[{"date_updated":"2023-08-22T09:53:01Z","year":"2020","citation":{"chicago":"Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” <i>Advanced Science</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/advs.202001724\">https://doi.org/10.1002/advs.202001724</a>.","ieee":"A. Tian <i>et al.</i>, “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” <i>Advanced Science</i>, vol. 7, no. 21. Wiley, 2020.","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)."},"isi":1,"external_id":{"isi":["000573860700001"]},"doi":"10.1002/advs.202001724","day":"04","abstract":[{"text":"Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.","lang":"eng"}],"volume":7,"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.","ddc":["570"],"_id":"8592","author":[{"first_name":"Anhao","last_name":"Tian","full_name":"Tian, Anhao"},{"full_name":"Kang, Bo","last_name":"Kang","first_name":"Bo"},{"full_name":"Li, Baizhou","first_name":"Baizhou","last_name":"Li"},{"full_name":"Qiu, Biying","last_name":"Qiu","first_name":"Biying"},{"first_name":"Wenhong","last_name":"Jiang","full_name":"Jiang, Wenhong"},{"first_name":"Fangjie","last_name":"Shao","full_name":"Shao, Fangjie"},{"full_name":"Gao, Qingqing","last_name":"Gao","first_name":"Qingqing"},{"full_name":"Liu, Rui","last_name":"Liu","first_name":"Rui"},{"full_name":"Cai, Chengwei","last_name":"Cai","first_name":"Chengwei"},{"full_name":"Jing, Rui","last_name":"Jing","first_name":"Rui"},{"full_name":"Wang, Wei","last_name":"Wang","first_name":"Wei"},{"full_name":"Chen, Pengxiang","last_name":"Chen","first_name":"Pengxiang"},{"full_name":"Liang, Qinghui","last_name":"Liang","first_name":"Qinghui"},{"first_name":"Lili","last_name":"Bao","full_name":"Bao, Lili"},{"first_name":"Jianghong","last_name":"Man","full_name":"Man, Jianghong"},{"full_name":"Wang, Yan","first_name":"Yan","last_name":"Wang"},{"last_name":"Shi","first_name":"Yu","full_name":"Shi, Yu"},{"first_name":"Jin","last_name":"Li","full_name":"Li, Jin"},{"last_name":"Yang","first_name":"Minmin","full_name":"Yang, Minmin"},{"full_name":"Wang, Lisha","last_name":"Wang","first_name":"Lisha"},{"first_name":"Jianmin","last_name":"Zhang","full_name":"Zhang, 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"},{"first_name":"Xiuwu","last_name":"Bian","full_name":"Bian, Xiuwu"},{"full_name":"Wang, Ying‐Jie","last_name":"Wang","first_name":"Ying‐Jie"},{"full_name":"Liu, Chong","first_name":"Chong","last_name":"Liu"}],"issue":"21","publication_status":"published","date_created":"2020-10-01T09:44:13Z","article_processing_charge":"No","department":[{"_id":"SiHi"}],"title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","intvolume":"         7","ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-12-10T14:07:24Z","publisher":"Wiley","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2020-11-04T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["2198-3844"]},"oa":1,"file":[{"date_created":"2020-12-10T14:07:24Z","file_size":7835833,"checksum":"92818c23ecc70e35acfa671f3cfb9909","date_updated":"2020-12-10T14:07:24Z","file_name":"2020_AdvScience_Tian.pdf","content_type":"application/pdf","success":1,"relation":"main_file","access_level":"open_access","file_id":"8938","creator":"dernst"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Advanced Science","has_accepted_license":"1","oa_version":"Published Version","project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"month":"11","article_number":"2001724","language":[{"iso":"eng"}],"keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"]},{"intvolume":"        11","title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","date_created":"2020-11-09T07:49:36Z","department":[{"_id":"EM-Fac"}],"article_processing_charge":"No","publication_status":"published","author":[{"first_name":"Linda","last_name":"Schulte","full_name":"Schulte, Linda"},{"full_name":"Mao, Jiafei","first_name":"Jiafei","last_name":"Mao"},{"last_name":"Reitz","first_name":"Julian","full_name":"Reitz, Julian"},{"full_name":"Sreeramulu, Sridhar","first_name":"Sridhar","last_name":"Sreeramulu"},{"full_name":"Kudlinzki, Denis","first_name":"Denis","last_name":"Kudlinzki"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"first_name":"Jakob","last_name":"Meier-Credo","full_name":"Meier-Credo, Jakob"},{"full_name":"Saxena, Krishna","last_name":"Saxena","first_name":"Krishna"},{"last_name":"Buhr","first_name":"Florian","full_name":"Buhr, Florian"},{"full_name":"Langer, Julian D.","first_name":"Julian D.","last_name":"Langer"},{"first_name":"Martin","last_name":"Blackledge","full_name":"Blackledge, Martin"},{"first_name":"Achilleas S.","last_name":"Frangakis","full_name":"Frangakis, Achilleas S."},{"full_name":"Glaubitz, Clemens","first_name":"Clemens","last_name":"Glaubitz"},{"last_name":"Schwalbe","first_name":"Harald","full_name":"Schwalbe, Harald"}],"scopus_import":"1","_id":"8744","article_type":"original","publisher":"Springer Nature","file_date_updated":"2020-11-09T07:56:24Z","quality_controlled":"1","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"}],"day":"04","doi":"10.1038/s41467-020-19372-x","external_id":{"isi":["000592028600001"]},"isi":1,"citation":{"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>.","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).","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.","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>","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>","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.","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>."},"year":"2020","date_updated":"2023-08-22T12:36:07Z","ddc":["570"],"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.","article_number":"5569","month":"11","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":"2020-11-04T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"8745","creator":"dernst","success":1,"relation":"main_file","access_level":"open_access","date_updated":"2020-11-09T07:56:24Z","content_type":"application/pdf","file_name":"2020_NatureComm_Schulte.pdf","date_created":"2020-11-09T07:56:24Z","file_size":1670898,"checksum":"b2688f0347e69e6629bba582077278c5"}]},{"ddc":["570"],"volume":11,"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. ","external_id":{"isi":["000603078000003"]},"isi":1,"year":"2020","citation":{"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>","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.","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).","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."},"date_updated":"2023-08-24T11:01:50Z","abstract":[{"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.","lang":"eng"}],"day":"22","doi":"10.1038/s41467-020-20286-x","file_date_updated":"2020-12-28T08:16:10Z","quality_controlled":"1","article_type":"original","publisher":"Springer Nature","author":[{"last_name":"Fäßler","first_name":"Florian","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","first_name":"Georgi A","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wan, William","first_name":"William","last_name":"Wan"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"8971","intvolume":"        11","title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","date_created":"2020-12-23T08:25:45Z","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"article_processing_charge":"No","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/"}]},"file":[{"date_created":"2020-12-28T08:16:10Z","checksum":"55d43ea0061cc4027ba45e966e1db8cc","file_size":3958727,"date_updated":"2020-12-28T08:16:10Z","file_name":"2020_NatureComm_Faessler.