:31:08Z","volume":34,"file":[{"relation":"main_file","checksum":"84e92d40e67936c739628315c238daf9","file_size":4406772,"creator":"dernst","file_name":"2020_GenesDevelopment_Kang.pdf","content_type":"application/pdf","file_id":"11136","date_created":"2022-04-08T07:12:33Z","success":1,"access_level":"open_access","date_updated":"2022-04-08T07:12:33Z"}],"external_id":{"pmid":["32499403"]},"oa_version":"Published Version","date_published":"2020-04-28T00:00:00Z","publication":"Genes & Development","issue":"13-14","ddc":["570"],"author":[{"last_name":"Kang","full_name":"Kang, Hyeseon","first_name":"Hyeseon"},{"full_name":"Shokhirev, Maxim N.","first_name":"Maxim N.","last_name":"Shokhirev"},{"first_name":"Zhichao","full_name":"Xu, Zhichao","last_name":"Xu"},{"full_name":"Chandran, Sahaana","first_name":"Sahaana","last_name":"Chandran"},{"last_name":"Dixon","full_name":"Dixon, Jesse R.","first_name":"Jesse R."},{"orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"HETZER, Martin W","last_name":"HETZER"}],"doi":"10.1101/gad.335794.119","publisher":"Cold Spring Harbor Laboratory Press","language":[{"iso":"eng"}],"file_date_updated":"2022-04-08T07:12:33Z","type":"journal_article","day":"28","has_accepted_license":"1","keyword":["Developmental Biology","Genetics"],"citation":{"ama":"Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. <i>Genes &#38; Development</i>. 2020;34(13-14):913-930. doi:<a href=\"https://doi.org/10.1101/gad.335794.119\">10.1101/gad.335794.119</a>","short":"H. Kang, M.N. Shokhirev, Z. Xu, S. Chandran, J.R. Dixon, M. Hetzer, Genes &#38; Development 34 (2020) 913–930.","ieee":"H. Kang, M. N. Shokhirev, Z. Xu, S. Chandran, J. R. Dixon, and M. Hetzer, “Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation,” <i>Genes &#38; Development</i>, vol. 34, no. 13–14. Cold Spring Harbor Laboratory Press, pp. 913–930, 2020.","mla":"Kang, Hyeseon, et al. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” <i>Genes &#38; Development</i>, vol. 34, no. 13–14, Cold Spring Harbor Laboratory Press, 2020, pp. 913–30, doi:<a href=\"https://doi.org/10.1101/gad.335794.119\">10.1101/gad.335794.119</a>.","apa":"Kang, H., Shokhirev, M. N., Xu, Z., Chandran, S., Dixon, J. R., &#38; Hetzer, M. (2020). Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.335794.119\">https://doi.org/10.1101/gad.335794.119</a>","ista":"Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. 2020. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes &#38; Development. 34(13–14), 913–930.","chicago":"Kang, Hyeseon, Maxim N. Shokhirev, Zhichao Xu, Sahaana Chandran, Jesse R. Dixon, and Martin Hetzer. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory Press, 2020. <a href=\"https://doi.org/10.1101/gad.335794.119\">https://doi.org/10.1101/gad.335794.119</a>."},"intvolume":"        34","status":"public","abstract":[{"lang":"eng","text":"During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division."}],"extern":"1","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","month":"04","_id":"11057","oa":1,"title":"Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation","publication_status":"published","article_type":"original"}]