[{"issue":"2","citation":{"chicago":"Zhou, Haoxin, Hryhoriy Polshyn, Takashi Taniguchi, Kenji Watanabe, and Andrea F. Young. “Skyrmion Solids in Monolayer Graphene.” <i>Nature Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41567-019-0729-8\">https://doi.org/10.1038/s41567-019-0729-8</a>.","ieee":"H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, and A. F. Young, “Skyrmion solids in monolayer graphene,” <i>Nature Physics</i>, vol. 16, no. 2. Springer Nature, pp. 154–158, 2020.","apa":"Zhou, H., Polshyn, H., Taniguchi, T., Watanabe, K., &#38; Young, A. F. (2020). Skyrmion solids in monolayer graphene. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-019-0729-8\">https://doi.org/10.1038/s41567-019-0729-8</a>","ista":"Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. 2020. Skyrmion solids in monolayer graphene. Nature Physics. 16(2), 154–158.","mla":"Zhou, Haoxin, et al. “Skyrmion Solids in Monolayer Graphene.” <i>Nature Physics</i>, vol. 16, no. 2, Springer Nature, 2020, pp. 154–58, doi:<a href=\"https://doi.org/10.1038/s41567-019-0729-8\">10.1038/s41567-019-0729-8</a>.","ama":"Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. Skyrmion solids in monolayer graphene. <i>Nature Physics</i>. 2020;16(2):154-158. doi:<a href=\"https://doi.org/10.1038/s41567-019-0729-8\">10.1038/s41567-019-0729-8</a>","short":"H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, A.F. Young, Nature Physics 16 (2020) 154–158."},"date_updated":"2022-01-31T07:10:07Z","abstract":[{"lang":"eng","text":"Partially filled Landau levels host competing electronic orders. For example, electron solids may prevail close to integer filling of the Landau levels before giving way to fractional quantum Hall liquids at higher carrier density1,2. Here, we report the observation of an electron solid with non-collinear spin texture in monolayer graphene, consistent with solidification of skyrmions3—topological spin textures characterized by quantized electrical charge4,5. We probe the spin texture of the solids using a modified Corbino geometry that allows ferromagnetic magnons to be launched and detected6,7. We find that magnon transport is highly efficient when one Landau level is filled (ν=1), consistent with quantum Hall ferromagnetic spin polarization. However, even minimal doping immediately quenches the magnon signal while leaving the vanishing low-temperature charge conductivity unchanged. Our results can be understood by the formation of a solid of charged skyrmions near ν=1, whose non-collinear spin texture leads to rapid magnon decay. Data near fractional fillings show evidence of several fractional skyrmion solids, suggesting that graphene hosts a highly tunable landscape of coupled spin and charge orders."}],"language":[{"iso":"eng"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":16,"type":"journal_article","page":"154-158","publisher":"Springer Nature","day":"01","extern":"1","_id":"10701","article_type":"original","title":"Skyrmion solids in monolayer graphene","quality_controlled":"1","oa_version":"Preprint","doi":"10.1038/s41567-019-0729-8","external_id":{"arxiv":["1904.11485"]},"acknowledgement":"We acknowledge discussions with B. Halperin, C. Huang, A. Macdonald and M. Zalatel. Experimental work at UCSB was supported by the Army Research Office under awards nos. MURI W911NF-16-1-0361 and W911NF-16-1-0482. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by MEXT (Japan) and CREST (JPMJCR15F3), JST. A.F.Y. acknowledges the support of the David and Lucile Packard Foundation and and Alfred. P. Sloan Foundation.","publication":"Nature Physics","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1904.11485","open_access":"1"}],"date_published":"2020-02-01T00:00:00Z","publication_status":"published","date_created":"2022-01-28T12:04:09Z","arxiv":1,"author":[{"full_name":"Zhou, Haoxin","last_name":"Zhou","first_name":"Haoxin"},{"orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy","last_name":"Polshyn"},{"full_name":"Taniguchi, Takashi","first_name":"Takashi","last_name":"Taniguchi"},{"full_name":"Watanabe, Kenji","first_name":"Kenji","last_name":"Watanabe"},{"last_name":"Young","first_name":"Andrea F.","full_name":"Young, Andrea F."}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"intvolume":"        16","year":"2020","status":"public","month":"02"},{"date_updated":"2024-10-09T20:58:18Z","language":[{"iso":"eng"}],"abstract":[{"text":"We introduce in this paper AMT2.0, a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended signal temporal logic, which integrates timed regular expressions within signal temporal logic. The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal. We demonstrate the tool functionality on several running examples and case studies, and evaluate its performance.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","volume":22,"keyword":["Information Systems","Software"],"issue":"6","citation":{"chicago":"Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10009-020-00582-z\">https://doi.org/10.1007/s10009-020-00582-z</a>.","ieee":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 22, no. 6. Springer Nature, pp. 741–758, 2020.","apa":"Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., &#38; Ulus, D. (2020). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10009-020-00582-z\">https://doi.org/10.1007/s10009-020-00582-z</a>","ista":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2020. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 22(6), 741–758.","mla":"Nickovic, Dejan, et al. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 22, no. 6, Springer Nature, 2020, pp. 741–58, doi:<a href=\"https://doi.org/10.1007/s10009-020-00582-z\">10.1007/s10009-020-00582-z</a>.","ama":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. <i>International Journal on Software Tools for Technology Transfer</i>. 2020;22(6):741-758. doi:<a href=\"https://doi.org/10.1007/s10009-020-00582-z\">10.1007/s10009-020-00582-z</a>","short":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, International Journal on Software Tools for Technology Transfer 22 (2020) 741–758."},"publisher":"Springer Nature","day":"03","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"299"}]},"article_type":"original","_id":"10861","page":"741-758","publication":"International Journal on Software Tools for Technology Transfer","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic","external_id":{"isi":["000555398600001"]},"doi":"10.1007/s10009-020-00582-z","oa_version":"None","date_created":"2022-03-18T10:10:53Z","isi":1,"publication_identifier":{"issn":["1433-2779"],"eissn":["1433-2787"]},"intvolume":"        22","author":[{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lebeltel","first_name":"Olivier","full_name":"Lebeltel, Olivier"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"first_name":"Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ulus, Dogan","first_name":"Dogan","last_name":"Ulus"}],"year":"2020","month":"08","status":"public","date_published":"2020-08-03T00:00:00Z","publication_status":"published","department":[{"_id":"ToHe"}]},{"_id":"10862","article_type":"original","publisher":"Elsevier","day":"15","type":"journal_article","volume":279,"keyword":["Analysis"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"We consider the sum of two large Hermitian matrices A and B with a Haar unitary conjugation bringing them into a general relative position. We prove that the eigenvalue density on the scale slightly above the local eigenvalue spacing is asymptotically given by the free additive convolution of the laws of A and B as the dimension of the matrix increases. This implies optimal rigidity of the eigenvalues and optimal rate of convergence in Voiculescu's theorem. Our previous works [4], [5] established these results in the bulk spectrum, the current paper completely settles the problem at the spectral edges provided they have the typical square-root behavior. The key element of our proof is to compensate the deterioration of the stability of the subordination equations by sharp error estimates that properly account for the local density near the edge. Our results also hold if the Haar unitary matrix is replaced by the Haar orthogonal matrix.","lang":"eng"}],"date_updated":"2025-04-15T08:05:01Z","citation":{"ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Spectral rigidity for addition of random matrices at the regular edge,” <i>Journal of Functional Analysis</i>, vol. 279, no. 7. Elsevier, 2020.