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8975","creator":"dernst"}],"type":"journal_article","date_published":"2020-12-22T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["2041-1723"]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Nature Communications","article_number":"6437","month":"12","project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"name":"Protein structure and function in filopodia across scales","grant_number":"M02495","call_identifier":"FWF","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"oa_version":"Published Version"},{"abstract":[{"text":"Aggregation of organic molecules can drastically affect their physicochemical properties. For instance, the optical properties of BODIPY dyes are inherently related to the degree of aggregation and the mutual orientation of BODIPY units within these aggregates. Whereas the noncovalent aggregation of various BODIPY dyes has been studied in diverse media, the ill-defined nature of these aggregates has made it difficult to elucidate the structure–property relationships. Here, we studied the encapsulation of three structurally simple BODIPY derivatives within the hydrophobic cavity of a water-soluble, flexible PdII6L4 coordination cage. The cavity size allowed for the selective encapsulation of two dye molecules, irrespective of the substitution pattern on the BODIPY core. Working with a model, a pentamethyl-substituted derivative, we found that the mutual orientation of two BODIPY units in the cage’s cavity was remarkably similar to that in the crystalline state of the free dye, allowing us to isolate and characterize the smallest possible noncovalent H-type BODIPY aggregate, namely, an H-dimer. Interestingly, a CF3-substituted BODIPY, known for forming J-type aggregates, was also encapsulated as an H-dimer. Taking advantage of the dynamic nature of encapsulation, we developed a system in which reversible switching between H- and J-aggregates can be induced for multiple cycles simply by addition and subsequent destruction of the cage. We expect that the ability to rapidly and reversibly manipulate the optical properties of supramolecular inclusion complexes in aqueous media will open up avenues for developing detection systems that operate within biological environments.","lang":"eng"}],"doi":"10.1021/jacs.0c08589","day":"04","external_id":{"pmid":["33006898"]},"date_updated":"2023-08-07T10:09:54Z","year":"2020","citation":{"mla":"Gemen, Julius, et al. “Modulating the Optical Properties of BODIPY Dyes by Noncovalent Dimerization within a Flexible Coordination Cage.” <i>Journal of the American Chemical Society</i>, vol. 142, no. 41, American Chemical Society, 2020, pp. 17721–29, doi:<a href=\"https://doi.org/10.1021/jacs.0c08589\">10.1021/jacs.0c08589</a>.","short":"J. Gemen, J. Ahrens, L.J.W. Shimon, R. Klajn, Journal of the American Chemical Society 142 (2020) 17721–17729.","ista":"Gemen J, Ahrens J, Shimon LJW, Klajn R. 2020. Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage. Journal of the American Chemical Society. 142(41), 17721–17729.","ama":"Gemen J, Ahrens J, Shimon LJW, Klajn R. Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage. <i>Journal of the American Chemical Society</i>. 2020;142(41):17721-17729. doi:<a href=\"https://doi.org/10.1021/jacs.0c08589\">10.1021/jacs.0c08589</a>","apa":"Gemen, J., Ahrens, J., Shimon, L. J. W., &#38; Klajn, R. (2020). Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.0c08589\">https://doi.org/10.1021/jacs.0c08589</a>","ieee":"J. Gemen, J. Ahrens, L. J. W. Shimon, and R. Klajn, “Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage,” <i>Journal of the American Chemical Society</i>, vol. 142, no. 41. American Chemical Society, pp. 17721–17729, 2020.","chicago":"Gemen, Julius, Johannes Ahrens, Linda J. W. Shimon, and Rafal Klajn. “Modulating the Optical Properties of BODIPY Dyes by Noncovalent Dimerization within a Flexible Coordination Cage.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/jacs.0c08589\">https://doi.org/10.1021/jacs.0c08589</a>."},"extern":"1","volume":142,"title":"Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage","intvolume":"       142","publication_status":"published","article_processing_charge":"No","date_created":"2023-08-01T09:36:10Z","author":[{"full_name":"Gemen, Julius","last_name":"Gemen","first_name":"Julius"},{"first_name":"Johannes","last_name":"Ahrens","full_name":"Ahrens, Johannes"},{"full_name":"Shimon, Linda J. W.","last_name":"Shimon","first_name":"Linda J. W."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal"}],"issue":"41","_id":"13362","pmid":1,"scopus_import":"1","article_type":"original","publisher":"American Chemical Society","page":"17721-17729","quality_controlled":"1","oa":1,"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"date_published":"2020-10-04T00:00:00Z","type":"journal_article","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1021/jacs.0c08589","open_access":"1"}],"month":"10","oa_version":"Published Version","publication":"Journal of the American Chemical Society","language":[{"iso":"eng"}],"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"]},{"type":"journal_article","date_published":"2020-08-14T00:00:00Z","oa":1,"publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1021/jacs.0c06146","open_access":"1"}],"publication":"Journal of the American Chemical Society","month":"08","oa_version":"Published Version","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"language":[{"iso":"eng"}],"external_id":{"pmid":["32791832"]},"citation":{"short":"M. Canton, A.B. Grommet, L. Pesce, J. Gemen, S. Li, Y. Diskin-Posner, A. Credi, G.M. Pavan, J. Andréasson, R. Klajn, Journal of the American Chemical Society 142 (2020) 14557–14565.","mla":"Canton, Martina, et al. “Improving Fatigue Resistance of Dihydropyrene by Encapsulation within a Coordination Cage.” <i>Journal of the American Chemical Society</i>, vol. 142, no. 34, American Chemical Society, 2020, pp. 14557–65, doi:<a href=\"https://doi.org/10.1021/jacs.0c06146\">10.1021/jacs.0c06146</a>.","ista":"Canton M, Grommet AB, Pesce L, Gemen J, Li S, Diskin-Posner Y, Credi A, Pavan GM, Andréasson J, Klajn R. 2020. Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage. Journal of the American Chemical Society. 142(34), 14557–14565.","ama":"Canton M, Grommet AB, Pesce L, et al. Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage. <i>Journal of the American Chemical Society</i>. 2020;142(34):14557-14565. doi:<a href=\"https://doi.org/10.1021/jacs.0c06146\">10.1021/jacs.0c06146</a>","apa":"Canton, M., Grommet, A. B., Pesce, L., Gemen, J., Li, S., Diskin-Posner, Y., … Klajn, R. (2020). Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.0c06146\">https://doi.org/10.1021/jacs.0c06146</a>","ieee":"M. Canton <i>et al.</i>, “Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage,” <i>Journal of the American Chemical Society</i>, vol. 142, no. 34. American Chemical Society, pp. 14557–14565, 2020.","chicago":"Canton, Martina, Angela B. Grommet, Luca Pesce, Julius Gemen, Shiming Li, Yael Diskin-Posner, Alberto Credi, Giovanni M. Pavan, Joakim Andréasson, and Rafal Klajn. “Improving Fatigue Resistance of Dihydropyrene by Encapsulation within a Coordination Cage.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/jacs.0c06146\">https://doi.org/10.1021/jacs.0c06146</a>."},"year":"2020","date_updated":"2023-08-07T10:15:38Z","abstract":[{"lang":"eng","text":"Photochromic molecules undergo reversible isomerization upon irradiation with light at different wavelengths, a process that can alter their physical and chemical properties. For instance, dihydropyrene (DHP) is a deep-colored compound that isomerizes to light-brown cyclophanediene (CPD) upon irradiation with visible light. CPD can then isomerize back to DHP upon irradiation with UV light or thermally in the dark. Conversion between DHP and CPD is thought to proceed via a biradical intermediate; bimolecular events involving this unstable intermediate thus result in rapid decomposition and poor cycling performance. Here, we show that the reversible isomerization of DHP can be stabilized upon confinement within a PdII6L4 coordination cage. By protecting this reactive intermediate using the cage, each isomerization reaction proceeds to higher yield, which significantly decreases the fatigue experienced by the system upon repeated photocycling. Although molecular confinement is known to help stabilize reactive species, this effect is not typically employed to protect reactive intermediates and thus improve reaction yields. We envisage that performing reactions under confinement will not only improve the cyclic performance of photochromic molecules, but may also increase the amount of product obtainable from traditionally low-yielding organic reactions."}],"day":"14","doi":"10.1021/jacs.0c06146","extern":"1","volume":142,"issue":"34","author":[{"last_name":"Canton","first_name":"Martina","full_name":"Canton, Martina"},{"first_name":"Angela B.","last_name":"Grommet","full_name":"Grommet, Angela B."