[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-19720-x","relation":"erratum"}]},"file":[{"file_id":"8585","creator":"dernst","relation":"main_file","access_level":"open_access","success":1,"date_updated":"2020-09-28T13:16:15Z","file_name":"2020_NatureComm_Prehal.pdf","content_type":"application/pdf","date_created":"2020-09-28T13:16:15Z","checksum":"eada7bc8dd16a49390137cff882ef328","file_size":1822469}],"oa":1,"publication_identifier":{"issn":["2041-1723"]},"date_published":"2020-09-24T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"month":"09","article_number":"4838","oa_version":"Published Version","publication":"Nature Communications","has_accepted_license":"1","ddc":["530"],"volume":11,"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."}],"doi":"10.1038/s41467-020-18610-6","day":"24","isi":1,"external_id":{"isi":["000573756600004"]},"date_updated":"2023-08-22T09:37:24Z","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>","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>","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>.","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>.","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","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."},"year":"2020","article_type":"original","publisher":"Springer Nature","file_date_updated":"2020-09-28T13:16:15Z","quality_controlled":"1","title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","intvolume":"        11","publication_status":"published","department":[{"_id":"StFr"}],"article_processing_charge":"No","date_created":"2020-09-25T07:23:13Z","author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"full_name":"Fitzek, Harald","last_name":"Fitzek","first_name":"Harald"},{"last_name":"Kothleitner","first_name":"Gerald","full_name":"Kothleitner, Gerald"},{"last_name":"Presser","first_name":"Volker","full_name":"Presser, Volker"},{"full_name":"Gollas, Bernhard","last_name":"Gollas","first_name":"Bernhard"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"full_name":"Abbas, Qamar","first_name":"Qamar","last_name":"Abbas"}],"_id":"8568"},{"file":[{"file_id":"8938","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2020-12-10T14:07:24Z","file_name":"2020_AdvScience_Tian.pdf","content_type":"application/pdf","date_created":"2020-12-10T14:07:24Z","checksum":"92818c23ecc70e35acfa671f3cfb9909","file_size":7835833}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["2198-3844"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2020-11-04T00:00:00Z","keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"oa_version":"Published Version","article_number":"2001724","month":"11","has_accepted_license":"1","publication":"Advanced Science","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.","volume":7,"ddc":["570"],"day":"04","doi":"10.1002/advs.202001724","abstract":[{"lang":"eng","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."}],"citation":{"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.","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>.","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>","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.","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)."},"year":"2020","date_updated":"2023-08-22T09:53:01Z","external_id":{"isi":["000573860700001"]},"isi":1,"publisher":"Wiley","article_type":"original","ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-12-10T14:07:24Z","date_created":"2020-10-01T09:44:13Z","article_processing_charge":"No","department":[{"_id":"SiHi"}],"publication_status":"published","intvolume":"         7","title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","_id":"8592","issue":"21","author":[{"first_name":"Anhao","last_name":"Tian","full_name":"Tian, Anhao"},{"first_name":"Bo","last_name":"Kang","full_name":"Kang, Bo"},{"full_name":"Li, Baizhou","last_name":"Li","first_name":"Baizhou"},{"first_name":"Biying","last_name":"Qiu","full_name":"Qiu, Biying"},{"first_name":"Wenhong","last_name":"Jiang","full_name":"Jiang, Wenhong"},{"full_name":"Shao, Fangjie","first_name":"Fangjie","last_name":"Shao"},{"first_name":"Qingqing","last_name":"Gao","full_name":"Gao, Qingqing"},{"last_name":"Liu","first_name":"Rui","full_name":"Liu, Rui"},{"full_name":"Cai, Chengwei","first_name":"Chengwei","last_name":"Cai"},{"first_name":"Rui","last_name":"Jing","full_name":"Jing, Rui"},{"full_name":"Wang, Wei","last_name":"Wang","first_name":"Wei"},{"last_name":"Chen","first_name":"Pengxiang","full_name":"Chen, Pengxiang"},{"full_name":"Liang, Qinghui","last_name":"Liang","first_name":"Qinghui"},{"first_name":"Lili","last_name":"Bao","full_name":"Bao, Lili"},{"full_name":"Man, Jianghong","first_name":"Jianghong","last_name":"Man"},{"full_name":"Wang, Yan","last_name":"Wang","first_name":"Yan"},{"last_name":"Shi","first_name":"Yu","full_name":"Shi, Yu"},{"first_name":"Jin","last_name":"Li","full_name":"Li, Jin"},{"full_name":"Yang, Minmin","first_name":"Minmin","last_name":"Yang"},{"first_name":"Lisha","last_name":"Wang","full_name":"Wang, Lisha"},{"full_name":"Zhang, Jianmin","last_name":"Zhang","first_name":"Jianmin"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"},{"first_name":"Junming","last_name":"Zhu","full_name":"Zhu, Junming"},{"full_name":"Bian, Xiuwu","first_name":"Xiuwu","last_name":"Bian"},{"last_name":"Wang","first_name":"Ying‐Jie","full_name":"Wang, Ying‐Jie"},{"full_name":"Liu, Chong","last_name":"Liu","first_name":"Chong"}]},{"has_accepted_license":"1","publication":"Nature Communications","oa_version":"Published Version","article_number":"5569","month":"11","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2020-11-04T00:00:00Z","publication_identifier":{"issn":["2041-1723"]},"oa":1,"file":[{"relation":"main_file","access_level":"open_access","success":1,"file_id":"8745","creator":"dernst","date_created":"2020-11-09T07:56:24Z","file_size":1670898,"checksum":"b2688f0347e69e6629bba582077278c5","date_updated":"2020-11-09T07:56:24Z","file_name":"2020_NatureComm_Schulte.pdf","content_type":"application/pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","scopus_import":"1","_id":"8744","author":[{"full_name":"Schulte, Linda","last_name":"Schulte","first_name":"Linda"},{"full_name":"Mao, Jiafei","last_name":"Mao","first_name":"Jiafei"},{"first_name":"Julian","last_name":"Reitz","full_name":"Reitz, Julian"},{"first_name":"Sridhar","last_name":"Sreeramulu","full_name":"Sreeramulu, Sridhar"},{"full_name":"Kudlinzki, Denis","first_name":"Denis","last_name":"Kudlinzki"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Meier-Credo, Jakob","last_name":"Meier-Credo","first_name":"Jakob"},{"first_name":"Krishna","last_name":"Saxena","full_name":"Saxena, Krishna"},{"first_name":"Florian","last_name":"Buhr","full_name":"Buhr, Florian"},{"full_name":"Langer, Julian D.","last_name":"Langer","first_name":"Julian D."},{"full_name":"Blackledge, Martin","first_name":"Martin","last_name":"Blackledge"},{"first_name":"Achilleas S.","last_name":"Frangakis","full_name":"Frangakis, Achilleas S."},{"full_name":"Glaubitz, Clemens","last_name":"Glaubitz","first_name":"Clemens"},{"first_name":"Harald","last_name":"Schwalbe","full_name":"Schwalbe, Harald"}],"article_processing_charge":"No","date_created":"2020-11-09T07:49:36Z","department":[{"_id":"EM-Fac"}],"publication_status":"published","intvolume":"        11","title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","quality_controlled":"1","file_date_updated":"2020-11-09T07:56:24Z","publisher":"Springer Nature","article_type":"original","citation":{"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.","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).","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>.","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>.","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.","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>","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>"},"year":"2020","date_updated":"2023-08-22T12:36:07Z","external_id":{"isi":["000592028600001"]},"isi":1,"day":"04","doi":"10.1038/s41467-020-19372-x","abstract":[{"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.","lang":"eng"}],"volume":11,"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.","ddc":["570"]},{"file":[{"relation":"main_file","success":1,"access_level":"open_access","creator":"dernst","file_id":"8768","file_size":2498594,"checksum":"555456dd0e47bcf9e0994bcb95577e88","date_created":"2020-11-18T07:26:10Z","file_name":"2020_PlosCompBio_Kaveh.pdf","content_type":"application/pdf","date_updated":"2020-11-18T07:26:10Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2020-11-05T00:00:00Z","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"language":[{"iso":"eng"}],"oa_version":"Published Version","article_number":"e1008402","month":"11","has_accepted_license":"1","publication":"PLOS Computational Biology","volume":16,"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.","ddc":["000"],"day":"05","doi":"10.1371/journal.pcbi.1008402","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."