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” <i>Journal of Functional Analysis</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jfa.2020.108639\">https://doi.org/10.1016/j.jfa.2020.108639</a>.","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2020). Spectral rigidity for addition of random matrices at the regular edge. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2020.108639\">https://doi.org/10.1016/j.jfa.2020.108639</a>","ista":"Bao Z, Erdös L, Schnelli K. 2020. Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. 279(7), 108639.","mla":"Bao, Zhigang, et al. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” <i>Journal of Functional Analysis</i>, vol. 279, no. 7, 108639, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jfa.2020.108639\">10.1016/j.jfa.2020.108639</a>.","ama":"Bao Z, Erdös L, Schnelli K. Spectral rigidity for addition of random matrices at the regular edge. <i>Journal of Functional Analysis</i>. 2020;279(7). doi:<a href=\"https://doi.org/10.1016/j.jfa.2020.108639\">10.1016/j.jfa.2020.108639</a>","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 279 (2020)."},"article_number":"108639","issue":"7","month":"10","status":"public","year":"2020","publication_identifier":{"issn":["0022-1236"]},"intvolume":"       279","author":[{"last_name":"Bao","first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475"},{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","first_name":"László","last_name":"Erdös"},{"full_name":"Schnelli, Kevin","first_name":"Kevin","last_name":"Schnelli"}],"arxiv":1,"date_created":"2022-03-18T10:18:59Z","isi":1,"department":[{"_id":"LaEr"}],"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1708.01597","open_access":"1"}],"date_published":"2020-10-15T00:00:00Z","ec_funded":1,"corr_author":"1","article_processing_charge":"No","publication":"Journal of Functional Analysis","acknowledgement":"Partially supported by ERC Advanced Grant RANMAT No. 338804.","doi":"10.1016/j.jfa.2020.108639","external_id":{"isi":["000559623200009"],"arxiv":["1708.01597"]},"oa_version":"Preprint","quality_controlled":"1","title":"Spectral rigidity for addition of random matrices at the regular edge","scopus_import":"1"},{"page":"5323-5329","_id":"10866","article_type":"original","day":"01","publisher":"American Chemical Society","citation":{"chicago":"Duan, Jiahua, Nathaniel Capote-Robayna, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Ivan Prieto Gonzalez, Javier Martín-Sánchez, Alexey Y. Nikitin, and Pablo Alonso-González. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">https://doi.org/10.1021/acs.nanolett.0c01673</a>.","ieee":"J. Duan <i>et al.</i>, “Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs,” <i>Nano Letters</i>, vol. 20, no. 7. American Chemical Society, pp. 5323–5329, 2020.","apa":"Duan, J., Capote-Robayna, N., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Prieto Gonzalez, I., Martín-Sánchez, J., … Alonso-González, P. (2020). Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">https://doi.org/10.1021/acs.nanolett.0c01673</a>","ista":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, Álvarez-Pérez G, Prieto Gonzalez I, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2020. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 20(7), 5323–5329.","mla":"Duan, Jiahua, et al. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” <i>Nano Letters</i>, vol. 20, no. 7, American Chemical Society, 2020, pp. 5323–29, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">10.1021/acs.nanolett.0c01673</a>.","ama":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, et al. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. <i>Nano Letters</i>. 2020;20(7):5323-5329. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">10.1021/acs.nanolett.0c01673</a>","short":"J. Duan, N. Capote-Robayna, J. Taboada-Gutiérrez, G. Álvarez-Pérez, I. Prieto Gonzalez, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Nano Letters 20 (2020) 5323–5329."},"issue":"7","volume":20,"type":"journal_article","keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"Recent discoveries have shown that, when two layers of van der Waals (vdW) materials are superimposed with a relative twist angle between them, the electronic properties of the coupled system can be dramatically altered. Here, we demonstrate that a similar concept can be extended to the optics realm, particularly to propagating phonon polaritons–hybrid light-matter interactions. To do this, we fabricate stacks composed of two twisted slabs of a vdW crystal (α-MoO3) supporting anisotropic phonon polaritons (PhPs), and image the propagation of the latter when launched by localized sources. Our images reveal that, under a critical angle, the PhPs isofrequency curve undergoes a topological transition, in which the propagation of PhPs is strongly guided (canalization regime) along predetermined directions without geometric spreading. These results demonstrate a new degree of freedom (twist angle) for controlling the propagation of polaritons at the nanoscale with potential for nanoimaging, (bio)-sensing, or heat management.","lang":"eng"}],"date_updated":"2023-09-05T12:05:58Z","department":[{"_id":"NanoFab"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.14599"}],"date_published":"2020-07-01T00:00:00Z","month":"07","status":"public","year":"2020","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"intvolume":"        20","author":[{"last_name":"Duan","first_name":"Jiahua","full_name":"Duan, Jiahua"},{"full_name":"Capote-Robayna, Nathaniel","first_name":"Nathaniel","last_name":"Capote-Robayna"},{"full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier","last_name":"Taboada-Gutiérrez"},{"full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo","last_name":"Álvarez-Pérez"},{"orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Prieto Gonzalez, Ivan","first_name":"Ivan","last_name":"Prieto Gonzalez"},{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"full_name":"Nikitin, Alexey Y.","last_name":"Nikitin","first_name":"Alexey Y."},{"last_name":"Alonso-González","first_name":"Pablo","full_name":"Alonso-González, Pablo"}],"arxiv":1,"date_created":"2022-03-18T11:37:38Z","isi":1,"external_id":{"arxiv":["2004.14599"],"isi":["000548893200082"],"pmid":["32530634"]},"doi":"10.1021/acs.nanolett.0c01673","oa_version":"Preprint","quality_controlled":"1","title":"Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs","scopus_import":"1","article_processing_charge":"No","pmid":1,"publication":"Nano Letters","acknowledgement":"J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the\r\nGovernment of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA20-PF-BP19-053,\r\nrespectively). J. M-S acknowledges financial support through the Ramón y Cajal Program from\r\nthe Government of Spain (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of\r\nScience, Innovation and Universities (national project no. MAT201788358-C3-3-R). P.A.-G.\r\nacknowledges support from the European Research Council under starting grant no. 715496,\r\n2DNANOPTICA."},{"article_processing_charge":"No","acknowledgement":" Supported by the Russian Foundation for Basic Research grant 18-01-00036.","publication":"International Mathematics Research Notices","external_id":{"isi":["000522852700002"],"arxiv":["1702.07513"]},"oa_version":"Preprint","doi":"10.1093/imrn/rny037","scopus_import":"1","quality_controlled":"1","title":"Waist of balls in hyperbolic and spherical spaces","year":"2020","month":"02","status":"public","arxiv":1,"date_created":"2022-03-18T11:39:30Z","isi":1,"publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"intvolume":"      2020","author":[{"first_name":"Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"full_name":"Karasev, Roman","last_name":"Karasev","first_name":"Roman"}],"publication_status":"published","department":[{"_id":"HeEd"}],"date_published":"2020-02-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.07513"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":2020,"type":"journal_article","keyword":["General Mathematics"],"date_updated":"2023-08-24T14:19:55Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In this paper we find a tight estimate for Gromov’s waist of the balls in spaces of constant curvature, deduce the estimates for the balls in Riemannian manifolds with upper bounds on the curvature (CAT(ϰ)-spaces), and establish similar result for normed spaces."