},{"first_name":"Luca","last_name":"Pesce","full_name":"Pesce, Luca"},{"full_name":"Gemen, Julius","first_name":"Julius","last_name":"Gemen"},{"first_name":"Shiming","last_name":"Li","full_name":"Li, Shiming"},{"last_name":"Diskin-Posner","first_name":"Yael","full_name":"Diskin-Posner, Yael"},{"first_name":"Alberto","last_name":"Credi","full_name":"Credi, Alberto"},{"first_name":"Giovanni M.","last_name":"Pavan","full_name":"Pavan, Giovanni M."},{"last_name":"Andréasson","first_name":"Joakim","full_name":"Andréasson, Joakim"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal"}],"scopus_import":"1","_id":"13364","pmid":1,"intvolume":"       142","title":"Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage","article_processing_charge":"No","date_created":"2023-08-01T09:36:59Z","publication_status":"published","quality_controlled":"1","page":"14557-14565","article_type":"original","publisher":"American Chemical Society"},{"oa_version":"Published Version","month":"04","publication":"Journal of the American Chemical Society","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"oa":1,"type":"journal_article","date_published":"2020-04-30T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1021/jacs.0c03444","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_created":"2023-08-01T09:37:12Z","article_processing_charge":"No","publication_status":"published","intvolume":"       142","title":"Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage","scopus_import":"1","_id":"13365","pmid":1,"issue":"21","author":[{"last_name":"Pesce","first_name":"Luca","full_name":"Pesce, Luca"},{"last_name":"Perego","first_name":"Claudio","full_name":"Perego, Claudio"},{"first_name":"Angela B.","last_name":"Grommet","full_name":"Grommet, Angela B."},{"last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"full_name":"Pavan, Giovanni M.","last_name":"Pavan","first_name":"Giovanni M."}],"publisher":"American Chemical Society","article_type":"original","quality_controlled":"1","page":"9792-9802","day":"30","doi":"10.1021/jacs.0c03444","abstract":[{"text":"Photoswitchable molecules are employed for many applications, from the development of active materials to the design of stimuli-responsive molecular systems and light-powered molecular machines. To fully exploit their potential, we must learn ways to control the mechanism and kinetics of their photoinduced isomerization. One possible strategy involves confinement of photoresponsive switches such as azobenzenes or spiropyrans within crowded molecular environments, which may allow control over their light-induced conversion. However, the molecular factors that influence and control the switching process under realistic conditions and within dynamic molecular regimes often remain difficult to ascertain. As a case study, here we have employed molecular models to probe the isomerization of azobenzene guests within a Pd(II)-based coordination cage host in water. Atomistic molecular dynamics and metadynamics simulations allow us to characterize the flexibility of the cage in the solvent, the (rare) guest encapsulation and release events, and the relative probability/kinetics of light-induced isomerization of azobenzene analogues in these host–guest systems. In this way, we can reconstruct the mechanism of azobenzene switching inside the cage cavity and explore key molecular factors that may control this event. We obtain a molecular-level insight on the effects of crowding and host–guest interactions on azobenzene isomerization. The detailed picture elucidated by this study may enable the rational design of photoswitchable systems whose reactivity can be controlled via host–guest interactions.","lang":"eng"}],"year":"2020","citation":{"mla":"Pesce, Luca, et al. “Molecular Factors Controlling the Isomerization of Azobenzenes in the Cavity of a Flexible Coordination Cage.” <i>Journal of the American Chemical Society</i>, vol. 142, no. 21, American Chemical Society, 2020, pp. 9792–802, doi:<a href=\"https://doi.org/10.1021/jacs.0c03444\">10.1021/jacs.0c03444</a>.","short":"L. Pesce, C. Perego, A.B. Grommet, R. Klajn, G.M. Pavan, Journal of the American Chemical Society 142 (2020) 9792–9802.","ista":"Pesce L, Perego C, Grommet AB, Klajn R, Pavan GM. 2020. Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage. Journal of the American Chemical Society. 142(21), 9792–9802.","apa":"Pesce, L., Perego, C., Grommet, A. B., Klajn, R., &#38; Pavan, G. M. (2020). Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.0c03444\">https://doi.org/10.1021/jacs.0c03444</a>","ama":"Pesce L, Perego C, Grommet AB, Klajn R, Pavan GM. Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage. <i>Journal of the American Chemical Society</i>. 2020;142(21):9792-9802. doi:<a href=\"https://doi.org/10.1021/jacs.0c03444\">10.1021/jacs.0c03444</a>","chicago":"Pesce, Luca, Claudio Perego, Angela B. Grommet, Rafal Klajn, and Giovanni M. Pavan. “Molecular Factors Controlling the Isomerization of Azobenzenes in the Cavity of a Flexible Coordination Cage.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/jacs.0c03444\">https://doi.org/10.1021/jacs.0c03444</a>.","ieee":"L. Pesce, C. Perego, A. B. Grommet, R. Klajn, and G. M. Pavan, “Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage,” <i>Journal of the American Chemical Society</i>, vol. 142, no. 21. American Chemical Society, pp. 9792–9802, 2020."},"date_updated":"2023-08-07T10:18:53Z","external_id":{"pmid":["32353237"]},"volume":142,"extern":"1"},{"volume":36,"extern":"1","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>","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.","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>.","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>.","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.","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","external_id":{"pmid":["33381818"]},"day":"01","doi":"10.1093/bioinformatics/btaa843","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"}],"quality_controlled":"1","page":"i919-i927","publisher":"Oxford University Press","article_type":"original","scopus_import":"1","_id":"14125","pmid":1,"issue":"Supplement_2","author":[{"last_name":"Stark","first_name":"Stefan G","full_name":"Stark, Stefan G"},{"full_name":"Ficek, Joanna","first_name":"Joanna","last_name":"Ficek"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco"},{"full_name":"Bonilla, Ximena","first_name":"Ximena","last_name":"Bonilla"},{"full_name":"Chevrier, Stéphane","first_name":"Stéphane","last_name":"Chevrier"},{"last_name":"Singer","first_name":"Franziska","full_name":"Singer, Franziska"},{"last_name":"Aebersold","first_name":"Rudolf","full_name":"Aebersold, Rudolf"},{"first_name":"Faisal S","last_name":"Al-Quaddoomi","full_name":"Al-Quaddoomi, Faisal S"},{"full_name":"Albinus, Jonas","last_name":"Albinus","first_name":"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","first_name":"Per-Olof","last_name":"Attinger"},{"full_name":"Bacac, Marina","last_name":"Bacac","first_name":"Marina"},{"first_name":"Daniel","last_name":"Baumhoer","full_name":"Baumhoer, Daniel"},{"full_name":"Beck-Schimmer, Beatrice","last_name":"Beck-Schimmer","first_name":"Beatrice"},{"first_name":"Niko","last_name":"Beerenwinkel","full_name":"Beerenwinkel, Niko"},{"last_name":"Beisel","first_name":"Christian","full_name":"Beisel, Christian"},{"last_name":"Bernasconi","first_name":"Lara","full_name":"Bernasconi, Lara"},{"first_name":"Anne","last_name":"Bertolini","full_name":"Bertolini, Anne"},{"first_name":"Bernd","last_name":"Bodenmiller","full_name":"Bodenmiller, Bernd"},{"full_name":"Bonilla, Ximena","first_name":"Ximena","last_name":"Bonilla"},{"full_name":"Casanova, Ruben","first_name":"Ruben","last_name":"Casanova"},{"last_name":"Chevrier","first_name":"Stéphane","full_name":"Chevrier, Stéphane"},{"first_name":"Natalia","last_name":"Chicherova","full_name":"Chicherova, Natalia"},{"last_name":"D'Costa","first_name":"Maya","full_name":"D'Costa, Maya"},{"last_name":"Danenberg","first_name":"Esther","full_name":"Danenberg, Esther"},{"full_name":"Davidson, Natalie","first_name":"Natalie","last_name":"Davidson"},{"full_name":"gan, Monica-Andreea Dră","last_name":"gan","first_name":"Monica-Andreea