}],"citation":{"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>.","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","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>","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>","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.","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>."},"year":"2020","date_updated":"2023-08-22T12:49:18Z","external_id":{"isi":["000591317200004"]},"isi":1,"publisher":"Public Library of Science","article_type":"original","quality_controlled":"1","file_date_updated":"2020-11-18T07:26:10Z","department":[{"_id":"KrCh"}],"date_created":"2020-11-18T07:20:23Z","article_processing_charge":"No","publication_status":"published","intvolume":"        16","title":"The Moran process on 2-chromatic graphs","scopus_import":"1","_id":"8767","issue":"11","author":[{"first_name":"Kamran","last_name":"Kaveh","full_name":"Kaveh, Kamran"},{"first_name":"Alex","last_name":"McAvoy","full_name":"McAvoy, Alex"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Nowak, Martin A.","first_name":"Martin A.","last_name":"Nowak"}]},{"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"oa_version":"Published Version","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"grant_number":"M02495","name":"Protein structure and function in filopodia across scales","call_identifier":"FWF","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"month":"12","article_number":"6437","publication":"Nature Communications","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"publication_identifier":{"issn":["2041-1723"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2020-12-22T00:00:00Z","type":"journal_article","file":[{"content_type":"application/pdf","file_name":"2020_NatureComm_Faessler.pdf","date_updated":"2020-12-28T08:16:10Z","checksum":"55d43ea0061cc4027ba45e966e1db8cc","file_size":3958727,"date_created":"2020-12-28T08:16:10Z","creator":"dernst","file_id":"8975","relation":"main_file","access_level":"open_access","success":1}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","description":"News on IST Homepage","relation":"press_release"}]},"publication_status":"published","date_created":"2020-12-23T08:25:45Z","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"article_processing_charge":"No","title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","intvolume":"        11","_id":"8971","scopus_import":"1","author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","first_name":"Florian","last_name":"Fäßler"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","last_name":"Dimchev","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin"},{"full_name":"Wan, William","last_name":"Wan","first_name":"William"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"publisher":"Springer Nature","article_type":"original","quality_controlled":"1","file_date_updated":"2020-12-28T08:16:10Z","doi":"10.1038/s41467-020-20286-x","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."}],"date_updated":"2023-08-24T11:01:50Z","citation":{"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.","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>.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","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>.","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.","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>","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>"},"year":"2020","isi":1,"external_id":{"isi":["000603078000003"]},"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. ","volume":11,"ddc":["570"]},{"external_id":{"pmid":["32910969"]},"year":"2020","citation":{"chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>.","ieee":"H. V. D. Rosa <i>et al.</i>, “Molecular recognition at septin interfaces: The switches hold the key,” <i>Journal of Molecular Biology</i>, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. 2020;432(21):5784-5801. doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., &#38; Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801.","mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>.","short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801."},"date_updated":"2024-02-28T12:37:54Z","abstract":[{"text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.","lang":"eng"}],"day":"02","doi":"10.1016/j.jmb.2020.09.001","volume":432,"issue":"21","author":[{"last_name":"Rosa","first_name":"Higor Vinícius Dias","full_name":"Rosa, Higor Vinícius Dias"},{"full_name":"Leonardo, Diego Antonio","last_name":"Leonardo","first_name":"Diego Antonio"},{"full_name":"Brognara, Gabriel","first_name":"Gabriel","last_name":"Brognara","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"first_name":"José","last_name":"Brandão-Neto","full_name":"Brandão-Neto, José"},{"full_name":"D'Muniz Pereira, Humberto","first_name":"Humberto","last_name":"D'Muniz Pereira"},{"full_name":"Araújo, Ana Paula Ulian","last_name":"Araújo","first_name":"Ana Paula Ulian"},{"first_name":"Richard Charles","last_name":"Garratt","full_name":"Garratt, Richard Charles"}],"pmid":1,"_id":"15036","intvolume":"       432","title":"Molecular recognition at septin interfaces: The switches hold the key","department":[{"_id":"MaLo"}],"article_processing_charge":"No","date_created":"2024-02-28T08:50:34Z","publication_status":"published","quality_controlled":"1","page":"5784-5801","article_type":"original","publisher":"Elsevier","type":"journal_article","date_published":"2020-10-02T00:00:00Z","oa":1,"publication_identifier":{"issn":["0022-2836"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jmb.2020.09.001"}],"publication":"Journal of Molecular Biology","month":"10","oa_version":"Published Version","keyword":["Molecular Biology","Structural Biology"],"language":[{"iso":"eng"}]},{"volume":13,"ddc":["580"],"date_updated":"2024-02-28T12:41:52Z","citation":{"apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">https://doi.org/10.1016/j.molp.2020.02.012</a>","ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. <i>Molecular Plant</i>. 2020;13(5):717-731. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">10.1016/j.molp.2020.02.012</a>","ieee":"J. Moulinier-Anzola <i>et al.</i>, “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” <i>Molecular Plant</i>, vol. 13, no. 5. Elsevier, pp. 717–731, 2020.","chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” <i>Molecular Plant</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">https://doi.org/10.1016/j.molp.2020.02.012</a>.","mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” <i>Molecular Plant</i>, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">10.1016/j.molp.2020.02.012</a>.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.","ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731."},"year":"2020","external_id":{"pmid":["32087370"]},"doi":"10.1016/j.molp.2020.02.012","day":"04","abstract":[{"text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.","lang":"eng"}],"page":"717-731","quality_controlled":"1","file_date_updated":"2024-02-28T12:39:56Z","publisher":"Elsevier","article_type":"original","_id":"15037","pmid":1,"author":[{"full_name":"Moulinier-Anzola, Jeanette","last_name":"Moulinier-Anzola","first_name":"Jeanette"},{"full_name":"Schwihla, Maximilian","last_name":"Schwihla","first_name":"Maximilian"},{"full_name":"De-Araújo, Lucinda","first_name":"Lucinda","last_name":"De-Araújo"},{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","full_name":"Artner, Christina","last_name":"Artner","first_name":"Christina"},{"full_name":"Jörg, Lisa","first_name":"Lisa","last_name":"Jörg"},{"first_name":"Nataliia","last_name":"Konstantinova","full_name":"Konstantinova, Nataliia"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"first_name":"Barbara","last_name":"Korbei","full_name":"Korbei, Barbara"}],"issue":"5","publication_status":"published","date_created":"2024-02-28T08:55:56Z","department":[{"_id":"EvBe"}],"article_processing_charge":"No","title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","intvolume":"        13","file":[{"file_size":3089212,"checksum":"c538a5008f7827f62d17d40a3bfabe65","date_created":"2024-02-28T12:39:56Z","file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","content_type":"application/pdf","date_updated":"2024-02-28T12:39:56Z","relation":"main_file","success":1,"access_level":"open_access","creator":"dernst","file_id":"15038"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2020-05-04T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["1674-2052"]},"oa":1,"language":[{"iso":"eng"}],"keyword":["Plant Science","Molecular Biology"],"publication":"Molecular Plant","has_accepted_license":"1","oa_version":"Published Version","month":"05"},{"oa_version":"None","month":"04","publication":"Nature Nanotechnology","language":[{"iso":"eng"}],"keyword":["Electrical and Electronic Engineering","Condensed Matter Physics","General Materials Science","Biomedical Engineering","Atomic and Molecular Physics","and Optics","Bioengineering"],"publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"date_published":"2020-04-17T00:00:00Z","type":"journal_article","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2023-08-01T09:37:39Z","article_processing_charge":"No","title":"Chemical reactivity under nanoconfinement","intvolume":"        15","pmid":1,"_id":"13367","scopus_import":"1","author":[{"full_name":"Grommet, Angela B.","last_name":"Grommet","first_name":"Angela B."