}],"citation":{"ieee":"A. Akopyan and R. Karasev, “Waist of balls in hyperbolic and spherical spaces,” <i>International Mathematics Research Notices</i>, vol. 2020, no. 3. Oxford University Press, pp. 669–697, 2020.","chicago":"Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/imrn/rny037\">https://doi.org/10.1093/imrn/rny037</a>.","apa":"Akopyan, A., &#38; Karasev, R. (2020). Waist of balls in hyperbolic and spherical spaces. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rny037\">https://doi.org/10.1093/imrn/rny037</a>","ista":"Akopyan A, Karasev R. 2020. Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. 2020(3), 669–697.","mla":"Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” <i>International Mathematics Research Notices</i>, vol. 2020, no. 3, Oxford University Press, 2020, pp. 669–97, doi:<a href=\"https://doi.org/10.1093/imrn/rny037\">10.1093/imrn/rny037</a>.","ama":"Akopyan A, Karasev R. Waist of balls in hyperbolic and spherical spaces. <i>International Mathematics Research Notices</i>. 2020;2020(3):669-697. doi:<a href=\"https://doi.org/10.1093/imrn/rny037\">10.1093/imrn/rny037</a>","short":"A. Akopyan, R. Karasev, International Mathematics Research Notices 2020 (2020) 669–697."},"issue":"3","article_type":"original","_id":"10867","day":"01","publisher":"Oxford University Press","page":"669-697"},{"status":"public","month":"06","year":"2020","author":[{"full_name":"Cho, Ukrae H.","first_name":"Ukrae H.","last_name":"Cho"},{"full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W"}],"intvolume":"       106","publication_identifier":{"issn":["0896-6273"]},"date_created":"2022-04-07T07:43:36Z","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2020.05.031","open_access":"1"}],"date_published":"2020-06-17T00:00:00Z","article_processing_charge":"No","pmid":1,"publication":"Neuron","doi":"10.1016/j.neuron.2020.05.031","oa_version":"Published Version","external_id":{"pmid":["32553207"]},"title":"Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging","quality_controlled":"1","scopus_import":"1","article_type":"review","_id":"11054","extern":"1","publisher":"Elsevier","day":"17","page":"899-911","keyword":["General Neuroscience"],"volume":106,"type":"journal_article","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"In recent years, the nuclear pore complex (NPC) has emerged as a key player in genome regulation and cellular homeostasis. New discoveries have revealed that the NPC has multiple cellular functions besides mediating the molecular exchange between the nucleus and the cytoplasm. In this review, we discuss non-transport aspects of the NPC focusing on the NPC-genome interaction, the extreme longevity of the NPC proteins, and NPC dysfunction in age-related diseases. The examples summarized herein demonstrate that the NPC, which first evolved to enable the biochemical communication between the nucleus and the cytoplasm, now doubles as the gatekeeper of cellular identity and aging."}],"language":[{"iso":"eng"}],"date_updated":"2024-10-14T11:15:26Z","citation":{"ama":"Cho UH, Hetzer M. Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. <i>Neuron</i>. 2020;106(6):899-911. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.05.031\">10.1016/j.neuron.2020.05.031</a>","short":"U.H. Cho, M. Hetzer, Neuron 106 (2020) 899–911.","mla":"Cho, Ukrae H., and Martin Hetzer. “Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging.” <i>Neuron</i>, vol. 106, no. 6, Elsevier, 2020, pp. 899–911, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.05.031\">10.1016/j.neuron.2020.05.031</a>.","ista":"Cho UH, Hetzer M. 2020. Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. Neuron. 106(6), 899–911.","ieee":"U. H. Cho and M. Hetzer, “Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging,” <i>Neuron</i>, vol. 106, no. 6. Elsevier, pp. 899–911, 2020.","chicago":"Cho, Ukrae H., and Martin Hetzer. “Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.05.031\">https://doi.org/10.1016/j.neuron.2020.05.031</a>.","apa":"Cho, U. H., &#38; Hetzer, M. (2020). Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.05.031\">https://doi.org/10.1016/j.neuron.2020.05.031</a>"},"issue":"6"},{"publication_status":"published","date_published":"2020-09-08T00:00:00Z","year":"2020","month":"09","status":"public","date_created":"2022-04-07T07:43:48Z","publication_identifier":{"issn":["2050-084X"]},"intvolume":"         9","author":[{"full_name":"Bersini, Simone","last_name":"Bersini","first_name":"Simone"},{"full_name":"Schulte, Roberta","first_name":"Roberta","last_name":"Schulte"},{"full_name":"Huang, Ling","last_name":"Huang","first_name":"Ling"},{"full_name":"Tsai, Hannah","last_name":"Tsai","first_name":"Hannah"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W"}],"file":[{"relation":"main_file","checksum":"f8b3821349a194050be02570d8fe7d4b","success":1,"file_size":4399825,"file_id":"11132","content_type":"application/pdf","creator":"dernst","date_updated":"2022-04-08T06:53:10Z","date_created":"2022-04-08T06:53:10Z","access_level":"open_access","file_name":"2020_eLife_Bersini.pdf"}],"ddc":["570"],"external_id":{"pmid":["32896271"]},"doi":"10.7554/elife.54383","oa_version":"Published Version","file_date_updated":"2022-04-08T06:53:10Z","scopus_import":"1","quality_controlled":"1","title":"Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome","article_processing_charge":"No","publication":"eLife","pmid":1,"_id":"11055","article_type":"original","day":"08","publisher":"eLife Sciences Publications","extern":"1","citation":{"mla":"Bersini, Simone, et al. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>, vol. 9, e54383, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>.","ama":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>","short":"S. Bersini, R. Schulte, L. Huang, H. Tsai, M. Hetzer, ELife 9 (2020).","chicago":"Bersini, Simone, Roberta Schulte, Ling Huang, Hannah Tsai, and Martin Hetzer. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>.","ieee":"S. Bersini, R. Schulte, L. Huang, H. Tsai, and M. Hetzer, “Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","apa":"Bersini, S., Schulte, R., Huang, L., Tsai, H., &#38; Hetzer, M. (2020). Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>","ista":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. 2020. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. eLife. 9, e54383."},"article_number":"e54383","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":9,"type":"journal_article","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"date_updated":"2024-10-14T11:17:02Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Vascular dysfunctions are a common feature of multiple age-related diseases. However, modeling healthy and pathological aging of the human vasculature represents an unresolved experimental challenge. Here, we generated induced vascular endothelial cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial junction stability, as vascular aging markers. A functional assay performed on PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which plays a key role in both vascular calcification and endothelial barrier damage observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered the functionality of the vascular barrier in vitro, hence representing a potential future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These results show that iVECs and iSMCs retain disease-related signatures, allowing modeling of vascular aging and HGPS in vitro."