Dră"},{"full_name":"Dummer, Reinhard","first_name":"Reinhard","last_name":"Dummer"},{"first_name":"Stefanie","last_name":"Engler","full_name":"Engler, Stefanie"},{"last_name":"Erkens","first_name":"Martin","full_name":"Erkens, Martin"},{"first_name":"Katja","last_name":"Eschbach","full_name":"Eschbach, Katja"},{"last_name":"Esposito","first_name":"Cinzia","full_name":"Esposito, Cinzia"},{"last_name":"Fedier","first_name":"André","full_name":"Fedier, André"},{"full_name":"Ferreira, Pedro","first_name":"Pedro","last_name":"Ferreira"},{"first_name":"Joanna","last_name":"Ficek","full_name":"Ficek, Joanna"},{"full_name":"Frei, Anja L","first_name":"Anja L","last_name":"Frei"},{"first_name":"Bruno","last_name":"Frey","full_name":"Frey, Bruno"},{"last_name":"Goetze","first_name":"Sandra","full_name":"Goetze, Sandra"},{"full_name":"Grob, Linda","first_name":"Linda","last_name":"Grob"},{"full_name":"Gut, Gabriele","first_name":"Gabriele","last_name":"Gut"},{"full_name":"Günther, Detlef","last_name":"Günther","first_name":"Detlef"},{"last_name":"Haberecker","first_name":"Martina","full_name":"Haberecker, Martina"},{"first_name":"Pirmin","last_name":"Haeuptle","full_name":"Haeuptle, Pirmin"},{"first_name":"Viola","last_name":"Heinzelmann-Schwarz","full_name":"Heinzelmann-Schwarz, Viola"},{"last_name":"Herter","first_name":"Sylvia","full_name":"Herter, Sylvia"},{"last_name":"Holtackers","first_name":"Rene","full_name":"Holtackers, Rene"},{"first_name":"Tamara","last_name":"Huesser","full_name":"Huesser, Tamara"},{"first_name":"Anja","last_name":"Irmisch","full_name":"Irmisch, Anja"},{"first_name":"Francis","last_name":"Jacob","full_name":"Jacob, Francis"},{"full_name":"Jacobs, Andrea","first_name":"Andrea","last_name":"Jacobs"},{"last_name":"Jaeger","first_name":"Tim M","full_name":"Jaeger, Tim M"},{"first_name":"Katharina","last_name":"Jahn","full_name":"Jahn, Katharina"},{"full_name":"James, Alva R","first_name":"Alva R","last_name":"James"},{"last_name":"Jermann","first_name":"Philip M","full_name":"Jermann, Philip M"},{"full_name":"Kahles, André","last_name":"Kahles","first_name":"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"},{"full_name":"Kuipers, Jack","first_name":"Jack","last_name":"Kuipers"},{"full_name":"Kunze, Christian P","first_name":"Christian P","last_name":"Kunze"},{"full_name":"Kurzeder, Christian","first_name":"Christian","last_name":"Kurzeder"},{"full_name":"Lehmann, Kjong-Van","first_name":"Kjong-Van","last_name":"Lehmann"},{"full_name":"Levesque, Mitchell","last_name":"Levesque","first_name":"Mitchell"},{"first_name":"Sebastian","last_name":"Lugert","full_name":"Lugert, Sebastian"},{"first_name":"Gerd","last_name":"Maass","full_name":"Maass, Gerd"},{"full_name":"Manz, Markus","last_name":"Manz","first_name":"Markus"},{"full_name":"Markolin, Philipp","first_name":"Philipp","last_name":"Markolin"},{"full_name":"Mena, Julien","last_name":"Mena","first_name":"Julien"},{"full_name":"Menzel, Ulrike","first_name":"Ulrike","last_name":"Menzel"},{"full_name":"Metzler, Julian M","first_name":"Julian M","last_name":"Metzler"},{"last_name":"Miglino","first_name":"Nicola","full_name":"Miglino, Nicola"},{"full_name":"Milani, Emanuela S","last_name":"Milani","first_name":"Emanuela S"},{"full_name":"Moch, Holger","first_name":"Holger","last_name":"Moch"},{"first_name":"Simone","last_name":"Muenst","full_name":"Muenst, Simone"},{"first_name":"Riccardo","last_name":"Murri","full_name":"Murri, Riccardo"},{"full_name":"Ng, Charlotte KY","last_name":"Ng","first_name":"Charlotte KY"},{"first_name":"Stefan","last_name":"Nicolet","full_name":"Nicolet, Stefan"},{"first_name":"Marta","last_name":"Nowak","full_name":"Nowak, Marta"},{"full_name":"Pedrioli, Patrick GA","last_name":"Pedrioli","first_name":"Patrick GA"},{"full_name":"Pelkmans, Lucas","first_name":"Lucas","last_name":"Pelkmans"},{"full_name":"Piscuoglio, Salvatore","first_name":"Salvatore","last_name":"Piscuoglio"},{"last_name":"Prummer","first_name":"Michael","full_name":"Prummer, Michael"},{"full_name":"Ritter, Mathilde","last_name":"Ritter","first_name":"Mathilde"},{"full_name":"Rommel, Christian","first_name":"Christian","last_name":"Rommel"},{"first_name":"María L","last_name":"Rosano-González","full_name":"Rosano-González, María L"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"first_name":"Natascha","last_name":"Santacroce","full_name":"Santacroce, Natascha"},{"last_name":"Castillo","first_name":"Jacobo Sarabia del","full_name":"Castillo, Jacobo Sarabia del"},{"full_name":"Schlenker, Ramona","first_name":"Ramona","last_name":"Schlenker"},{"full_name":"Schwalie, Petra C","last_name":"Schwalie","first_name":"Petra C"},{"last_name":"Schwan","first_name":"Severin","full_name":"Schwan, 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","first_name":"Sujana","last_name":"Sivapatham"},{"last_name":"Snijder","first_name":"Berend","full_name":"Snijder, Berend"},{"full_name":"Sobottka, Bettina","last_name":"Sobottka","first_name":"Bettina"},{"full_name":"Sreedharan, Vipin T","first_name":"Vipin T","last_name":"Sreedharan"},{"last_name":"Stark","first_name":"Stefan","full_name":"Stark, Stefan"},{"first_name":"Daniel J","last_name":"Stekhoven","full_name":"Stekhoven, Daniel J"},{"last_name":"Theocharides","first_name":"Alexandre PA","full_name":"Theocharides, Alexandre PA"},{"first_name":"Tinu M","last_name":"Thomas","full_name":"Thomas, Tinu M"},{"full_name":"Tolnay, Markus","first_name":"Markus","last_name":"Tolnay"},{"full_name":"Tosevski, Vinko","first_name":"Vinko","last_name":"Tosevski"},{"last_name":"Toussaint","first_name":"Nora C","full_name":"Toussaint, Nora C"},{"first_name":"Mustafa A","last_name":"Tuncel","full_name":"Tuncel, Mustafa A"},{"full_name":"Tusup, Marina","last_name":"Tusup","first_name":"Marina"},{"last_name":"Drogen","first_name":"Audrey Van","full_name":"Drogen, Audrey Van"},{"last_name":"Vetter","first_name":"Marcus","full_name":"Vetter, Marcus"},{"last_name":"Vlajnic","first_name":"Tatjana","full_name":"Vlajnic, Tatjana"},{"last_name":"Weber","first_name":"Sandra","full_name":"Weber, Sandra"},{"full_name":"Weber, Walter P","first_name":"Walter P","last_name":"Weber"},{"full_name":"Wegmann, Rebekka","last_name":"Wegmann","first_name":"Rebekka"},{"full_name":"Weller, Michael","last_name":"Weller","first_name":"Michael"},{"first_name":"Fabian","last_name":"Wendt","full_name":"Wendt, Fabian"},{"last_name":"Wey","first_name":"Norbert","full_name":"Wey, Norbert"},{"full_name":"Wicki, Andreas","last_name":"Wicki","first_name":"Andreas"},{"last_name":"Wollscheid","first_name":"Bernd","full_name":"Wollscheid, Bernd"},{"full_name":"Yu, Shuqing","first_name":"Shuqing","last_name":"Yu"},{"full_name":"Ziegler, Johanna","first_name":"Johanna","last_name":"Ziegler"},{"full_name":"Zimmermann, Marc","last_name":"Zimmermann","first_name":"Marc"},{"last_name":"Zoche","first_name":"Martin","full_name":"Zoche, Martin"},{"full_name":"Zuend, Gregor","last_name":"Zuend","first_name":"Gregor"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"first_name":"Kjong-Van","last_name":"Lehmann","full_name":"Lehmann, Kjong-Van"}],"date_created":"2023-08-21T12:28:20Z","department":[{"_id":"FrLo"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        36","title":"SCIM: Universal single-cell matching with unpaired feature sets","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bioinformatics/btaa843"}],"status":"public","related_material":{"link":[{"url":"https://github.com/ratschlab/scim","relation":"software"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_published":"2020-12-01T00:00:00Z","publication_identifier":{"eissn":["1367-4811"]},"oa":1,"keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"language":[{"iso":"eng"}],"publication":"Bioinformatics","oa_version":"Published Version","month":"12"},{"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]).","volume":182,"extern":"1","date_updated":"2021-11-26T08:58:37Z","citation":{"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.","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>.","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>.","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>"},"year":"2020","external_id":{"pmid":["32814015"]},"doi":"10.1016/j.cell.2020.07.021","day":"18","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"}],"page":"1140-1155.e18","quality_controlled":"1","publisher":"Elsevier","article_type":"original","_id":"10348","pmid":1,"scopus_import":"1","author":[{"full_name":"Pfitzner, Anna-Katharina","last_name":"Pfitzner","first_name":"Anna-Katharina"},{"full_name":"Mercier, Vincent","first_name":"Vincent","last_name":"Mercier"},{"last_name":"Jiang","first_name":"Xiuyun","full_name":"Jiang, Xiuyun"},{"full_name":"Moser