},{"full_name":"Feller, Moran","last_name":"Feller","first_name":"Moran"},{"first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"publisher":"Springer Nature","article_type":"original","page":"256-271","quality_controlled":"1","doi":"10.1038/s41565-020-0652-2","day":"17","abstract":[{"text":"Confining molecules can fundamentally change their chemical and physical properties. Confinement effects are considered instrumental at various stages of the origins of life, and life continues to rely on layers of compartmentalization to maintain an out-of-equilibrium state and efficiently synthesize complex biomolecules under mild conditions. As interest in synthetic confined systems grows, we are realizing that the principles governing reactivity under confinement are the same in abiological systems as they are in nature. In this Review, we categorize the ways in which nanoconfinement effects impact chemical reactivity in synthetic systems. Under nanoconfinement, chemical properties can be modulated to increase reaction rates, enhance selectivity and stabilize reactive species. Confinement effects also lead to changes in physical properties. The fluorescence of light emitters, the colours of dyes and electronic communication between electroactive species can all be tuned under confinement. Within each of these categories, we elucidate design principles and strategies that are widely applicable across a range of confined systems, specifically highlighting examples of different nanocompartments that influence reactivity in similar ways.","lang":"eng"}],"date_updated":"2023-08-07T10:29:06Z","citation":{"apa":"Grommet, A. B., Feller, M., &#38; Klajn, R. (2020). Chemical reactivity under nanoconfinement. <i>Nature Nanotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41565-020-0652-2\">https://doi.org/10.1038/s41565-020-0652-2</a>","ama":"Grommet AB, Feller M, Klajn R. Chemical reactivity under nanoconfinement. <i>Nature Nanotechnology</i>. 2020;15:256-271. doi:<a href=\"https://doi.org/10.1038/s41565-020-0652-2\">10.1038/s41565-020-0652-2</a>","ieee":"A. B. Grommet, M. Feller, and R. Klajn, “Chemical reactivity under nanoconfinement,” <i>Nature Nanotechnology</i>, vol. 15. Springer Nature, pp. 256–271, 2020.","chicago":"Grommet, Angela B., Moran Feller, and Rafal Klajn. “Chemical Reactivity under Nanoconfinement.” <i>Nature Nanotechnology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41565-020-0652-2\">https://doi.org/10.1038/s41565-020-0652-2</a>.","mla":"Grommet, Angela B., et al. “Chemical Reactivity under Nanoconfinement.” <i>Nature Nanotechnology</i>, vol. 15, Springer Nature, 2020, pp. 256–71, doi:<a href=\"https://doi.org/10.1038/s41565-020-0652-2\">10.1038/s41565-020-0652-2</a>.","short":"A.B. Grommet, M. Feller, R. Klajn, Nature Nanotechnology 15 (2020) 256–271.","ista":"Grommet AB, Feller M, Klajn R. 2020. Chemical reactivity under nanoconfinement. Nature Nanotechnology. 15, 256–271."},"year":"2020","external_id":{"pmid":["32303705"]},"volume":15,"extern":"1"},{"main_file_link":[{"url":"https://arxiv.org/abs/2001.09951","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"eissn":["1361-6455"],"issn":["0953-4075"]},"oa":1,"date_published":"2020-06-17T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"keyword":["Condensed Matter Physics","Atomic and Molecular Physics","and Optics"],"oa_version":"Preprint","month":"06","article_number":"144003","publication":"Journal of Physics B: Atomic, Molecular and Optical Physics","volume":53,"extern":"1","doi":"10.1088/1361-6455/ab8e56","arxiv":1,"day":"17","abstract":[{"lang":"eng","text":"The interaction of strong near-infrared (NIR) laser pulses with wide-bandgap dielectrics produces high harmonics in the extreme ultraviolet (XUV) wavelength range. These observations have opened up the possibility of attosecond metrology in solids, which would benefit from a precise measurement of the emission times of individual harmonics with respect to the NIR laser field. Here we show that, when high-harmonics are detected from the input surface of a magnesium oxide crystal, a bichromatic probing of the XUV emission shows a clear synchronization largely consistent with a semiclassical model of electron–hole recollisions in bulk solids. On the other hand, the bichromatic spectrogram of harmonics originating from the exit surface of the 200 μm-thick crystal is strongly modified, indicating the influence of laser field distortions during propagation. Our tracking of sub-cycle electron and hole re-collisions at XUV energies is relevant to the development of solid-state sources of attosecond pulses."}],"date_updated":"2023-08-22T07:36:36Z","citation":{"ieee":"G. Vampa <i>et al.</i>, “Attosecond synchronization of extreme ultraviolet high harmonics from crystals,” <i>Journal of Physics B: Atomic, Molecular and Optical Physics</i>, vol. 53, no. 14. IOP Publishing, 2020.","chicago":"Vampa, Giulio, Jian Lu, Yong Sing You, Denitsa Rangelova Baykusheva, Mengxi Wu, Hanzhe Liu, Kenneth J Schafer, Mette B Gaarde, David A Reis, and Shambhu Ghimire. “Attosecond Synchronization of Extreme Ultraviolet High Harmonics from Crystals.” <i>Journal of Physics B: Atomic, Molecular and Optical Physics</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/1361-6455/ab8e56\">https://doi.org/10.1088/1361-6455/ab8e56</a>.","apa":"Vampa, G., Lu, J., You, Y. S., Baykusheva, D. R., Wu, M., Liu, H., … Ghimire, S. (2020). Attosecond synchronization of extreme ultraviolet high harmonics from crystals. <i>Journal of Physics B: Atomic, Molecular and Optical Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6455/ab8e56\">https://doi.org/10.1088/1361-6455/ab8e56</a>","ama":"Vampa G, Lu J, You YS, et al. Attosecond synchronization of extreme ultraviolet high harmonics from crystals. <i>Journal of Physics B: Atomic, Molecular and Optical Physics</i>. 2020;53(14). doi:<a href=\"https://doi.org/10.1088/1361-6455/ab8e56\">10.1088/1361-6455/ab8e56</a>","ista":"Vampa G, Lu J, You YS, Baykusheva DR, Wu M, Liu H, Schafer KJ, Gaarde MB, Reis DA, Ghimire S. 2020. Attosecond synchronization of extreme ultraviolet high harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical Physics. 53(14), 144003.","short":"G. Vampa, J. Lu, Y.S. You, D.R. Baykusheva, M. Wu, H. Liu, K.J. Schafer, M.B. Gaarde, D.A. Reis, S. Ghimire, Journal of Physics B: Atomic, Molecular and Optical Physics 53 (2020).","mla":"Vampa, Giulio, et al. “Attosecond Synchronization of Extreme Ultraviolet High Harmonics from Crystals.” <i>Journal of Physics B: Atomic, Molecular and Optical Physics</i>, vol. 53, no. 14, 144003, IOP Publishing, 2020, doi:<a href=\"https://doi.org/10.1088/1361-6455/ab8e56\">10.1088/1361-6455/ab8e56</a>."},"year":"2020","external_id":{"arxiv":["2001.09951"]},"publisher":"IOP Publishing","article_type":"original","quality_controlled":"1","publication_status":"published","article_processing_charge":"No","date_created":"2023-08-09T13:09:51Z","title":"Attosecond synchronization of extreme ultraviolet high harmonics from crystals","intvolume":"        53","_id":"13998","scopus_import":"1","author":[{"full_name":"Vampa, Giulio","first_name":"Giulio","last_name":"Vampa"},{"last_name":"Lu","first_name":"Jian","full_name":"Lu, Jian"},{"full_name":"You, Yong Sing","first_name":"Yong Sing","last_name":"You"},{"first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Wu, Mengxi","last_name":"Wu","first_name":"Mengxi"},{"full_name":"Liu, Hanzhe","last_name":"Liu","first_name":"Hanzhe"},{"full_name":"Schafer, Kenneth J","last_name":"Schafer","first_name":"Kenneth J"},{"full_name":"Gaarde, Mette B","last_name":"Gaarde","first_name":"Mette B"},{"full_name":"Reis, David A","first_name":"David A","last_name":"Reis"},{"first_name":"Shambhu","last_name":"Ghimire","full_name":"Ghimire, Shambhu"}],"issue":"14"},{"external_id":{"pmid":["33381818"]},"year":"2020","citation":{"apa":"Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer, F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired feature sets. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>","ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. <i>Bioinformatics</i>. 2020;36(Supplement_2):i919-i927. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>","chicago":"Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” <i>Bioinformatics</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>.","ieee":"S. G. Stark <i>et al.</i>, “SCIM: Universal single-cell matching with unpaired feature sets,” <i>Bioinformatics</i>, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.","short":"S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927.","mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” <i>Bioinformatics</i>, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>.","ista":"Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927."},"date_updated":"2023-09-11T10:21:00Z","abstract":[{"text":"Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively.","lang":"eng"}],"day":"01","doi":"10.1093/bioinformatics/btaa843","extern":"1","volume":36,"issue":"Supplement_2","author":[{"full_name":"Stark, Stefan G","last_name":"Stark","first_name":"Stefan G"},{"full_name":"Ficek, Joanna","last_name":"Ficek","first_name":"Joanna"},{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Ximena","last_name":"Bonilla","full_name":"Bonilla, Ximena"},{"full_name":"Chevrier, Stéphane","first_name":"Stéphane","last_name":"Chevrier"},{"full_name":"Singer, Franziska","last_name":"Singer","first_name":"Franziska"},{"last_name":"Aebersold","first_name":"Rudolf","full_name":"Aebersold, Rudolf"},{"last_name":"Al-Quaddoomi","first_name":"Faisal S","full_name":"Al-Quaddoomi, Faisal S"},{"last_name":"Albinus","first_name":"Jonas","full_name":"Albinus, Jonas"},{"first_name":"Ilaria","last_name":"Alborelli","full_name":"Alborelli, Ilaria"},{"last_name":"Andani","first_name":"Sonali","full_name":"Andani, Sonali"},{"full_name":"Attinger, Per-Olof","last_name":"Attinger","first_name":"Per-Olof"},{"full_name":"Bacac, Marina","first_name":"Marina","last_name":"Bacac"},{"last_name":"Baumhoer","first_name":"Daniel","full_name":"Baumhoer, Daniel"},{"last_name":"Beck-Schimmer","first_name":"Beatrice","full_name":"Beck-Schimmer, Beatrice"},{"last_name":"Beerenwinkel","first_name":"Niko","full_name":"Beerenwinkel, Niko"},{"last_name":"Beisel","first_name":"Christian","full_name":"Beisel, Christian"},{"first_name":"Lara","last_name":"Bernasconi","full_name":"Bernasconi, Lara"},{"full_name":"Bertolini, Anne","first_name":"Anne","last_name":"Bertolini"},{"last_name":"Bodenmiller","first_name":"Bernd","full_name":"Bodenmiller, Bernd"},{"full_name":"Bonilla, Ximena","first_name":"Ximena","last_name":"Bonilla"},{"last_name":"Casanova","first_name":"Ruben","full_name":"Casanova, Ruben"},{"full_name":"Chevrier, Stéphane","last_name":"Chevrier","first_name":"Stéphane"},{"full_name":"Chicherova, Natalia","first_name":"Natalia","last_name":"Chicherova"},{"full_name":"D'Costa, Maya","last_name":"D'Costa","first_name":"Maya"},{"full_name":"Danenberg, Esther","first_name":"Esther","last_name":"Danenberg"},{"last_name":"Davidson","first_name":"Natalie","full_name":"Davidson, Natalie"},{"last_name":"gan","first_name":"Monica-Andreea Dră","full_name":"gan, Monica-Andreea Dră"},{"full_name":"Dummer, Reinhard","first_name":"Reinhard","last_name":"Dummer"},{"full_name":"Engler, Stefanie","first_name":"Stefanie","last_name":"Engler"},{"full_name":"Erkens, Martin","last_name":"Erkens","first_name":"Martin"},{"full_name":"Eschbach, Katja","last_name":"Eschbach","first_name":"Katja"},{"first_name":"Cinzia","last_name":"Esposito","full_name":"Esposito, Cinzia"},{"full_name":"Fedier, André","first_name":"André","last_name":"Fedier"},{"first_name":"Pedro","last_name":"Ferreira","full_name":"Ferreira, Pedro"},{"first_name":"Joanna","last_name":"Ficek","full_name":"Ficek, Joanna"},{"full_name":"Frei, Anja L","last_name":"Frei","first_name":"Anja L"},{"last_name":"Frey","first_name":"Bruno","full_name":"Frey, Bruno"},{"full_name":"Goetze, Sandra","first_name":"Sandra","last_name":"Goetze"},{"full_name":"Grob, Linda","last_name":"Grob","first_name":"Linda"},{"full_name":"Gut, Gabriele","last_name":"Gut","first_name":"Gabriele"},{"full_name":"Günther, Detlef","first_name":"Detlef","last_name":"Günther"},{"last_name":"Haberecker","first_name":"Martina","full_name":"Haberecker, Martina"},{"full_name":"Haeuptle, Pirmin","first_name":"Pirmin","last_name":"Haeuptle"},{"last_name":"Heinzelmann-Schwarz","first_name":"Viola","full_name":"Heinzelmann-Schwarz, Viola"},{"full_name":"Herter, Sylvia","last_name":"Herter","first_name":"Sylvia"},{"first_name":"Rene","last_name":"Holtackers","full_name":"Holtackers, Rene"},{"first_name":"Tamara","last_name":"Huesser","full_name":"Huesser, Tamara"},{"last_name":"Irmisch","first_name":"Anja","full_name":"Irmisch, Anja"},{"first_name":"Francis","last_name":"Jacob","full_name":"Jacob, Francis"},{"full_name":"Jacobs, Andrea","last_name":"Jacobs","first_name":"Andrea"},{"first_name":"Tim M","last_name":"Jaeger","full_name":"Jaeger, Tim M"},{"full_name":"Jahn, Katharina","first_name":"Katharina","last_name":"Jahn"},{"full_name":"James, Alva R","last_name":"James","first_name":"Alva R"},{"full_name":"Jermann, Philip M","last_name":"Jermann","first_name":"Philip M"},{"last_name":"Kahles","first_name":"André","full_name":"Kahles, André"},{"full_name":"Kahraman, Abdullah","last_name":"Kahraman","first_name":"Abdullah"},{"first_name":"Viktor H","last_name":"Koelzer","full_name":"Koelzer, Viktor H"},{"full_name":"Kuebler, Werner","first_name":"Werner","last_name":"Kuebler"},{"first_name":"Jack","last_name":"Kuipers","full_name":"Kuipers, Jack"},{"first_name":"Christian P","last_name":"Kunze","full_name":"Kunze, Christian P"},{"first_name":"Christian","last_name":"Kurzeder","full_name":"Kurzeder, Christian"},{"first_name":"Kjong-Van","last_name":"Lehmann","full_name":"Lehmann, Kjong-Van"},{"last_name":"Levesque","first_name":"Mitchell","full_name":"Levesque, Mitchell"},{"last_name":"Lugert","first_name":"Sebastian","full_name":"Lugert, Sebastian"},{"full_name":"Maass, Gerd","last_name":"Maass","first_name":"Gerd"},{"first_name":"Markus","last_name":"Manz","full_name":"Manz, Markus"},{"full_name":"Markolin, Philipp","last_name":"Markolin","first_name":"Philipp"},{"first_name":"Julien","last_name":"Mena","full_name":"Mena, Julien"},{"first_name":"Ulrike","last_name":"Menzel","full_name":"Menzel, Ulrike"},{"first_name":"Julian M","last_name":"Metzler","full_name":"Metzler, Julian M"},{"last_name":"Miglino","first_name":"Nicola","full_name":"Miglino, Nicola"},{"full_name":"Milani, Emanuela S","first_name":"Emanuela S","last_name":"Milani"},{"full_name":"Moch, Holger","last_name":"Moch","first_name":"Holger"},{"first_name":"Simone","last_name":"Muenst","full_name":"Muenst, Simone"},{"full_name":"Murri, Riccardo","first_name":"Riccardo","last_name":"Murri"},{"full_name":"Ng, Charlotte KY","first_name":"Charlotte KY","last_name":"Ng"},{"last_name":"Nicolet","first_name":"Stefan","full_name":"Nicolet, Stefan"},{"full_name":"Nowak, Marta","last_name":"Nowak","first_name":"Marta"},{"full_name":"Pedrioli, Patrick GA","last_name":"Pedrioli","first_name":"Patrick GA"},{"first_name":"Lucas","last_name":"Pelkmans","full_name":"Pelkmans, Lucas"},{"full_name":"Piscuoglio, Salvatore","last_name":"Piscuoglio","first_name":"Salvatore"},{"last_name":"Prummer","first_name":"Michael","full_name":"Prummer, Michael"},{"last_name":"Ritter","first_name":"Mathilde","full_name":"Ritter, Mathilde"},{"full_name":"Rommel, Christian","first_name":"Christian","last_name":"Rommel"},{"full_name":"Rosano-González, María L","last_name":"Rosano-González","first_name":"María L"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"full_name":"Santacroce, Natascha","last_name":"Santacroce","first_name":"Natascha"},{"first_name":"Jacobo Sarabia del","last_name":"Castillo","full_name":"Castillo, Jacobo Sarabia del"},{"first_name":"Ramona","last_name":"Schlenker","full_name":"Schlenker, Ramona"},{"first_name":"Petra C","last_name":"Schwalie","full_name":"Schwalie, Petra C"},{"full_name":"Schwan, Severin","last_name":"Schwan","first_name":"Severin"},{"full_name":"Schär, Tobias","first_name":"Tobias","last_name":"Schär"},{"last_name":"Senti","first_name":"Gabriela","full_name":"Senti, Gabriela"},{"full_name":"Singer, Franziska","last_name":"Singer","first_name":"Franziska"},{"full_name":"Sivapatham, Sujana","last_name":"Sivapatham","first_name":"Sujana"},{"full_name":"Snijder, Berend","last_name":"Snijder","first_name":"Berend"},{"first_name":"Bettina","last_name":"Sobottka","full_name":"Sobottka, Bettina"},{"first_name":"Vipin