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":4,"type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology","Biomedical Engineering","Biomaterials"],"date_updated":"2024-10-14T11:18:07Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Aging of the circulatory system correlates with the pathogenesis of a large spectrum of diseases. However, it is largely unknown which factors drive the age-dependent or pathological decline of the vasculature and how vascular defects relate to tissue aging. The goal of the study is to design a multianalytical approach to identify how the cellular microenvironment (i.e., fibroblasts) and serum from healthy donors of different ages or Alzheimer disease (AD) patients can modulate the functionality of organ-specific vascular endothelial cells (VECs). Long-living human microvascular networks embedding VECs and fibroblasts from skin biopsies are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate that fibroblasts from young donors restore the functionality of aged endothelial cells, an effect also achieved by serum from young donors. New biomarkers of vascular aging are validated in human biopsies and it is shown that young serum induces angiopoietin-like-4, which can restore compromised vascular barriers. This strategy is then employed to characterize transcriptional/functional changes induced on the blood–brain barrier by AD serum, demonstrating the importance of PTP4A3 in the regulation of permeability. Features of vascular degeneration during aging and AD are recapitulated, and a tool to identify novel biomarkers that can be exploited to develop future therapeutics modulating vascular function is established."}],"citation":{"ista":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. 2020. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. Advanced Biosystems. 4(5), 2000044.","ieee":"S. Bersini, R. Arrojo e Drigo, L. Huang, M. N. Shokhirev, and M. Hetzer, “Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease,” <i>Advanced Biosystems</i>, vol. 4, no. 5. Wiley, 2020.","chicago":"Bersini, Simone, Rafael Arrojo e Drigo, Ling Huang, Maxim N. Shokhirev, and Martin Hetzer. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” <i>Advanced Biosystems</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/adbi.202000044\">https://doi.org/10.1002/adbi.202000044</a>.","apa":"Bersini, S., Arrojo e Drigo, R., Huang, L., Shokhirev, M. N., &#38; Hetzer, M. (2020). Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. <i>Advanced Biosystems</i>. Wiley. <a href=\"https://doi.org/10.1002/adbi.202000044\">https://doi.org/10.1002/adbi.202000044</a>","ama":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. <i>Advanced Biosystems</i>. 2020;4(5). doi:<a href=\"https://doi.org/10.1002/adbi.202000044\">10.1002/adbi.202000044</a>","short":"S. Bersini, R. Arrojo e Drigo, L. Huang, M.N. Shokhirev, M. Hetzer, Advanced Biosystems 4 (2020).","mla":"Bersini, Simone, et al. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” <i>Advanced Biosystems</i>, vol. 4, no. 5, 2000044, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/adbi.202000044\">10.1002/adbi.202000044</a>."},"article_number":"2000044","issue":"5","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"article_type":"original","_id":"11056","publisher":"Wiley","day":"01","extern":"1","article_processing_charge":"No","publication":"Advanced Biosystems","pmid":1,"file":[{"creator":"dernst","file_id":"11134","content_type":"application/pdf","success":1,"checksum":"5584d9a1609812dc75c02ce1e35d2ec0","file_size":2490829,"access_level":"open_access","file_name":"2020_AdvancedBiosystems_Bersini.pdf","date_created":"2022-04-08T07:06:05Z","date_updated":"2022-04-08T07:06:05Z","relation":"main_file"}],"ddc":["570"],"doi":"10.1002/adbi.202000044","oa_version":"Published Version","external_id":{"pmid":["32402127"]},"file_date_updated":"2022-04-08T07:06:05Z","scopus_import":"1","quality_controlled":"1","title":"Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease","year":"2020","month":"05","status":"public","date_created":"2022-04-07T07:43:57Z","publication_identifier":{"issn":["2366-7478","2366-7478"]},"intvolume":"         4","author":[{"full_name":"Bersini, Simone","first_name":"Simone","last_name":"Bersini"},{"first_name":"Rafael","last_name":"Arrojo e Drigo","full_name":"Arrojo e Drigo, Rafael"},{"full_name":"Huang, Ling","first_name":"Ling","last_name":"Huang"},{"full_name":"Shokhirev, Maxim N.","first_name":"Maxim N.","last_name":"Shokhirev"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W"}],"publication_status":"published","date_published":"2020-05-01T00:00:00Z"},{"author":[{"full_name":"Kang, Hyeseon","last_name":"Kang","first_name":"Hyeseon"},{"full_name":"Shokhirev, Maxim N.","first_name":"Maxim N.","last_name":"Shokhirev"},{"full_name":"Xu, Zhichao","first_name":"Zhichao","last_name":"Xu"},{"last_name":"Chandran","first_name":"Sahaana","full_name":"Chandran, Sahaana"},{"full_name":"Dixon, Jesse R.","last_name":"Dixon","first_name":"Jesse R."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W"}],"publication_identifier":{"issn":["0890-9369","1549-5477"]},"intvolume":"        34","date_created":"2022-04-07T07:44:09Z","status":"public","month":"04","year":"2020","date_published":"2020-04-28T00:00:00Z","publication_status":"published","publication":"Genes & Development","pmid":1,"article_processing_charge":"No","title":"Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation","quality_controlled":"1","scopus_import":"1","doi":"10.1101/gad.335794.119","external_id":{"pmid":["32499403"]},"file_date_updated":"2022-04-08T07:12:33Z","oa_version":"Published Version","ddc":["570"],"file":[{"access_level":"open_access","file_name":"2020_GenesDevelopment_Kang.pdf","date_updated":"2022-04-08T07:12:33Z","date_created":"2022-04-08T07:12:33Z","file_id":"11136","content_type":"application/pdf","creator":"dernst","success":1,"checksum":"84e92d40e67936c739628315c238daf9","file_size":4406772,"relation":"main_file"}],"extern":"1","publisher":"Cold Spring Harbor Laboratory Press","day":"28","article_type":"original","_id":"11057","page":"913-930","abstract":[{"lang":"eng","text":"During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division."}],"language":[{"iso":"eng"}],"date_updated":"2024-10-14T11:18:25Z","keyword":["Developmental Biology","Genetics"],"volume":34,"type":"journal_article","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"13-14","citation":{"ista":"Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. 2020. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes &#38; Development. 34(13–14), 913–930.","chicago":"Kang, Hyeseon, Maxim N. Shokhirev, Zhichao Xu, Sahaana Chandran, Jesse R. Dixon, and Martin Hetzer. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory Press, 2020. <a href=\"https://doi.org/10.1101/gad.335794.119\">https://doi.org/10.1101/gad.335794.119</a>.","ieee":"H. Kang, M. N. Shokhirev, Z. Xu, S. Chandran, J. R. Dixon, and M. Hetzer, “Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation,” <i>Genes &#38; Development</i>, vol. 34, no. 13–14. Cold Spring Harbor Laboratory Press, pp. 913–930, 2020.","apa":"Kang, H., Shokhirev, M. N., Xu, Z., Chandran, S., Dixon, J. R., &#38; Hetzer, M. (2020). Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.335794.119\">https://doi.org/10.1101/gad.335794.119</a>","ama":"Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. <i>Genes &#38; Development</i>. 2020;34(13-14):913-930. doi:<a href=\"https://doi.org/10.1101/gad.335794.119\">10.1101/gad.335794.119</a>","short":"H. Kang, M.N. Shokhirev, Z. Xu, S. Chandran, J.R. Dixon, M. Hetzer, Genes &#38; Development 34 (2020) 913–930.","mla":"Kang, Hyeseon, et al. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” <i>Genes &#38; Development</i>, vol. 34, no. 13–14, Cold Spring Harbor Laboratory Press, 2020, pp. 913–30, doi:<a href=\"https://doi.org/10.1101/gad.335794.119\">10.1101/gad.335794.119</a>."}},{"citation":{"apa":"Bersini, S., Lytle, N. K., Schulte, R., Huang, L., Wahl, G. M., &#38; Hetzer, M. (2020). Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.201900623\">https://doi.org/10.26508/lsa.201900623</a>","chicago":"Bersini, Simone, Nikki K Lytle, Roberta Schulte, Ling Huang, Geoffrey M Wahl, and Martin Hetzer. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” <i>Life Science Alliance</i>. Life Science Alliance, 2020. <a href=\"https://doi.org/10.26508/lsa.201900623\">https://doi.org/10.26508/lsa.201900623</a>.","ieee":"S. Bersini, N. K. Lytle, R. Schulte, L. Huang, G. M. Wahl, and M. Hetzer, “Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling,” <i>Life Science Alliance</i>, vol. 3, no. 1. Life Science Alliance, 2020.","ista":"Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. 