von Filseck, Joachim","last_name":"Moser von Filseck","first_name":"Joachim"},{"full_name":"Baum, Buzz","first_name":"Buzz","last_name":"Baum"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"last_name":"Roux","first_name":"Aurélien","full_name":"Roux, Aurélien"}],"issue":"5","publication_status":"published","article_processing_charge":"No","date_created":"2021-11-26T08:02:27Z","title":"An ESCRT-III polymerization sequence drives membrane deformation and fission","intvolume":"       182","main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S0092867420309296"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","date_published":"2020-08-18T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0092-8674"]},"oa":1,"language":[{"iso":"eng"}],"keyword":["general biochemistry","genetics and molecular biology"],"publication":"Cell","oa_version":"Published Version","month":"08"},{"publication_identifier":{"issn":["2050-084X"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2019-10-10T00:00:00Z","type":"journal_article","file":[{"date_updated":"2022-04-08T08:18:01Z","content_type":"application/pdf","file_name":"2019_eLife_Buchwalter.pdf","date_created":"2022-04-08T08:18:01Z","checksum":"1e8672a1e9c3dc0a2d3d0dad89673616","file_size":6984654,"file_id":"11138","creator":"dernst","access_level":"open_access","relation":"main_file","success":1}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13079"}]},"status":"public","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","oa_version":"Published Version","month":"10","article_number":"e49796","publication":"eLife","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"doi":"10.7554/elife.49796","day":"10","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-05-31T06:36:22Z","year":"2019","citation":{"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>.","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.","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>","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>","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>."},"external_id":{"pmid":["31599721"]},"volume":8,"extern":"1","ddc":["570"],"publication_status":"published","date_created":"2022-04-07T07:45:02Z","article_processing_charge":"No","title":"Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress","intvolume":"         8","_id":"11060","pmid":1,"scopus_import":"1","author":[{"first_name":"Abigail","last_name":"Buchwalter","full_name":"Buchwalter, Abigail"},{"first_name":"Roberta","last_name":"Schulte","full_name":"Schulte, Roberta"},{"last_name":"Tsai","first_name":"Hsiao","full_name":"Tsai, Hsiao"},{"full_name":"Capitanio, Juliana","first_name":"Juliana","last_name":"Capitanio"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"publisher":"eLife Sciences Publications","article_type":"original","quality_controlled":"1","file_date_updated":"2022-04-08T08:18:01Z"},{"doi":"10.1038/s41467-019-10490-9","day":"19","abstract":[{"lang":"eng","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."}],"date_updated":"2021-01-12T08:19:03Z","citation":{"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.","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>","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.","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>."},"year":"2019","external_id":{"pmid":["31217444"]},"volume":10,"extern":"1","publication_status":"published","article_processing_charge":"No","date_created":"2020-09-17T10:28:25Z","title":"Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex","intvolume":"        10","_id":"8405","pmid":1,"author":[{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"first_name":"Leandro F.","last_name":"Estrozi","full_name":"Estrozi, Leandro F."},{"first_name":"Charles D.","last_name":"Schwieters","full_name":"Schwieters, Charles D."},{"last_name":"Effantin","first_name":"Gregory","full_name":"Effantin, Gregory"},{"first_name":"Pavel","last_name":"Macek","full_name":"Macek, Pavel"},{"last_name":"Sounier","first_name":"Remy","full_name":"Sounier, Remy"},{"full_name":"Sivertsen, Astrid C.","last_name":"Sivertsen","first_name":"Astrid C."},{"full_name":"Schmidt, Elena","last_name":"Schmidt","first_name":"Elena"},{"full_name":"Kerfah, Rime","first_name":"Rime","last_name":"Kerfah"},{"first_name":"Guillaume","last_name":"Mas","full_name":"Mas, Guillaume"},{"first_name":"Jacques-Philippe","last_name":"Colletier","full_name":"Colletier, Jacques-Philippe"},{"full_name":"Güntert, Peter","last_name":"Güntert","first_name":"Peter"},{"first_name":"Adrien","last_name":"Favier","full_name":"Favier, Adrien"},{"full_name":"Schoehn, Guy","last_name":"Schoehn","first_name":"Guy"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"},{"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":[{"url":"https://doi.org/10.1038/s41467-019-10490-9","open_access":"1"}],"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"]},{"article_type":"original","publisher":"Elsevier","language":[{"iso":"eng"}],"keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"page":"180-186","quality_controlled":"1","month":"09","title":"Relaxing with liquids and solids – A perspective on biomolecular dynamics","intvolume":"       306","oa_version":"Submitted Version","publication_status":"published","article_processing_charge":"No","date_created":"2020-09-17T10:28:47Z","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda"}],"publication":"Journal of Magnetic Resonance","_id":"8407","pmid":1,"extern":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":306,"doi":"10.1016/j.jmr.2019.07.025","publication_identifier":{"issn":["1090-7807"]},"day":"01","date_published":"2019-09-01T00:00:00Z","external_id":{"pmid":["31350165"]},"type":"journal_article","date_updated":"2021-01-12T08:19:04Z","year":"2019","citation":{"chicago":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jmr.2019.07.025\">https://doi.org/10.1016/j.jmr.2019.07.025</a>.","ieee":"P. Schanda, “Relaxing with liquids and solids – A perspective on biomolecular dynamics,” <i>Journal of Magnetic Resonance</i>, vol. 306. Elsevier, pp. 180–186, 2019.","apa":"Schanda, P. (2019). Relaxing with liquids and solids – A perspective on biomolecular dynamics. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2019.07.025\">https://doi.org/10.1016/j.jmr.2019.07.025</a>","ama":"Schanda P. Relaxing with liquids and solids – A perspective on biomolecular dynamics. <i>Journal of Magnetic Resonance</i>. 2019;306:180-186. doi:<a href=\"https://doi.org/10.1016/j.jmr.2019.07.025\">10.1016/j.jmr.2019.07.025</a>","ista":"Schanda P. 2019. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 306, 180–186.","short":"P. Schanda, Journal of Magnetic Resonance 306 (2019) 180–186.","mla":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” <i>Journal of Magnetic Resonance</i>, vol. 306, Elsevier, 2019, pp. 180–86, doi:<a href=\"https://doi.org/10.1016/j.jmr.2019.07.025\">10.1016/j.jmr.2019.07.025</a>."}},{"extern":"1","volume":141,"abstract":[{"text":"Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artefact-free dynamics measurements, and allows probing motions effectively without molecular-weight limitations. The application to the TET2 enzyme assembly of ~0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (ps-ms). We quantitatively probe ring flip motions, and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.","lang":"eng"}],"day":"14","doi":"10.1021/jacs.9b04219","external_id":{"pmid":["31199882"]},"year":"2019","citation":{"ista":"Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. 2019. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 141(28), 11183–11195.","short":"D.F. Gauto, P. Macek, A. Barducci, H. Fraga, A. Hessel, T. Terauchi, D. Gajan, Y. Miyanoiri, J. Boisbouvier, R. Lichtenecker, M. Kainosho, P. Schanda, Journal of the American Chemical Society 141 (2019) 11183–11195.","mla":"Gauto, Diego F., et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” <i>Journal of the American Chemical Society</i>, vol. 141, no. 28, American Chemical Society, 2019, pp. 11183–95, doi:<a href=\"https://doi.org/10.1021/jacs.9b04219\">10.1021/jacs.9b04219</a>.","ieee":"D. F. Gauto <i>et al.