T","last_name":"Sreedharan","full_name":"Sreedharan, Vipin T"},{"full_name":"Stark, Stefan","first_name":"Stefan","last_name":"Stark"},{"full_name":"Stekhoven, Daniel J","first_name":"Daniel J","last_name":"Stekhoven"},{"full_name":"Theocharides, Alexandre PA","first_name":"Alexandre PA","last_name":"Theocharides"},{"first_name":"Tinu M","last_name":"Thomas","full_name":"Thomas, Tinu M"},{"first_name":"Markus","last_name":"Tolnay","full_name":"Tolnay, Markus"},{"last_name":"Tosevski","first_name":"Vinko","full_name":"Tosevski, Vinko"},{"last_name":"Toussaint","first_name":"Nora C","full_name":"Toussaint, Nora C"},{"full_name":"Tuncel, Mustafa A","first_name":"Mustafa A","last_name":"Tuncel"},{"full_name":"Tusup, Marina","first_name":"Marina","last_name":"Tusup"},{"last_name":"Drogen","first_name":"Audrey Van","full_name":"Drogen, Audrey Van"},{"full_name":"Vetter, Marcus","last_name":"Vetter","first_name":"Marcus"},{"first_name":"Tatjana","last_name":"Vlajnic","full_name":"Vlajnic, Tatjana"},{"full_name":"Weber, Sandra","last_name":"Weber","first_name":"Sandra"},{"first_name":"Walter P","last_name":"Weber","full_name":"Weber, Walter P"},{"full_name":"Wegmann, Rebekka","first_name":"Rebekka","last_name":"Wegmann"},{"full_name":"Weller, Michael","last_name":"Weller","first_name":"Michael"},{"full_name":"Wendt, Fabian","last_name":"Wendt","first_name":"Fabian"},{"full_name":"Wey, Norbert","first_name":"Norbert","last_name":"Wey"},{"full_name":"Wicki, Andreas","first_name":"Andreas","last_name":"Wicki"},{"full_name":"Wollscheid, Bernd","first_name":"Bernd","last_name":"Wollscheid"},{"first_name":"Shuqing","last_name":"Yu","full_name":"Yu, Shuqing"},{"full_name":"Ziegler, Johanna","first_name":"Johanna","last_name":"Ziegler"},{"last_name":"Zimmermann","first_name":"Marc","full_name":"Zimmermann, Marc"},{"full_name":"Zoche, Martin","first_name":"Martin","last_name":"Zoche"},{"full_name":"Zuend, Gregor","first_name":"Gregor","last_name":"Zuend"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"last_name":"Lehmann","first_name":"Kjong-Van","full_name":"Lehmann, Kjong-Van"}],"scopus_import":"1","pmid":1,"_id":"14125","intvolume":"        36","title":"SCIM: Universal single-cell matching with unpaired feature sets","department":[{"_id":"FrLo"}],"date_created":"2023-08-21T12:28:20Z","article_processing_charge":"No","publication_status":"published","quality_controlled":"1","page":"i919-i927","article_type":"original","publisher":"Oxford University Press","type":"journal_article","date_published":"2020-12-01T00:00:00Z","oa":1,"publication_identifier":{"eissn":["1367-4811"]},"related_material":{"link":[{"relation":"software","url":"https://github.com/ratschlab/scim"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bioinformatics/btaa843"}],"publication":"Bioinformatics","month":"12","oa_version":"Published Version","keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"keyword":["general biochemistry","genetics and molecular biology"],"month":"08","oa_version":"Published Version","publication":"Cell","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S0092867420309296","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["0092-8674"]},"date_published":"2020-08-18T00:00:00Z","type":"journal_article","article_type":"original","publisher":"Elsevier","page":"1140-1155.e18","quality_controlled":"1","title":"An ESCRT-III polymerization sequence drives membrane deformation and fission","intvolume":"       182","publication_status":"published","date_created":"2021-11-26T08:02:27Z","article_processing_charge":"No","author":[{"last_name":"Pfitzner","first_name":"Anna-Katharina","full_name":"Pfitzner, Anna-Katharina"},{"first_name":"Vincent","last_name":"Mercier","full_name":"Mercier, Vincent"},{"full_name":"Jiang, Xiuyun","first_name":"Xiuyun","last_name":"Jiang"},{"first_name":"Joachim","last_name":"Moser von Filseck","full_name":"Moser von Filseck, Joachim"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Roux, Aurélien","last_name":"Roux","first_name":"Aurélien"}],"issue":"5","pmid":1,"_id":"10348","scopus_import":"1","extern":"1","volume":182,"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]).","abstract":[{"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.","lang":"eng"}],"doi":"10.1016/j.cell.2020.07.021","day":"18","external_id":{"pmid":["32814015"]},"date_updated":"2021-11-26T08:58:37Z","year":"2020","citation":{"short":"A.-K. Pfitzner, V. Mercier, X. Jiang, J. Moser von Filseck, B. Baum, A. Šarić, A. Roux, Cell 182 (2020) 1140–1155.e18.","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>.","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.","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>","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>","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.","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>."}},{"publication_status":"published","department":[{"_id":"XiFe"}],"date_created":"2023-01-16T09:16:10Z","article_processing_charge":"No","title":"AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization","intvolume":"        16","pmid":1,"_id":"12189","scopus_import":"1","author":[{"full_name":"Christophorou, Nicolas","first_name":"Nicolas","last_name":"Christophorou"},{"full_name":"She, Wenjing","last_name":"She","first_name":"Wenjing"},{"last_name":"Long","first_name":"Jincheng","full_name":"Long, Jincheng"},{"full_name":"Hurel, Aurélie","first_name":"Aurélie","last_name":"Hurel"},{"first_name":"Sébastien","last_name":"Beaubiat","full_name":"Beaubiat, Sébastien"},{"full_name":"Idir, Yassir","last_name":"Idir","first_name":"Yassir"},{"full_name":"Tagliaro-Jahns, Marina","first_name":"Marina","last_name":"Tagliaro-Jahns"},{"full_name":"Chambon, Aurélie","first_name":"Aurélie","last_name":"Chambon"},{"full_name":"Solier, Victor","first_name":"Victor","last_name":"Solier"},{"first_name":"Daniel","last_name":"Vezon","full_name":"Vezon, Daniel"},{"full_name":"Grelon, Mathilde","last_name":"Grelon","first_name":"Mathilde"},{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"full_name":"Bouché, Nicolas","first_name":"Nicolas","last_name":"Bouché"},{"last_name":"Mézard","first_name":"Christine","full_name":"Mézard, Christine"}],"issue":"6","publisher":"Public Library of Science (PLoS)","article_type":"original","quality_controlled":"1","doi":"10.1371/journal.pgen.1008894","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"}],"date_updated":"2023-05-08T10:54:39Z","citation":{"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.","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>.","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).","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>.","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.","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>","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>"},"year":"2020","external_id":{"pmid":["32598340"]},"acknowledgement":"The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.","volume":16,"extern":"1","oa_version":"Published Version","month":"06","article_number":"e1008894","publication":"PLOS Genetics","language":[{"iso":"eng"}],"keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"publication_identifier":{"issn":["1553-7404"]},"oa":1,"date_published":"2020-06-29T00:00:00Z","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public"},{"date_published":"2019-01-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["1471-0056"],"eissn":["1471-0064"]},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","publication":"Nature Reviews Genetics","oa_version":"None","month":"01","language":[{"iso":"eng"}],"keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"date_updated":"2022-07-18T08:31:42Z","citation":{"mla":"Buchwalter, Abigail, et al. “Coaching from the Sidelines: The Nuclear Periphery in Genome Regulation.” <i>Nature Reviews Genetics</i>, vol. 20, no. 1, Springer Nature, 2019, pp. 39–50, doi:<a href=\"https://doi.org/10.1038/s41576-018-0063-5\">10.1038/s41576-018-0063-5</a>.","short":"A. Buchwalter, J.M. Kaneshiro, M. Hetzer, Nature Reviews Genetics 20 (2019) 39–50.","ista":"Buchwalter A, Kaneshiro JM, Hetzer M. 2019. Coaching from the sidelines: The nuclear periphery in genome regulation. Nature Reviews Genetics. 20(1), 39–50.","ama":"Buchwalter A, Kaneshiro JM, Hetzer M. Coaching from the sidelines: The nuclear periphery in genome regulation. <i>Nature Reviews Genetics</i>. 