2020. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Science Alliance. 3(1), e201900623.","mla":"Bersini, Simone, et al. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” <i>Life Science Alliance</i>, vol. 3, no. 1, e201900623, Life Science Alliance, 2020, doi:<a href=\"https://doi.org/10.26508/lsa.201900623\">10.26508/lsa.201900623</a>.","short":"S. Bersini, N.K. Lytle, R. Schulte, L. Huang, G.M. Wahl, M. Hetzer, Life Science Alliance 3 (2020).","ama":"Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. <i>Life Science Alliance</i>. 2020;3(1). doi:<a href=\"https://doi.org/10.26508/lsa.201900623\">10.26508/lsa.201900623</a>"},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","article_number":"e201900623","issue":"1","volume":3,"type":"journal_article","keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"Nucleoporin 93 (Nup93) expression inversely correlates with the survival of triple-negative breast cancer patients. However, our knowledge of Nup93 function in breast cancer besides its role as structural component of the nuclear pore complex is not understood. Combination of functional assays and genetic analyses suggested that chromatin interaction of Nup93 partially modulates the expression of genes associated with actin cytoskeleton remodeling and epithelial to mesenchymal transition, resulting in impaired invasion of triple-negative, claudin-low breast cancer cells. Nup93 depletion induced stress fiber formation associated with reduced cell migration/proliferation and impaired expression of mesenchymal-like genes. Silencing LIMCH1, a gene responsible for actin cytoskeleton remodeling and up-regulated upon Nup93 depletion, partially restored the invasive phenotype of cancer cells. Loss of Nup93 led to significant defects in tumor establishment/propagation in vivo, whereas patient samples revealed that high Nup93 and low LIMCH1 expression correlate with late tumor stage. Our approach identified Nup93 as contributor of triple-negative, claudin-low breast cancer cell invasion and paves the way to study the role of nuclear envelope proteins during breast cancer tumorigenesis.","lang":"eng"}],"date_updated":"2024-10-14T11:18:41Z","_id":"11058","article_type":"original","extern":"1","publisher":"Life Science Alliance","day":"01","ddc":["570"],"file_date_updated":"2022-04-08T07:33:01Z","external_id":{"pmid":["31959624"]},"oa_version":"Published Version","doi":"10.26508/lsa.201900623","file":[{"file_size":2653960,"success":1,"checksum":"3bf33e7e93bef7823287807206b69b38","file_id":"11137","creator":"dernst","content_type":"application/pdf","date_updated":"2022-04-08T07:33:01Z","date_created":"2022-04-08T07:33:01Z","file_name":"2020_LifeScienceAlliance_Bersini.pdf","access_level":"open_access","relation":"main_file"}],"quality_controlled":"1","title":"Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling","scopus_import":"1","article_processing_charge":"No","pmid":1,"publication":"Life Science Alliance","publication_status":"published","date_published":"2020-01-01T00:00:00Z","month":"01","status":"public","year":"2020","intvolume":"         3","publication_identifier":{"issn":["2575-1077"]},"author":[{"full_name":"Bersini, Simone","first_name":"Simone","last_name":"Bersini"},{"first_name":"Nikki K","last_name":"Lytle","full_name":"Lytle, Nikki K"},{"full_name":"Schulte, Roberta","last_name":"Schulte","first_name":"Roberta"},{"last_name":"Huang","first_name":"Ling","full_name":"Huang, Ling"},{"last_name":"Wahl","first_name":"Geoffrey M","full_name":"Wahl, Geoffrey M"},{"first_name":"Martin W","last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"date_created":"2022-04-07T07:44:18Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","article_processing_charge":"No","date_updated":"2023-10-18T08:32:34Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We discus noise channels in coherent electro-optic up-conversion between microwave and optical fields, in particular due to optical heating. We also report on a novel configuration, which promises to be flexible and highly efficient."}],"publication":"OSA Quantum 2.0 Conference","oa_version":"None","citation":{"mla":"Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” <i>OSA Quantum 2.0 Conference</i>, QTu8A.1, Optica Publishing Group, 2020, doi:<a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">10.1364/QUANTUM.2020.QTu8A.1</a>.","ama":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise channels in electro-optic microwave to optical up-conversion. In: <i>OSA Quantum 2.0 Conference</i>. Optica Publishing Group; 2020. doi:<a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">10.1364/QUANTUM.2020.QTu8A.1</a>","short":"N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA Quantum 2.0 Conference, Optica Publishing Group, 2020.","ieee":"N. J. Lambert, S. Mobassem, A. R. Rueda Sanchez, and H. G. L. Schwefel, “New designs and noise channels in electro-optic microwave to optical up-conversion,” in <i>OSA Quantum 2.0 Conference</i>, Washington, DC, United States, 2020.","chicago":"Lambert, Nicholas J., Sonia Mobassem, Alfredo R Rueda Sanchez, and Harald G.L. Schwefel. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” In <i>OSA Quantum 2.0 Conference</i>. Optica Publishing Group, 2020. <a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">https://doi.org/10.1364/QUANTUM.2020.QTu8A.1</a>.","apa":"Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., &#38; Schwefel, H. G. L. (2020). New designs and noise channels in electro-optic microwave to optical up-conversion. In <i>OSA Quantum 2.0 Conference</i>. Washington, DC, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">https://doi.org/10.1364/QUANTUM.2020.QTu8A.1</a>","ista":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. 2020. New designs and noise channels in electro-optic microwave to optical up-conversion. OSA Quantum 2.0 Conference. OSA: Optical Society of America, OSA Technical Digest, , QTu8A.1."},"doi":"10.1364/QUANTUM.2020.QTu8A.1","article_number":"QTu8A.1","alternative_title":["OSA Technical Digest"],"conference":{"start_date":"2020-09-14","location":"Washington, DC, United States","name":"OSA: Optical Society of America","end_date":"2020-09-17"},"scopus_import":"1","quality_controlled":"1","title":"New designs and noise channels in electro-optic microwave to optical up-conversion","year":"2020","month":"01","_id":"10328","status":"public","day":"01","publisher":"Optica Publishing Group","date_created":"2021-11-21T23:01:31Z","publication_identifier":{"isbn":["9-781-5575-2820-9"]},"author":[{"first_name":"Nicholas J.","last_name":"Lambert","full_name":"Lambert, Nicholas J."},{"full_name":"Mobassem, Sonia","last_name":"Mobassem","first_name":"Sonia"},{"orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","last_name":"Rueda Sanchez"},{"full_name":"Schwefel, Harald G.L.","first_name":"Harald G.L.","last_name":"Schwefel"}],"publication_status":"published","department":[{"_id":"JoFi"}],"date_published":"2020-01-01T00:00:00Z"},{"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2"}],"date_published":"2020-12-16T00:00:00Z","month":"12","status":"public","year":"2020","intvolume":"       117","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"author":[{"first_name":"Johannes","last_name":"Krausser","full_name":"Krausser, Johannes"},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."},{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"}],"date_created":"2021-11-25T15:07:09Z","doi":"10.1073/pnas.2007694117","oa_version":"Published Version","external_id":{"pmid":["33328273"]},"quality_controlled":"1","title":"Physical mechanisms of amyloid nucleation on fluid membranes","scopus_import":"1","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","pmid":1,"acknowledgement":"We thank T. C. T. Michaels for reading the manuscript. This work was supported by the Academy of Medical Science (J.K. and A.Š.), the Cambridge Center for Misfolding Diseases (T.P.J.K.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council Grant PhysProt Agreement 337969, the Wellcome Trust (A.Š. and T.P.J.K.), the Royal Society (A.Š.), the Medical Research Council (J.K. and A.