</i>, “Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR,” <i>Journal of the American Chemical Society</i>, vol. 141, no. 28. American Chemical Society, pp. 11183–11195, 2019.","chicago":"Gauto, Diego F., Pavel Macek, Alessandro Barducci, Hugo Fraga, Audrey Hessel, Tsutomu Terauchi, David Gajan, et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/jacs.9b04219\">https://doi.org/10.1021/jacs.9b04219</a>.","ama":"Gauto DF, Macek P, Barducci A, et al. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. <i>Journal of the American Chemical Society</i>. 2019;141(28):11183-11195. doi:<a href=\"https://doi.org/10.1021/jacs.9b04219\">10.1021/jacs.9b04219</a>","apa":"Gauto, D. F., Macek, P., Barducci, A., Fraga, H., Hessel, A., Terauchi, T., … Schanda, P. (2019). Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.9b04219\">https://doi.org/10.1021/jacs.9b04219</a>"},"date_updated":"2021-01-12T08:19:04Z","article_type":"original","publisher":"American Chemical Society","quality_controlled":"1","page":"11183-11195","intvolume":"       141","title":"Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR","article_processing_charge":"No","date_created":"2020-09-17T10:29:00Z","publication_status":"published","issue":"28","author":[{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"last_name":"Macek","first_name":"Pavel","full_name":"Macek, Pavel"},{"first_name":"Alessandro","last_name":"Barducci","full_name":"Barducci, Alessandro"},{"full_name":"Fraga, Hugo","first_name":"Hugo","last_name":"Fraga"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"first_name":"Tsutomu","last_name":"Terauchi","full_name":"Terauchi, Tsutomu"},{"last_name":"Gajan","first_name":"David","full_name":"Gajan, David"},{"last_name":"Miyanoiri","first_name":"Yohei","full_name":"Miyanoiri, Yohei"},{"full_name":"Boisbouvier, Jerome","last_name":"Boisbouvier","first_name":"Jerome"},{"full_name":"Lichtenecker, Roman","last_name":"Lichtenecker","first_name":"Roman"},{"full_name":"Kainosho, Masatsune","first_name":"Masatsune","last_name":"Kainosho"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"pmid":1,"_id":"8408","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"issn":["0002-7863","1520-5126"]},"type":"journal_article","date_published":"2019-06-14T00:00:00Z","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"language":[{"iso":"eng"}],"month":"06","oa_version":"Submitted Version","publication":"Journal of the American Chemical Society"},{"month":"01","oa_version":"Submitted Version","publication":"Journal of the American Chemical Society","language":[{"iso":"eng"}],"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"publication_identifier":{"issn":["0002-7863","1520-5126"]},"date_published":"2019-01-08T00:00:00Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques","intvolume":"       141","publication_status":"published","article_processing_charge":"No","date_created":"2020-09-17T10:29:50Z","author":[{"last_name":"Rovó","first_name":"Petra","full_name":"Rovó, Petra"},{"first_name":"Colin A.","last_name":"Smith","full_name":"Smith, Colin A."},{"full_name":"Gauto, Diego","last_name":"Gauto","first_name":"Diego"},{"full_name":"de Groot, Bert L.","first_name":"Bert L.","last_name":"de Groot"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"full_name":"Linser, Rasmus","last_name":"Linser","first_name":"Rasmus"}],"issue":"2","_id":"8413","pmid":1,"article_type":"original","publisher":"American Chemical Society","page":"858-869","quality_controlled":"1","abstract":[{"lang":"eng","text":"NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains."}],"doi":"10.1021/jacs.8b09258","day":"08","external_id":{"pmid":["30620186"]},"date_updated":"2021-01-12T08:19:07Z","year":"2019","citation":{"apa":"Rovó, P., Smith, C. A., Gauto, D., de Groot, B. L., Schanda, P., &#38; Linser, R. (2019). Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.8b09258\">https://doi.org/10.1021/jacs.8b09258</a>","ama":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. <i>Journal of the American Chemical Society</i>. 2019;141(2):858-869. doi:<a href=\"https://doi.org/10.1021/jacs.8b09258\">10.1021/jacs.8b09258</a>","ieee":"P. Rovó, C. A. Smith, D. Gauto, B. L. de Groot, P. Schanda, and R. Linser, “Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques,” <i>Journal of the American Chemical Society</i>, vol. 141, no. 2. American Chemical Society, pp. 858–869, 2019.","chicago":"Rovó, Petra, Colin A. Smith, Diego Gauto, Bert L. de Groot, Paul Schanda, and Rasmus Linser. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/jacs.8b09258\">https://doi.org/10.1021/jacs.8b09258</a>.","mla":"Rovó, Petra, et al. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” <i>Journal of the American Chemical Society</i>, vol. 141, no. 2, American Chemical Society, 2019, pp. 858–69, doi:<a href=\"https://doi.org/10.1021/jacs.8b09258\">10.1021/jacs.8b09258</a>.","short":"P. Rovó, C.A. Smith, D. Gauto, B.L. de Groot, P. Schanda, R. Linser, Journal of the American Chemical Society 141 (2019) 858–869.","ista":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. 2019. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 141(2), 858–869."},"extern":"1","volume":141},{"type":"journal_article","date_published":"2019-09-12T00:00:00Z","oa":1,"publication_identifier":{"eissn":["2451-9294"],"issn":["2451-9308"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chempr.2019.08.012"}],"publication":"Chem","month":"09","oa_version":"Published Version","keyword":["Materials Chemistry","Biochemistry (medical)","General Chemical Engineering","Environmental Chemistry","Biochemistry","General Chemistry"],"language":[{"iso":"eng"}],"year":"2019","citation":{"ista":"Białek MJ, Klajn R. 2019. Diamond grows up. Chem. 5(9), 2283–2285.","short":"M.J. Białek, R. Klajn, Chem 5 (2019) 2283–2285.","mla":"Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” <i>Chem</i>, vol. 5, no. 9, Elsevier, 2019, pp. 2283–85, doi:<a href=\"https://doi.org/10.1016/j.chempr.2019.08.012\">10.1016/j.chempr.2019.08.012</a>.","ieee":"M. J. Białek and R. Klajn, “Diamond grows up,” <i>Chem</i>, vol. 5, no. 9. Elsevier, pp. 2283–2285, 2019.","chicago":"Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” <i>Chem</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.chempr.2019.08.012\">https://doi.org/10.1016/j.chempr.2019.08.012</a>.","apa":"Białek, M. J., &#38; Klajn, R. (2019). Diamond grows up. <i>Chem</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.chempr.2019.08.012\">https://doi.org/10.1016/j.chempr.2019.08.012</a>","ama":"Białek MJ, Klajn R. Diamond grows up. <i>Chem</i>. 2019;5(9):2283-2285. doi:<a href=\"https://doi.org/10.1016/j.chempr.2019.08.012\">10.1016/j.chempr.2019.08.012</a>"},"date_updated":"2023-08-07T10:46:50Z","abstract":[{"text":"Diamondoid nanoporous crystals represent a synthetically challenging class of materials that typically have been obtained from tetrahedral building blocks. In this issue of Chem, Stoddart and coworkers demonstrate that it is possible to generate diamondoid frameworks from a hexacationic building block lacking a tetrahedral symmetry. These results highlight the great potential of self-assembly for rapidly transforming small molecules into structurally complex functional materials.","lang":"eng"}],"day":"12","doi":"10.1016/j.chempr.2019.08.012","extern":"1","volume":5,"issue":"9","author":[{"first_name":"Michał J.","last_name":"Białek","full_name":"Białek, Michał J."