2019;20(1):39-50. doi:<a href=\"https://doi.org/10.1038/s41576-018-0063-5\">10.1038/s41576-018-0063-5</a>","apa":"Buchwalter, A., Kaneshiro, J. M., &#38; Hetzer, M. (2019). Coaching from the sidelines: The nuclear periphery in genome regulation. <i>Nature Reviews Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41576-018-0063-5\">https://doi.org/10.1038/s41576-018-0063-5</a>","chicago":"Buchwalter, Abigail, Jeanae M. Kaneshiro, and Martin Hetzer. “Coaching from the Sidelines: The Nuclear Periphery in Genome Regulation.” <i>Nature Reviews Genetics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41576-018-0063-5\">https://doi.org/10.1038/s41576-018-0063-5</a>.","ieee":"A. Buchwalter, J. M. Kaneshiro, and M. Hetzer, “Coaching from the sidelines: The nuclear periphery in genome regulation,” <i>Nature Reviews Genetics</i>, vol. 20, no. 1. Springer Nature, pp. 39–50, 2019."},"year":"2019","external_id":{"pmid":["30356165"]},"doi":"10.1038/s41576-018-0063-5","day":"01","abstract":[{"lang":"eng","text":"The genome is packaged and organized nonrandomly within the 3D space of the nucleus to promote efficient gene expression and to faithfully maintain silencing of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope membrane, which contains a set of proteins that actively participate in chromatin organization and gene regulation. Technological advances are providing views of genome organization at unprecedented resolution and are beginning to reveal the ways that cells co-opt the structures of the nuclear periphery for nuclear organization and gene regulation. These genome regulatory roles of proteins of the nuclear periphery have important influences on development, disease and ageing."}],"volume":20,"extern":"1","pmid":1,"_id":"11059","scopus_import":"1","author":[{"full_name":"Buchwalter, Abigail","last_name":"Buchwalter","first_name":"Abigail"},{"full_name":"Kaneshiro, Jeanae M.","first_name":"Jeanae M.","last_name":"Kaneshiro"},{"last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"issue":"1","publication_status":"published","article_processing_charge":"No","date_created":"2022-04-07T07:44:45Z","title":"Coaching from the sidelines: The nuclear periphery in genome regulation","intvolume":"        20","page":"39-50","quality_controlled":"1","publisher":"Springer Nature","article_type":"review"},{"file":[{"file_size":6984654,"checksum":"1e8672a1e9c3dc0a2d3d0dad89673616","date_created":"2022-04-08T08:18:01Z","content_type":"application/pdf","file_name":"2019_eLife_Buchwalter.pdf","date_updated":"2022-04-08T08:18:01Z","access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"11138"}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","related_material":{"record":[{"status":"public","id":"13079","relation":"research_data"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2019-10-10T00:00:00Z","publication_identifier":{"issn":["2050-084X"]},"oa":1,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"eLife","oa_version":"Published Version","article_number":"e49796","month":"10","volume":8,"ddc":["570"],"extern":"1","year":"2019","citation":{"ista":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. eLife. 8, e49796.","short":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, ELife 8 (2019).","mla":"Buchwalter, Abigail, et al. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” <i>ELife</i>, vol. 8, e49796, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.49796\">10.7554/elife.49796</a>.","ieee":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","chicago":"Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.49796\">https://doi.org/10.7554/elife.49796</a>.","apa":"Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., &#38; Hetzer, M. (2019). Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.49796\">https://doi.org/10.7554/elife.49796</a>","ama":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.49796\">10.7554/elife.49796</a>"},"date_updated":"2023-05-31T06:36:22Z","external_id":{"pmid":["31599721"]},"day":"10","doi":"10.7554/elife.49796","abstract":[{"lang":"eng","text":"The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs."}],"quality_controlled":"1","file_date_updated":"2022-04-08T08:18:01Z","publisher":"eLife Sciences Publications","article_type":"original","scopus_import":"1","_id":"11060","pmid":1,"author":[{"full_name":"Buchwalter, Abigail","last_name":"Buchwalter","first_name":"Abigail"},{"first_name":"Roberta","last_name":"Schulte","full_name":"Schulte, Roberta"},{"full_name":"Tsai, Hsiao","last_name":"Tsai","first_name":"Hsiao"},{"last_name":"Capitanio","first_name":"Juliana","full_name":"Capitanio, Juliana"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","first_name":"Martin W","last_name":"HETZER"}],"date_created":"2022-04-07T07:45:02Z","article_processing_charge":"No","publication_status":"published","intvolume":"         8","title":"Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress"},{"oa_version":"Published Version","month":"08","publication":"Cell Metabolism","keyword":["Cell Biology","Molecular Biology","Physiology"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1550-4131"]},"oa":1,"type":"journal_article","date_published":"2019-08-06T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cmet.2019.05.010"}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","date_created":"2022-04-07T07:45:21Z","article_processing_charge":"No","publication_status":"published","intvolume":"        30","title":"Age mosaicism across multiple scales in adult tissues","scopus_import":"1","pmid":1,"_id":"11062","issue":"2","author":[{"last_name":"Arrojo e Drigo","first_name":"Rafael","full_name":"Arrojo e Drigo, Rafael"},{"last_name":"Lev-Ram","first_name":"Varda","full_name":"Lev-Ram, Varda"},{"full_name":"Tyagi, Swati","last_name":"Tyagi","first_name":"Swati"},{"first_name":"Ranjan","last_name":"Ramachandra","full_name":"Ramachandra, Ranjan"},{"first_name":"Thomas","last_name":"Deerinck","full_name":"Deerinck, Thomas"},{"last_name":"Bushong","first_name":"Eric","full_name":"Bushong, Eric"},{"full_name":"Phan, Sebastien","last_name":"Phan","first_name":"Sebastien"},{"full_name":"Orphan, Victoria","first_name":"Victoria","last_name":"Orphan"},{"last_name":"Lechene","first_name":"Claude","full_name":"Lechene, Claude"},{"full_name":"Ellisman, Mark H.","first_name":"Mark H.","last_name":"Ellisman"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"publisher":"Elsevier","article_type":"original","quality_controlled":"1","page":"343-351.e3","day":"06","doi":"10.1016/j.cmet.2019.05.010","abstract":[{"text":"Most neurons are not replaced during an animal’s lifetime. This nondividing state is characterized by extreme longevity and age-dependent decline of key regulatory proteins. To study the lifespans of cells and proteins in adult tissues, we combined isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using 15N mapping, we show that liver and pancreas are composed of cells with vastly different ages, many as old as the animal. Strikingly, we also found that a subset of fibroblasts and endothelial cells, both known for their replicative potential, are characterized by the absence of cell division during adulthood. In addition, we show that the primary cilia of beta cells and neurons contains different structural regions with vastly different lifespans. Based on these results, we propose that age mosaicism across multiple scales is a fundamental principle of adult tissue, cell, and protein complex organization.","lang":"eng"}],"year":"2019","citation":{"apa":"Arrojo e Drigo, R., Lev-Ram, V., Tyagi, S., Ramachandra, R., Deerinck, T., Bushong, E., … Hetzer, M. (2019). Age mosaicism across multiple scales in adult tissues. <i>Cell Metabolism</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cmet.2019.05.010\">https://doi.org/10.1016/j.cmet.2019.05.010</a>","ama":"Arrojo e Drigo R, Lev-Ram V, Tyagi S, et al. Age mosaicism across multiple scales in adult tissues. <i>Cell Metabolism</i>. 2019;30(2):343-351.e3. doi:<a href=\"https://doi.org/10.1016/j.cmet.2019.05.010\">10.1016/j.cmet.2019.05.010</a>","ieee":"R. Arrojo e Drigo <i>et al.</i>, “Age mosaicism across multiple scales in adult tissues,” <i>Cell Metabolism</i>, vol. 30, no. 2. Elsevier, p. 343–351.e3, 2019.","chicago":"Arrojo e Drigo, Rafael, Varda Lev-Ram, Swati Tyagi, Ranjan Ramachandra, Thomas Deerinck, Eric Bushong, Sebastien Phan, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” <i>Cell Metabolism</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cmet.2019.05.010\">https://doi.org/10.1016/j.cmet.2019.05.010</a>.","short":"R. Arrojo e Drigo, V. Lev-Ram, S. Tyagi, R. Ramachandra, T. Deerinck, E. Bushong, S. Phan, V. Orphan, C. Lechene, M.H. Ellisman, M. Hetzer, Cell Metabolism 30 (2019) 343–351.e3.","mla":"Arrojo e Drigo, Rafael, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” <i>Cell Metabolism</i>, vol. 30, no. 2, Elsevier, 2019, p. 343–351.e3, doi:<a href=\"https://doi.org/10.1016/j.cmet.2019.05.010\">10.1016/j.cmet.2019.05.010</a>.","ista":"Arrojo e Drigo R, Lev-Ram V, Tyagi S, Ramachandra R, Deerinck T, Bushong E, Phan S, Orphan V, Lechene C, Ellisman MH, Hetzer M. 2019. Age mosaicism across multiple scales in adult tissues. Cell Metabolism. 