Š.), and the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by Engineering and Physical Sciences Research Council Grant EP/P020194/1.","page":"33090-33098","_id":"10336","article_type":"original","extern":"1","publisher":"National Academy of Sciences","day":"16","citation":{"chicago":"Krausser, Johannes, Tuomas P. J. Knowles, and Anđela Šarić. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2007694117\">https://doi.org/10.1073/pnas.2007694117</a>.","ieee":"J. Krausser, T. P. J. Knowles, and A. Šarić, “Physical mechanisms of amyloid nucleation on fluid membranes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 52. National Academy of Sciences, pp. 33090–33098, 2020.","apa":"Krausser, J., Knowles, T. P. J., &#38; Šarić, A. (2020). Physical mechanisms of amyloid nucleation on fluid membranes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2007694117\">https://doi.org/10.1073/pnas.2007694117</a>","ista":"Krausser J, Knowles TPJ, Šarić A. 2020. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 117(52), 33090–33098.","mla":"Krausser, Johannes, et al. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 52, National Academy of Sciences, 2020, pp. 33090–98, doi:<a href=\"https://doi.org/10.1073/pnas.2007694117\">10.1073/pnas.2007694117</a>.","ama":"Krausser J, Knowles TPJ, Šarić A. Physical mechanisms of amyloid nucleation on fluid membranes. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(52):33090-33098. doi:<a href=\"https://doi.org/10.1073/pnas.2007694117\">10.1073/pnas.2007694117</a>","short":"J. Krausser, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences 117 (2020) 33090–33098."},"issue":"52","volume":117,"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein–membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways—protein-rich and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity control the relative importance of those molecular pathways. We find that the membrane’s susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson’s disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context.","lang":"eng"}],"date_updated":"2021-11-25T15:35:58Z"},{"article_type":"original","_id":"10341","extern":"1","publisher":"Royal Society of Chemistry","day":"06","page":"10628-10639","OA_type":"hybrid","keyword":["condensed matter physics","general chemistry"],"volume":16,"type":"journal_article","oa":1,"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","abstract":[{"text":"Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2024-10-16T12:53:17Z","citation":{"mla":"Debets, V. E., et al. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” <i>Soft Matter</i>, vol. 16, no. 47, Royal Society of Chemistry, 2020, pp. 10628–39, doi:<a href=\"https://doi.org/10.1039/d0sm00712a\">10.1039/d0sm00712a</a>.","short":"V.E. Debets, L.M.C. Janssen, A. Šarić, Soft Matter 16 (2020) 10628–10639.","ama":"Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. <i>Soft Matter</i>. 2020;16(47):10628-10639. doi:<a href=\"https://doi.org/10.1039/d0sm00712a\">10.1039/d0sm00712a</a>","apa":"Debets, V. E., Janssen, L. M. C., &#38; Šarić, A. (2020). Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0sm00712a\">https://doi.org/10.1039/d0sm00712a</a>","ieee":"V. E. Debets, L. M. C. Janssen, and A. Šarić, “Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes,” <i>Soft Matter</i>, vol. 16, no. 47. Royal Society of Chemistry, pp. 10628–10639, 2020.","chicago":"Debets, V. E., L. M. C. Janssen, and Anđela Šarić. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/d0sm00712a\">https://doi.org/10.1039/d0sm00712a</a>.","ista":"Debets VE, Janssen LMC, Šarić A. 2020. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 16(47), 10628–10639."},"issue":"47","status":"public","month":"10","year":"2020","author":[{"full_name":"Debets, V. E.","last_name":"Debets","first_name":"V. E."},{"full_name":"Janssen, L. M. C.","last_name":"Janssen","first_name":"L. M. C."},{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"}],"intvolume":"        16","publication_identifier":{"issn":["1744-683X","1744-6848"]},"date_created":"2021-11-26T06:29:41Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.01.071761v1"}],"date_published":"2020-10-06T00:00:00Z","article_processing_charge":"No","pmid":1,"publication":"Soft Matter","acknowledgement":"We thank Jessica McQuade for her input at the start of the project. We acknowledge support from the ERASMUS Placement Programme (V. E. D.), the UCL Institute for the Physics of Living Systems (V. E. D. and A. Š.), the UCL Global Engagement Fund (L. M. C. J.), and the Royal Society (A. Š.).","oa_version":"Published Version","doi":"10.1039/d0sm00712a","external_id":{"pmid":["33084724"]},"OA_place":"publisher","title":"Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes","quality_controlled":"1","scopus_import":"1"},{"date_updated":"2024-10-16T12:56:52Z","abstract":[{"lang":"eng","text":"The blood-brain barrier is made of polarized brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Although transport across BECs is of paramount importance for nutrient uptake as well as ridding the brain of waste products, the intracellular sorting mechanisms that regulate successful receptor-mediated transcytosis in BECs remain to be elucidated. Here, we used a synthetic multivalent system with tunable avidity to the low-density lipoprotein receptor–related protein 1 (LRP1) to investigate the mechanisms of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modeling of transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting protein syndapin-2 on fast transport via tubule formation. We show that high-avidity cargo biases the LRP1 toward internalization associated with fast degradation, while mid-avidity augments the formation of syndapin-2 tubular carriers promoting a fast shuttling across."}],"language":[{"iso":"eng"}],"oa":1,"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","keyword":["multidisciplinary"],"type":"journal_article","volume":6,"issue":"48","article_number":"eabc4397 ","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","citation":{"short":"X. Tian, D.M. Leite, E. Scarpa, S. Nyberg, G. Fullstone, J. Forth, D. Matias, A. Apriceno, A. Poma, A. Duro-Castano, M. Vuyyuru, L. Harker-Kirschneck, A. Šarić, Z. Zhang, P. Xiang, B. Fang, Y. Tian, L. Luo, L. Rizzello, G. Battaglia, Science Advances 6 (2020).","ama":"Tian X, Leite DM, Scarpa E, et al. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. <i>Science Advances</i>. 2020;6(48). doi:<a href=\"https://doi.org/10.1126/sciadv.abc4397\">10.1126/sciadv.abc4397</a>","mla":"Tian, Xiaohe, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” <i>Science Advances</i>, vol. 6, no. 48, eabc4397, American Association for the Advancement of Science, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.abc4397\">10.1126/sciadv.abc4397</a>.","ista":"Tian X, Leite DM, Scarpa E, Nyberg S, Fullstone G, Forth J, Matias D, Apriceno A, Poma A, Duro-Castano A, Vuyyuru M, Harker-Kirschneck L, Šarić A, Zhang Z, Xiang P, Fang B, Tian Y, Luo L, Rizzello L, Battaglia G. 2020. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. 6(48), eabc4397.","apa":"Tian, X., Leite, D. M., Scarpa, E., Nyberg, S., Fullstone, G., Forth, J., … Battaglia, G. (2020). On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abc4397\">https://doi.org/10.1126/sciadv.abc4397</a>","ieee":"X. Tian <i>et al.</i>, “On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias,” <i>Science Advances</i>, vol. 6, no. 48. American Association for the Advancement of Science, 2020.","chicago":"Tian, Xiaohe, Diana M. Leite, Edoardo Scarpa, Sophie Nyberg, Gavin Fullstone, Joe Forth, Diana Matias, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” <i>Science Advances</i>. American Association for the Advancement of Science, 2020. <a href=\"https://doi.org/10.1126/sciadv.abc4397\">https://doi.org/10.1126/sciadv.abc4397</a>."},"day":"27","publisher":"American Association for the Advancement of Science","extern":"1","article_type":"original","_id":"10342","OA_type":"gold","DOAJ_listed":"1","acknowledgement":"Funding: G.B. thanks the ERC for the starting grant (MEViC 278793) and consolidator award (CheSSTaG 769798), EPSRC/BTG Healthcare Partnership (EP/I001697/1), EPSRC Established Career Fellowship (EP/N026322/1), EPSRC/SomaNautix Healthcare Partnership EP/R024723/1, and Children with Cancer UK for the research project (16-227). X.T. and G.B. thank that Anhui 100 Talent program for facilitating data sharing and research visits. A.D.