},{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"scopus_import":"1","_id":"13371","intvolume":"         5","title":"Diamond grows up","date_created":"2023-08-01T09:38:38Z","article_processing_charge":"No","publication_status":"published","quality_controlled":"1","page":"2283-2285","article_type":"original","publisher":"Elsevier"},{"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"type":"journal_article","date_published":"2019-02-06T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Published Version","month":"02","publication":"Journal of the American Chemical Society","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"language":[{"iso":"eng"}],"day":"06","doi":"10.1021/jacs.8b09638","abstract":[{"text":"The reversible photoisomerization of azobenzene has been utilized to construct a plethora of systems in which optical, electronic, catalytic, and other properties can be controlled by light. However, owing to azobenzene’s hydrophobic nature, most of these examples have been realized only in organic solvents, and systems operating in water are relatively scarce. Here, we show that by coadsorbing the inherently hydrophobic azobenzenes with water-solubilizing ligands on the same nanoparticulate platforms, it is possible to render them essentially water-soluble. To this end, we developed a modified nanoparticle functionalization procedure allowing us to precisely fine-tune the amount of azobenzene on the functionalized nanoparticles. Molecular dynamics simulations helped us to identify two distinct supramolecular architectures (depending on the length of the background ligand) on these nanoparticles, which can explain their excellent aqueous solubilities. Azobenzenes adsorbed on these water-soluble nanoparticles exhibit highly reversible photoisomerization upon exposure to UV and visible light. Importantly, the mixed-monolayer approach allowed us to systematically investigate how the background ligand affects the switching properties of azobenzene. We found that the nature of the background ligand has a profound effect on the kinetics of azobenzene switching. For example, a hydroxy-terminated background ligand is capable of accelerating the back-isomerization reaction by more than 6000-fold. These results pave the way toward the development of novel light-responsive nanomaterials operating in aqueous media and, in the long run, in biological environments.","lang":"eng"}],"citation":{"ama":"Chu Z, Han Y, Bian T, De S, Král P, Klajn R. Supramolecular control of azobenzene switching on nanoparticles. <i>Journal of the American Chemical Society</i>. 2019;141(5):1949-1960. doi:<a href=\"https://doi.org/10.1021/jacs.8b09638\">10.1021/jacs.8b09638</a>","apa":"Chu, Z., Han, Y., Bian, T., De, S., Král, P., &#38; Klajn, R. (2019). Supramolecular control of azobenzene switching on nanoparticles. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.8b09638\">https://doi.org/10.1021/jacs.8b09638</a>","ieee":"Z. Chu, Y. Han, T. Bian, S. De, P. Král, and R. Klajn, “Supramolecular control of azobenzene switching on nanoparticles,” <i>Journal of the American Chemical Society</i>, vol. 141, no. 5. American Chemical Society, pp. 1949–1960, 2019.","chicago":"Chu, Zonglin, Yanxiao Han, Tong Bian, Soumen De, Petr Král, and Rafal Klajn. “Supramolecular Control of Azobenzene Switching on Nanoparticles.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/jacs.8b09638\">https://doi.org/10.1021/jacs.8b09638</a>.","short":"Z. Chu, Y. Han, T. Bian, S. De, P. Král, R. Klajn, Journal of the American Chemical Society 141 (2019) 1949–1960.","mla":"Chu, Zonglin, et al. “Supramolecular Control of Azobenzene Switching on Nanoparticles.” <i>Journal of the American Chemical Society</i>, vol. 141, no. 5, American Chemical Society, 2019, pp. 1949–60, doi:<a href=\"https://doi.org/10.1021/jacs.8b09638\">10.1021/jacs.8b09638</a>.","ista":"Chu Z, Han Y, Bian T, De S, Král P, Klajn R. 2019. Supramolecular control of azobenzene switching on nanoparticles. Journal of the American Chemical Society. 141(5), 1949–1960."},"year":"2019","date_updated":"2023-08-07T10:51:12Z","external_id":{"pmid":["30595017"]},"volume":141,"extern":"1","date_created":"2023-08-01T09:39:19Z","article_processing_charge":"No","publication_status":"published","intvolume":"       141","title":"Supramolecular control of azobenzene switching on nanoparticles","scopus_import":"1","_id":"13373","pmid":1,"issue":"5","author":[{"first_name":"Zonglin","last_name":"Chu","full_name":"Chu, Zonglin"},{"first_name":"Yanxiao","last_name":"Han","full_name":"Han, Yanxiao"},{"last_name":"Bian","first_name":"Tong","full_name":"Bian, Tong"},{"first_name":"Soumen","last_name":"De","full_name":"De, Soumen"},{"full_name":"Král, Petr","last_name":"Král","first_name":"Petr"},{"last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"publisher":"American Chemical Society","article_type":"original","quality_controlled":"1","page":"1949-1960"},{"volume":26,"extern":"1","doi":"10.1016/j.chembiol.2019.09.002","day":"21","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"}],"date_updated":"2023-02-23T13:46:53Z","citation":{"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.","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>.","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>","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.","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>.","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."},"year":"2019","external_id":{"pmid":["31543461"]},"publisher":"Elsevier","article_type":"original","page":"1573-1585.e10","quality_controlled":"1","publication_status":"published","date_created":"2021-01-19T11:04:50Z","article_processing_charge":"No","title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1","intvolume":"        26","_id":"9018","pmid":1,"author":[{"id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","full_name":"Bakail, May M","orcid":"0000-0002-9592-1587","last_name":"Bakail","first_name":"May M"},{"full_name":"Gaubert, Albane","last_name":"Gaubert","first_name":"Albane"},{"last_name":"Andreani","first_name":"Jessica","full_name":"Andreani, Jessica"},{"first_name":"Gwenaëlle","last_name":"Moal","full_name":"Moal, Gwenaëlle"},{"full_name":"Pinna, Guillaume","last_name":"Pinna","first_name":"Guillaume"},{"last_name":"Boyarchuk","first_name":"Ekaterina","full_name":"Boyarchuk, Ekaterina"},{"last_name":"Gaillard","first_name":"Marie-Cécile","full_name":"Gaillard, Marie-Cécile"},{"full_name":"Courbeyrette, Regis","last_name":"Courbeyrette","first_name":"Regis"},{"last_name":"Mann","first_name":"Carl","full_name":"Mann, Carl"},{"full_name":"Thuret, Jean-Yves","first_name":"Jean-Yves","last_name":"Thuret"},{"last_name":"Guichard","first_name":"Bérengère","full_name":"Guichard, Bérengère"},{"first_name":"Brice","last_name":"Murciano","full_name":"Murciano, Brice"},{"last_name":"Richet","first_name":"Nicolas","full_name":"Richet, Nicolas"},{"last_name":"Poitou","first_name":"Adeline","full_name":"Poitou, Adeline"},{"full_name":"Frederic, Claire","first_name":"Claire","last_name":"Frederic"},{"full_name":"Le Du, Marie-Hélène","first_name":"Marie-Hélène","last_name":"Le Du"},{"last_name":"Agez","first_name":"Morgane","full_name":"Agez, Morgane"},{"last_name":"Roelants","first_name":"Caroline","full_name":"Roelants, Caroline"},{"full_name":"Gurard-Levin, Zachary A.","first_name":"Zachary A.","last_name":"Gurard-Levin"},{"first_name":"Geneviève","last_name":"Almouzni","full_name":"Almouzni, Geneviève"},{"first_name":"Nadia","last_name":"Cherradi","full_name":"Cherradi, Nadia"},{"last_name":"Guerois","first_name":"Raphael","full_name":"Guerois, Raphael"},{"last_name":"Ochsenbein","first_name":"Françoise","full_name":"Ochsenbein, Françoise"}],"issue":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chembiol.2019.09.002"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2451-9456"]},"oa":1,"date_published":"2019-11-21T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"oa_version":"Published Version","month":"11","publication":"Cell Chemical Biology"},{"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","relation":"main_file","access_level":"open_access","success":1}],"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)"},"oa":1,"publication_identifier":{"issn":["2041-1723"]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Nature Communications","article_number":"3380","month":"07","oa_version":"Published Version","ddc":["530"],"extern":"1","volume":10,"external_id":{"arxiv":["1909.07382"],"pmid":["31358762"]},"year":"2019","citation":{"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>","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>.","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.","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>.","ista":"Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing of colloidal monolayers. Nature Communications. 10(1), 3380."