30(2), 343–351.e3."},"date_updated":"2022-07-18T08:32:30Z","external_id":{"pmid":["31178361"]},"volume":30,"extern":"1"},{"doi":"10.1038/s41467-019-10490-9","day":"19","abstract":[{"text":"Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available.","lang":"eng"}],"date_updated":"2021-01-12T08:19:03Z","citation":{"short":"D.F. Gauto, L.F. Estrozi, C.D. Schwieters, G. Effantin, P. Macek, R. Sounier, A.C. Sivertsen, E. Schmidt, R. Kerfah, G. Mas, J.-P. Colletier, P. Güntert, A. Favier, G. Schoehn, P. Schanda, J. Boisbouvier, Nature Communications 10 (2019).","mla":"Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” <i>Nature Communications</i>, vol. 10, 2697, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-10490-9\">10.1038/s41467-019-10490-9</a>.","ista":"Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier J-P, Güntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J. 2019. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 10, 2697.","apa":"Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier, R., … Boisbouvier, J. (2019). Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-10490-9\">https://doi.org/10.1038/s41467-019-10490-9</a>","ama":"Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-10490-9\">10.1038/s41467-019-10490-9</a>","chicago":"Gauto, Diego F., Leandro F. Estrozi, Charles D. Schwieters, Gregory Effantin, Pavel Macek, Remy Sounier, Astrid C. Sivertsen, et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-10490-9\">https://doi.org/10.1038/s41467-019-10490-9</a>.","ieee":"D. F. Gauto <i>et al.</i>, “Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019."},"year":"2019","external_id":{"pmid":["31217444"]},"volume":10,"extern":"1","publication_status":"published","date_created":"2020-09-17T10:28:25Z","article_processing_charge":"No","title":"Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex","intvolume":"        10","pmid":1,"_id":"8405","author":[{"full_name":"Gauto, Diego F.","last_name":"Gauto","first_name":"Diego F."},{"full_name":"Estrozi, Leandro F.","first_name":"Leandro F.","last_name":"Estrozi"},{"first_name":"Charles D.","last_name":"Schwieters","full_name":"Schwieters, Charles D."},{"full_name":"Effantin, Gregory","first_name":"Gregory","last_name":"Effantin"},{"last_name":"Macek","first_name":"Pavel","full_name":"Macek, Pavel"},{"last_name":"Sounier","first_name":"Remy","full_name":"Sounier, Remy"},{"full_name":"Sivertsen, Astrid C.","first_name":"Astrid C.","last_name":"Sivertsen"},{"full_name":"Schmidt, Elena","last_name":"Schmidt","first_name":"Elena"},{"first_name":"Rime","last_name":"Kerfah","full_name":"Kerfah, Rime"},{"first_name":"Guillaume","last_name":"Mas","full_name":"Mas, Guillaume"},{"full_name":"Colletier, Jacques-Philippe","last_name":"Colletier","first_name":"Jacques-Philippe"},{"first_name":"Peter","last_name":"Güntert","full_name":"Güntert, Peter"},{"full_name":"Favier, Adrien","first_name":"Adrien","last_name":"Favier"},{"full_name":"Schoehn, Guy","last_name":"Schoehn","first_name":"Guy"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda"},{"full_name":"Boisbouvier, Jerome","last_name":"Boisbouvier","first_name":"Jerome"}],"publisher":"Springer Nature","article_type":"original","quality_controlled":"1","publication_identifier":{"issn":["2041-1723"]},"oa":1,"date_published":"2019-06-19T00:00:00Z","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-019-10490-9"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"06","article_number":"2697","publication":"Nature Communications","language":[{"iso":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"]},{"type":"journal_article","date_published":"2019-01-21T00:00:00Z","publication_identifier":{"issn":["1439-4235"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication":"ChemPhysChem","month":"01","oa_version":"Submitted Version","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"language":[{"iso":"eng"}],"external_id":{"pmid":["30444575"]},"citation":{"ista":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. 2019. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 20(2), 276–284.","short":"D. Marion, D.F. Gauto, I. Ayala, K. Giandoreggio-Barranco, P. Schanda, ChemPhysChem 20 (2019) 276–284.","mla":"Marion, Dominique, et al. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” <i>ChemPhysChem</i>, vol. 20, no. 2, Wiley, 2019, pp. 276–84, doi:<a href=\"https://doi.org/10.1002/cphc.201800935\">10.1002/cphc.201800935</a>.","chicago":"Marion, Dominique, Diego F. Gauto, Isabel Ayala, Karine Giandoreggio-Barranco, and Paul Schanda. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” <i>ChemPhysChem</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cphc.201800935\">https://doi.org/10.1002/cphc.201800935</a>.","ieee":"D. Marion, D. F. Gauto, I. Ayala, K. Giandoreggio-Barranco, and P. Schanda, “Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR,” <i>ChemPhysChem</i>, vol. 20, no. 2. Wiley, pp. 276–284, 2019.","ama":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. <i>ChemPhysChem</i>. 2019;20(2):276-284. doi:<a href=\"https://doi.org/10.1002/cphc.201800935\">10.1002/cphc.201800935</a>","apa":"Marion, D., Gauto, D. F., Ayala, I., Giandoreggio-Barranco, K., &#38; Schanda, P. (2019). Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. <i>ChemPhysChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cphc.201800935\">https://doi.org/10.1002/cphc.201800935</a>"},"year":"2019","date_updated":"2021-01-12T08:19:06Z","abstract":[{"text":"Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales can provide important insight into protein function. In magic‐angle‐spinning (MAS) NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion experiments in different regimes of radio‐frequency field strengths: at low RF field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type” relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.","lang":"eng"}],"day":"21","doi":"10.1002/cphc.201800935","extern":"1","volume":20,"issue":"2","author":[{"full_name":"Marion, Dominique","first_name":"Dominique","last_name":"Marion"},{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"last_name":"Ayala","first_name":"Isabel","full_name":"Ayala, Isabel"},{"last_name":"Giandoreggio-Barranco","first_name":"Karine","full_name":"Giandoreggio-Barranco, Karine"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"_id":"8411","pmid":1,"intvolume":"        20","title":"Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR","date_created":"2020-09-17T10:29:36Z","article_processing_charge":"No","publication_status":"published","quality_controlled":"1","page":"276-284","article_type":"original","publisher":"Wiley"},{"publisher":"Wiley","article_type":"original","page":"311-317","quality_controlled":"1","publication_status":"published","article_processing_charge":"No","date_created":"2020-09-17T10:29:43Z","title":"Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR","intvolume":"        20","pmid":1,"_id":"8412","author":[{"first_name":"Matthew D.","last_name":"Shannon","full_name":"Shannon, Matthew D."},{"full_name":"Theint, Theint","last_name":"Theint","first_name":"Theint"},{"first_name":"Dwaipayan","last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Dwaipayan"},{"last_name":"Surewicz","first_name":"Krystyna","full_name":"Surewicz, Krystyna"},{"last_name":"Surewicz","first_name":"Witold K.","full_name":"Surewicz, Witold K."},{"last_name":"Marion","first_name":"Dominique","full_name":"Marion, Dominique"},{"last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"full_name":"Jaroniec, Christopher P.","first_name":"Christopher P.","last_name":"Jaroniec"}],"issue":"2","volume":20,"extern":"1","doi":"10.1002/cphc.201800779","day":"21","abstract":[{"lang":"eng","text":"Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two‐state exchange process with a common exchange rate of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms, and an excited‐state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited‐state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid."}],"date_updated":"2021-01-12T08:19:06Z","citation":{"apa":"Shannon, M. D., Theint, T., Mukhopadhyay, D., Surewicz, K., Surewicz, W. K., Marion, D., … Jaroniec, C. P. (2019). Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. <i>ChemPhysChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cphc.201800779\">https://doi.org/10.1002/cphc.201800779</a>","ama":"Shannon MD, Theint T, Mukhopadhyay D, et al. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. <i>ChemPhysChem</i>. 2019;20(2):311-317. doi:<a href=\"https://doi.org/10.1002/cphc.201800779\">10.1002/cphc.201800779</a>","chicago":"Shannon, Matthew D., Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz, Witold K. Surewicz, Dominique Marion, Paul Schanda, and Christopher P. Jaroniec. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” <i>ChemPhysChem</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cphc.201800779\">https://doi.org/10.1002/cphc.201800779</a>.","ieee":"M. D. Shannon <i>et al.</i>, “Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR,” <i>ChemPhysChem</i>, vol. 20, no. 2. Wiley, pp. 311–317, 2019.","short":"M.D. Shannon, T. Theint, D. Mukhopadhyay, K. Surewicz, W.K. Surewicz, D. Marion, P. Schanda, C.P. Jaroniec, ChemPhysChem 20 (2019) 311–317.","mla":"Shannon, Matthew D., et al. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” <i>ChemPhysChem</i>, vol. 20, no. 2, Wiley, 2019, pp. 311–17, doi:<a href=\"https://doi.org/10.1002/cphc.201800779\">10.1002/cphc.201800779</a>.","ista":"Shannon MD, Theint T, Mukhopadhyay D, Surewicz K, Surewicz WK, Marion D, Schanda P, Jaroniec CP. 2019. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 20(2), 311–317."},"year":"2019","external_id":{"pmid":["30276945"]},"language":[{"iso":"eng"}],"keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"oa_version":"Submitted Version","month":"01","publication":"ChemPhysChem","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1439-4235"]},"date_published":"2019-01-21T00:00:00Z","type":"journal_article"},{"main_file_link":[{"url":"https://doi.org/10.1016/j.chembiol.2019.09.002","open_access":"1"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_published":"2019-11-21T00:00:00Z","publication_identifier":{"issn":["2451-9456"]},"oa":1,"keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"language":[{"iso":"eng"}],"publication":"Cell Chemical Biology","oa_version":"Published Version","month":"11","volume":26,"extern":"1","citation":{"short":"M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C. Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N. Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin, G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26 (2019) 1573–1585.e10.","mla":"Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” <i>Cell Chemical Biology</i>, vol. 26, no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:<a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">10.1016/j.chembiol.2019.09.002</a>.","ista":"Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C, Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11), 1573–1585.e10.","ama":"Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. <i>Cell Chemical Biology</i>. 2019;26(11):1573-1585.e10. doi:<a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">10.1016/j.chembiol.2019.09.002</a>","apa":"Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E., … Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. <i>Cell Chemical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">https://doi.org/10.1016/j.chembiol.2019.09.002</a>","chicago":"Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” <i>Cell Chemical Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">https://doi.org/10.1016/j.chembiol.2019.09.002</a>.","ieee":"M. M. Bakail <i>et al.</i>, “Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1,” <i>Cell Chemical Biology</i>, vol. 26, no. 11. Elsevier, p. 1573–1585.e10, 2019."},"year":"2019","date_updated":"2023-02-23T13:46:53Z","external_id":{"pmid":["31543461"]},"day":"21","doi":"10.1016/j.chembiol.2019.09.002","abstract":[{"text":"Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.","lang":"eng"}],"quality_controlled":"1","page":"1573-1585.e10","publisher":"Elsevier","article_type":"original","_id":"9018","pmid":1,"issue":"11","author":[{"id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M","last_name":"Bakail","orcid":"0000-0002-9592-1587","full_name":"Bakail, May M"},{"last_name":"Gaubert","first_name":"Albane","full_name":"Gaubert, Albane"},{"first_name":"Jessica","last_name":"Andreani","full_name":"Andreani, Jessica"},{"last_name":"Moal","first_name":"Gwenaëlle","full_name":"Moal, Gwenaëlle"},{"first_name":"Guillaume","last_name":"Pinna","full_name":"Pinna, Guillaume"},{"full_name":"Boyarchuk, Ekaterina","last_name":"Boyarchuk","first_name":"Ekaterina"},{"full_name":"Gaillard, Marie-Cécile","last_name":"Gaillard","first_name":"Marie-Cécile"},{"full_name":"Courbeyrette, Regis","last_name":"Courbeyrette","first_name":"Regis"},{"full_name":"Mann, Carl","first_name":"Carl","last_name":"Mann"},{"full_name":"Thuret, Jean-Yves","first_name":"Jean-Yves","last_name":"Thuret"},{"first_name":"Bérengère","last_name":"Guichard","full_name":"Guichard, Bérengère"},{"full_name":"Murciano, Brice","first_name":"Brice","last_name":"Murciano"},{"first_name":"Nicolas","last_name":"Richet","full_name":"Richet, Nicolas"},{"full_name":"Poitou, Adeline","last_name":"Poitou","first_name":"Adeline"},{"full_name":"Frederic, Claire","first_name":"Claire","last_name":"Frederic"},{"first_name":"Marie-Hélène","last_name":"Le Du","full_name":"Le Du, Marie-Hélène"},{"full_name":"Agez, Morgane","first_name":"Morgane","last_name":"Agez"},{"full_name":"Roelants, Caroline","first_name":"Caroline","last_name":"Roelants"},{"full_name":"Gurard-Levin, Zachary A.","last_name":"Gurard-Levin","first_name":"Zachary A."},{"full_name":"Almouzni, Geneviève","last_name":"Almouzni","first_name":"Geneviève"},{"last_name":"Cherradi","first_name":"Nadia","full_name":"Cherradi, Nadia"},{"last_name":"Guerois","first_name":"Raphael","full_name":"Guerois, Raphael"},{"full_name":"Ochsenbein, Françoise","first_name":"Françoise","last_name":"Ochsenbein"}],"article_processing_charge":"No","date_created":"2021-01-19T11:04:50Z","publication_status":"published","intvolume":"        26","title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1"},{"article_number":"3380","month":"07","oa_version":"Published Version","has_accepted_license":"1","publication":"Nature Communications","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"issn":["2041-1723"]},"type":"journal_article","date_published":"2019-07-29T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","file":[{"date_updated":"2021-02-02T13:47:21Z","content_type":"application/pdf","file_name":"2019_NatureComm_Ramananarivo.pdf","date_created":"2021-02-02T13:47:21Z","file_size":2820337,"checksum":"70c6e5d6fbea0932b0669505ab6633ec","file_id":"9061","creator":"cziletti","access_level":"open_access","relation":"main_file","success":1}],"intvolume":"        10","title":"Activity-controlled annealing of colloidal monolayers","article_processing_charge":"No","date_created":"2021-02-02T13:43:36Z","publication_status":"published","issue":"1","author":[{"full_name":"Ramananarivo, Sophie","last_name":"Ramananarivo","first_name":"Sophie"},{"first_name":"Etienne","last_name":"Ducrot","full_name":"Ducrot, Etienne"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci","first_name":"Jérémie A"}],"scopus_import":"1","_id":"9060","pmid":1,"article_type":"original","publisher":"Springer Nature","file_date_updated":"2021-02-02T13:47:21Z","quality_controlled":"1","abstract":[{"lang":"eng","text":"Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium."}],"day":"29","arxiv":1,"doi":"10.1038/s41467-019-11362-y","external_id":{"arxiv":["1909.07382"],"pmid":["31358762"]},"citation":{"ieee":"S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing of colloidal monolayers,” <i>Nature Communications</i>, vol. 10, no. 1. Springer Nature, 2019.","chicago":"Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled Annealing of Colloidal Monolayers.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-11362-y\">https://doi.org/10.1038/s41467-019-11362-y</a>.","apa":"Ramananarivo, S., Ducrot, E., &#38; Palacci, J. A. (2019). Activity-controlled annealing of colloidal monolayers. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-11362-y\">https://doi.org/10.1038/s41467-019-11362-y</a>","ama":"Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal monolayers. <i>Nature Communications</i>. 2019;10(1). doi:<a href=\"https://doi.org/10.1038/s41467-019-11362-y\">10.1038/s41467-019-11362-y</a>","ista":"Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing of colloidal monolayers. Nature Communications. 10(1), 3380.","short":"S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).","mla":"Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.” <i>Nature Communications</i>, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-11362-y\">10.1038/s41467-019-11362-y</a>."},"year":"2019","date_updated":"2023-02-23T13:47:59Z","ddc":["530"],"extern":"1","volume":10}]