-C. and L.R. acknowledge the Royal Society for a Newton fellowship and the Marie Skłodowska-Curie Actions for a European Fellowship. Author contributions: X.T. prepared and characterized POs, performed all the fast imaging in both conventional and STED microscopy, set up the initial BBB model, encapsulated the PtA2 in POs, and supervised the PtA2-PO animal work. D.M.L. prepared and characterized POs; performed all the permeability studies, PLA assays, WB and associated data analysis, and part of the colocalization assays; and performed experiments with the shRNA for knockdown of syndapin-2. E.S. prepared and characterized POs and performed part of colocalization assays and Cy7-labeled PO animal experiments. S.N. prepared and characterized POs and performed part of the colocalization and inhibition assays. G.F. designed, performed, and analyzed the agent-based simulations of transcytosis. J.F. designed the image-based algorithm to analyze the PLA data. D.M. prepared and characterized POs and helped with Cy7-labeled PO animal experiments. A.A. performed TEM imaging of the POs. A.P. and A.D.-C. synthesized the dye- and peptide-functionalized and pristine copolymers. M.V., L.H.-K., and A.Š. designed, performed, and analyzed the MD simulations. Z.Z. supervised and supported STED imaging. P.X., B.F., and Y.T. synthesized and characterized the PtA2 compound. L.L. performed some of the animal work. L.R. supported and helped with the BBB characterization. G.B. analyzed all fast imaging and supervised and coordinated the overall work. X.T., D.M.L., E.S., and G.B. wrote the manuscript. Competing interests: The authors declare that part of the work is associated with the UCL spin-out company SomaNautix Ltd. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.","pmid":1,"publication":"Science Advances","article_processing_charge":"No","scopus_import":"1","title":"On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias","quality_controlled":"1","file":[{"relation":"main_file","date_created":"2021-11-26T06:50:09Z","date_updated":"2021-11-26T06:50:09Z","file_name":"2020_SciAdv_Tian.pdf","access_level":"open_access","file_size":10381298,"success":1,"checksum":"3ba2eca975930cdb0b1ce1ae876885a7","file_id":"10343","creator":"cchlebak","content_type":"application/pdf"}],"OA_place":"publisher","doi":"10.1126/sciadv.abc4397","external_id":{"pmid":["33246953"]},"file_date_updated":"2021-11-26T06:50:09Z","oa_version":"Published Version","ddc":["611"],"date_created":"2021-11-26T06:40:28Z","author":[{"full_name":"Tian, Xiaohe","last_name":"Tian","first_name":"Xiaohe"},{"last_name":"Leite","first_name":"Diana M.","full_name":"Leite, Diana M."},{"first_name":"Edoardo","last_name":"Scarpa","full_name":"Scarpa, Edoardo"},{"last_name":"Nyberg","first_name":"Sophie","full_name":"Nyberg, Sophie"},{"last_name":"Fullstone","first_name":"Gavin","full_name":"Fullstone, Gavin"},{"full_name":"Forth, Joe","first_name":"Joe","last_name":"Forth"},{"first_name":"Diana","last_name":"Matias","full_name":"Matias, Diana"},{"last_name":"Apriceno","first_name":"Azzurra","full_name":"Apriceno, Azzurra"},{"full_name":"Poma, Alessandro","first_name":"Alessandro","last_name":"Poma"},{"first_name":"Aroa","last_name":"Duro-Castano","full_name":"Duro-Castano, Aroa"},{"last_name":"Vuyyuru","first_name":"Manish","full_name":"Vuyyuru, Manish"},{"last_name":"Harker-Kirschneck","first_name":"Lena","full_name":"Harker-Kirschneck, Lena"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Zhang","first_name":"Zhongping","full_name":"Zhang, Zhongping"},{"full_name":"Xiang, Pan","first_name":"Pan","last_name":"Xiang"},{"full_name":"Fang, Bin","first_name":"Bin","last_name":"Fang"},{"first_name":"Yupeng","last_name":"Tian","full_name":"Tian, Yupeng"},{"full_name":"Luo, Lei","last_name":"Luo","first_name":"Lei"},{"last_name":"Rizzello","first_name":"Loris","full_name":"Rizzello, Loris"},{"last_name":"Battaglia","first_name":"Giuseppe","full_name":"Battaglia, Giuseppe"}],"intvolume":"         6","publication_identifier":{"issn":["2375-2548"]},"year":"2020","status":"public","month":"11","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.04.04.025866v1","open_access":"1"}],"date_published":"2020-11-27T00:00:00Z","publication_status":"published"},{"year":"2020","month":"11","status":"public","date_created":"2021-11-26T07:10:43Z","intvolume":"       125","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"author":[{"first_name":"Joel C.","last_name":"Forster","full_name":"Forster, Joel C."},{"full_name":"Krausser, Johannes","first_name":"Johannes","last_name":"Krausser"},{"last_name":"Vuyyuru","first_name":"Manish R.","full_name":"Vuyyuru, Manish R."},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.02.27.968149v1"}],"date_published":"2020-11-23T00:00:00Z","article_processing_charge":"No","acknowledgement":"We acknowledge support from EPSRC (J. C. F.), MRC (B. B. and A. Š.), the ERC StG 802960 “NEPA” (J. K. and A. Š.), the Royal Society (A. Š.), and the United Kingdom Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC (EP/P020194/1).","pmid":1,"publication":"Physical Review Letters","file":[{"file_id":"10345","content_type":"application/pdf","creator":"cchlebak","success":1,"checksum":"fbf2e1415e332d6add90222d60401a1d","file_size":844353,"access_level":"open_access","file_name":"2020_PhysRevLett_Forster.pdf","date_created":"2021-11-26T07:16:49Z","date_updated":"2021-11-26T07:16:49Z","relation":"main_file"}],"OA_place":"publisher","ddc":["530"],"external_id":{"pmid":["33315453"]},"doi":"10.1103/physrevlett.125.228101","file_date_updated":"2021-11-26T07:16:49Z","oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","title":"Exploring the design rules for efficient membrane-reshaping nanostructures","article_type":"original","_id":"10344","day":"23","publisher":"American Physical Society","extern":"1","OA_type":"hybrid","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","oa":1,"type":"journal_article","volume":125,"date_updated":"2024-10-16T12:59:57Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In this study, we investigate the role of the surface patterning of nanostructures for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations and explore the solution space of ligand patterns on a nanoparticle that promote efficient and reliable cell uptake. Surprisingly, we find that in the regime of low ligand number the best-performing structures are characterized by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. Our approach reveals a set of nonintuitive design rules that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry."}],"citation":{"short":"J.C. Forster, J. Krausser, M.R. Vuyyuru, B. Baum, A. Šarić, Physical Review Letters 125 (2020).","ama":"Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. Exploring the design rules for efficient membrane-reshaping nanostructures. <i>Physical Review Letters</i>. 2020;125(22). doi:<a href=\"https://doi.org/10.1103/physrevlett.125.228101\">10.1103/physrevlett.125.228101</a>","mla":"Forster, Joel C., et al. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” <i>Physical Review Letters</i>, vol. 125, no. 22, 228101, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevlett.125.228101\">10.1103/physrevlett.125.228101</a>.","ista":"Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. 2020. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 125(22), 228101.","apa":"Forster, J. C., Krausser, J., Vuyyuru, M. R., Baum, B., &#38; Šarić, A. (2020). Exploring the design rules for efficient membrane-reshaping nanostructures. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.125.228101\">https://doi.org/10.1103/physrevlett.125.228101</a>","chicago":"Forster, Joel C., Johannes Krausser, Manish R. Vuyyuru, Buzz Baum, and Anđela Šarić. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevlett.125.228101\">https://doi.org/10.1103/physrevlett.125.228101</a>.","ieee":"J. C. Forster, J. Krausser, M. R. Vuyyuru, B. Baum, and A. Šarić, “Exploring the design rules for efficient membrane-reshaping nanostructures,” <i>Physical Review Letters</i>, vol. 125, no. 22. American Physical Society, 2020."