},"date_updated":"2023-02-23T13:47:59Z","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","file_date_updated":"2021-02-02T13:47:21Z","quality_controlled":"1","article_type":"original","publisher":"Springer Nature","issue":"1","author":[{"last_name":"Ramananarivo","first_name":"Sophie","full_name":"Ramananarivo, Sophie"},{"full_name":"Ducrot, Etienne","first_name":"Etienne","last_name":"Ducrot"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","last_name":"Palacci","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A"}],"scopus_import":"1","_id":"9060","pmid":1,"intvolume":"        10","title":"Activity-controlled annealing of colloidal monolayers","article_processing_charge":"No","date_created":"2021-02-02T13:43:36Z","publication_status":"published"},{"type":"journal_article","date_published":"2019-08-19T00:00:00Z","publication_identifier":{"issn":["0960-9822"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication":"Current Biology","month":"08","oa_version":"None","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"external_id":{"pmid":["31378616"]},"citation":{"ama":"Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. <i>Current Biology</i>. 2019;29(16):2676-2686.e3. doi:<a href=\"https://doi.org/10.1016/j.cub.2019.06.084\">10.1016/j.cub.2019.06.084</a>","apa":"Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., &#38; Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. <i>Current Biology</i>. Elsevier BV. <a href=\"https://doi.org/10.1016/j.cub.2019.06.084\">https://doi.org/10.1016/j.cub.2019.06.084</a>","ieee":"E. J. Lawrence <i>et al.</i>, “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” <i>Current Biology</i>, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019.","chicago":"Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” <i>Current Biology</i>. Elsevier BV, 2019. <a href=\"https://doi.org/10.1016/j.cub.2019.06.084\">https://doi.org/10.1016/j.cub.2019.06.084</a>.","mla":"Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” <i>Current Biology</i>, vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:<a href=\"https://doi.org/10.1016/j.cub.2019.06.084\">10.1016/j.cub.2019.06.084</a>.","short":"E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3.","ista":"Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3."},"year":"2019","date_updated":"2023-05-08T10:54:54Z","abstract":[{"text":"Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor.","lang":"eng"}],"day":"19","doi":"10.1016/j.cub.2019.06.084","extern":"1","volume":29,"acknowledgement":"We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.).","issue":"16","author":[{"first_name":"Emma J.","last_name":"Lawrence","full_name":"Lawrence, Emma J."},{"full_name":"Gao, Hongbo","last_name":"Gao","first_name":"Hongbo"},{"full_name":"Tock, Andrew J.","last_name":"Tock","first_name":"Andrew J."},{"last_name":"Lambing","first_name":"Christophe","full_name":"Lambing, Christophe"},{"first_name":"Alexander R.","last_name":"Blackwell","full_name":"Blackwell, Alexander R."},{"first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"full_name":"Henderson, Ian R.","last_name":"Henderson","first_name":"Ian R."}],"scopus_import":"1","_id":"12190","pmid":1,"intvolume":"        29","title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis","article_processing_charge":"No","date_created":"2023-01-16T09:16:33Z","department":[{"_id":"XiFe"}],"publication_status":"published","quality_controlled":"1","page":"2676-2686.e3","article_type":"original","publisher":"Elsevier BV"},{"abstract":[{"lang":"eng","text":"Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation."}],"day":"28","doi":"10.7554/elife.42530","external_id":{"unknown":["31135340"]},"citation":{"short":"S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).","mla":"He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” <i>ELife</i>, vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:<a href=\"https://doi.org/10.7554/elife.42530\">10.7554/elife.42530</a>.","ista":"He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530.","apa":"He, S., Vickers, M., Zhang, J., &#38; Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. <i>ELife</i>. eLife Sciences Publications, Ltd. <a href=\"https://doi.org/10.7554/elife.42530\">https://doi.org/10.7554/elife.42530</a>","ama":"He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.42530\">10.7554/elife.42530</a>","ieee":"S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” <i>eLife</i>, vol. 8. eLife Sciences Publications, Ltd, 2019.","chicago":"He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” <i>ELife</i>. eLife Sciences Publications, Ltd, 2019. <a href=\"https://doi.org/10.7554/elife.42530\">https://doi.org/10.7554/elife.42530</a>."},"year":"2019","date_updated":"2023-05-08T10:54:12Z","ddc":["580"],"extern":"1","volume":8,"acknowledgement":"We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF).","intvolume":"         8","title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","date_created":"2023-01-16T09:17:21Z","department":[{"_id":"XiFe"}],"article_processing_charge":"No","publication_status":"published","author":[{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"first_name":"Martin","last_name":"Vickers","full_name":"Vickers, Martin"},{"last_name":"Zhang","first_name":"Jingyi","full_name":"Zhang, Jingyi"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng","first_name":"Xiaoqi"}],"scopus_import":"1","_id":"12192","article_type":"original","publisher":"eLife Sciences Publications, Ltd","file_date_updated":"2023-02-07T09:42:46Z","quality_controlled":"1","oa":1,"publication_identifier":{"issn":["2050-084X"]},"type":"journal_article","date_published":"2019-05-28T00:00:00Z","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)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/"}],"file":[{"access_level":"open_access","success":1,"relation":"main_file","file_id":"12525","creator":"alisjak","date_created":"2023-02-07T09:42:46Z","file_size":2493837,"checksum":"ea6b89c20d59e5eb3646916fe5d568ad","date_updated":"2023-02-07T09:42:46Z","content_type":"application/pdf","file_name":"2019_elife_He.pdf"}],"article_number":"42530","month":"05","oa_version":"Published Version","has_accepted_license":"1","publication":"eLife","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"language":[{"iso":"eng"}]},{"oa_version":"Published Version","month":"09","publication":"Briefings in Functional Genomics","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-2649"],"eissn":["2041-2657"]},"oa":1,"type":"journal_article","date_published":"2018-09-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bfgp/ely007"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"CaHe"}],"date_created":"2022-03-18T12:40:35Z","article_processing_charge":"No","publication_status":"published","intvolume":"        17","title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","scopus_import":"1","_id":"10880","pmid":1,"issue":"5","author":[{"full_name":"Yuuta, Moriyama","orcid":"0000-0002-2853-8051","last_name":"Yuuta","first_name":"Moriyama","id":"4968E7C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kazuko","last_name":"Koshiba-Takeuchi","full_name":"Koshiba-Takeuchi, Kazuko"}],"publisher":"Oxford University Press","article_type":"original","quality_controlled":"1","page":"329-338","day":"01","doi":"10.1093/bfgp/ely007","abstract":[{"text":"Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Recently, it has been gradually revealed that WGD and subsequent fate changes of duplicated genes can facilitate phenotypic evolution. Here, we review the current understanding of the relationship between WGD and the acquisition of evolutionary novelties. We show some examples of this link and discuss how WGD and subsequent duplicated genes can facilitate phenotypic evolution as well as when such genomic doubling can be advantageous for adaptation.","lang":"eng"}],"citation":{"apa":"Yuuta, M., &#38; Koshiba-Takeuchi, K. (2018). Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>","ama":"Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. 2018;17(5):329-338. doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>","ieee":"M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications on the emergence of evolutionary novelties,” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.","chicago":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>.","mla":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>.","short":"M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338.","ista":"Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 17(5), 329–338."},"year":"2018","date_updated":"2023-09-19T15:11:22Z","external_id":{"isi":["000456054400004"],"pmid":["29579140"]},"isi":1,"acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","volume":17}]