},"article_number":"228101","issue":"22","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1"},{"status":"public","month":"09","year":"2020","author":[{"full_name":"Hafner, Anne E.","last_name":"Hafner","first_name":"Anne E."},{"full_name":"Gyori, Noemi G.","last_name":"Gyori","first_name":"Noemi G."},{"first_name":"Ciaran A.","last_name":"Bench","full_name":"Bench, Ciaran A."},{"full_name":"Davis, Luke K.","last_name":"Davis","first_name":"Luke K."},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"}],"intvolume":"       119","publication_identifier":{"issn":["0006-3495"]},"date_created":"2021-11-26T07:27:24Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.06.08.140061v1"}],"date_published":"2020-09-23T00:00:00Z","article_processing_charge":"No","pmid":1,"publication":"Biophysical Journal","acknowledgement":"We thank Melinda Duer, Patrick Mesquida, Lucy Colwell, Lucie Liu, Daan Frenkel, and Ivan Palaia for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.E.H., L.K.D., and A.Š.), Biotechnology and Biological Sciences Research Council LIDo programme (N.G.G. and C.A.B.), the Royal Society (A.Š.), and the UK Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC ( EP/P020194/1).","doi":"10.1016/j.bpj.2020.09.013","external_id":{"pmid":["33049216"]},"oa_version":"Published Version","OA_place":"publisher","title":"Modeling fibrillogenesis of collagen-mimetic molecules","quality_controlled":"1","scopus_import":"1","article_type":"original","_id":"10346","extern":"1","day":"23","publisher":"Cell Press","page":"1791-1799","OA_type":"hybrid","keyword":["biophysics"],"type":"journal_article","volume":119,"oa":1,"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","abstract":[{"text":"One of the most robust examples of self-assembly in living organisms is the formation of collagen architectures. Collagen type I molecules are a crucial component of the extracellular matrix, where they self-assemble into fibrils of well-defined axial striped patterns. This striped fibrillar pattern is preserved across the animal kingdom and is important for the determination of cell phenotype, cell adhesion, and tissue regulation and signaling. The understanding of the physical processes that determine such a robust morphology of self-assembled collagen fibrils is currently almost completely missing. Here, we develop a minimal coarse-grained computational model to identify the physical principles of the assembly of collagen-mimetic molecules. We find that screened electrostatic interactions can drive the formation of collagen-like filaments of well-defined striped morphologies. The fibril axial pattern is determined solely by the distribution of charges on the molecule and is robust to the changes in protein concentration, monomer rigidity, and environmental conditions. We show that the striped fibrillar pattern cannot be easily predicted from the interactions between two monomers but is an emergent result of multibody interactions. Our results can help address collagen remodeling in diseases and aging and guide the design of collagen scaffolds for biotechnological applications.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2024-10-16T13:05:34Z","citation":{"apa":"Hafner, A. E., Gyori, N. G., Bench, C. A., Davis, L. K., &#38; Šarić, A. (2020). Modeling fibrillogenesis of collagen-mimetic molecules. <i>Biophysical Journal</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">https://doi.org/10.1016/j.bpj.2020.09.013</a>","ieee":"A. E. Hafner, N. G. Gyori, C. A. Bench, L. K. Davis, and A. Šarić, “Modeling fibrillogenesis of collagen-mimetic molecules,” <i>Biophysical Journal</i>, vol. 119, no. 9. Cell Press, pp. 1791–1799, 2020.","chicago":"Hafner, Anne E., Noemi G. Gyori, Ciaran A. Bench, Luke K. Davis, and Anđela Šarić. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” <i>Biophysical Journal</i>. Cell Press, 2020. <a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">https://doi.org/10.1016/j.bpj.2020.09.013</a>.","ista":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. 2020. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 119(9), 1791–1799.","mla":"Hafner, Anne E., et al. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” <i>Biophysical Journal</i>, vol. 119, no. 9, Cell Press, 2020, pp. 1791–99, doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">10.1016/j.bpj.2020.09.013</a>.","short":"A.E. Hafner, N.G. Gyori, C.A. Bench, L.K. Davis, A. Šarić, Biophysical Journal 119 (2020) 1791–1799.","ama":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. Modeling fibrillogenesis of collagen-mimetic molecules. <i>Biophysical Journal</i>. 2020;119(9):1791-1799. doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">10.1016/j.bpj.2020.09.013</a>"},"issue":"9"},{"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["multidisciplinary"],"type":"journal_article","volume":117,"date_updated":"2021-11-26T08:59:06Z","abstract":[{"lang":"eng","text":"Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates, and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of amyloid-aggregation inhibition that reveals the fundamental thermodynamic and kinetic signatures characterizing effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimization of inhibitors of amyloid-fibril formation, revealing in particular the important role of on-rates in the binding of the inhibitors."}],"language":[{"iso":"eng"}],"citation":{"ieee":"T. C. T. Michaels <i>et al.</i>, “Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 39. National Academy of Sciences, pp. 24251–24257, 2020.","chicago":"Michaels, Thomas C. T., Anđela Šarić, Georg Meisl, Gabriella T. Heller, Samo Curk, Paolo Arosio, Sara Linse, Christopher M. Dobson, Michele Vendruscolo, and Tuomas P. J. Knowles. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2006684117\">https://doi.org/10.1073/pnas.2006684117</a>.","apa":"Michaels, T. C. T., Šarić, A., Meisl, G., Heller, G. T., Curk, S., Arosio, P., … Knowles, T. P. J. (2020). Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2006684117\">https://doi.org/10.1073/pnas.2006684117</a>","ista":"Michaels TCT, Šarić A, Meisl G, Heller GT, Curk S, Arosio P, Linse S, Dobson CM, Vendruscolo M, Knowles TPJ. 2020. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 117(39), 24251–24257.","mla":"Michaels, Thomas C. T., et al. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 39, National Academy of Sciences, 2020, pp. 24251–57, doi:<a href=\"https://doi.org/10.1073/pnas.2006684117\">10.1073/pnas.2006684117</a>.","ama":"Michaels TCT, Šarić A, Meisl G, et al. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(39):24251-24257. doi:<a href=\"https://doi.org/10.1073/pnas.2006684117\">10.1073/pnas.2006684117</a>","short":"T.C.T. Michaels, A. Šarić, G. Meisl, G.T. Heller, S. Curk, P. Arosio, S. Linse, C.M. Dobson, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences 117 (2020) 24251–24257."},"issue":"39","_id":"10347","article_type":"original","publisher":"National Academy of Sciences","day":"14","extern":"1","page":"24251-24257","article_processing_charge":"No","acknowledgement":"We acknowledge support from Peterhouse, Cambridge (T.C.T.M.); the Swiss National Science Foundation (T.C.T.M.); the Royal Society (A.S. and S.C.); the Academy of Medical Sciences (A.S.); Sidney Sussex College, Cambridge (G.M.); Newnham College, Cambridge (G.T.H.); the Wellcome Trust (T.P.J.K.); the Cambridge Center for Misfolding Diseases (T.P.J.K. and M.V.); the Biotechnology and Biological Sciences Research Council (T.P.J.K.); the Frances and Augustus Newman Foundation (T.P.J.K.); and the Synapsis Foundation for Alzheimer’s disease (P.A.). The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7/2007-2013) through the ERC Grant PhysProt (Agreement 337969).","pmid":1,"publication":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.2006684117","external_id":{"pmid":["32929030"]},"oa_version":"Published Version","scopus_import":"1","title":"Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors","quality_controlled":"1","year":"2020","status":"public","month":"09","date_created":"2021-11-26T07:48:27Z","author":[{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"full_name":"Heller, Gabriella T.","last_name":"Heller","first_name":"Gabriella T."},{"full_name":"Curk, Samo","first_name":"Samo","last_name":"Curk"},{"first_name":"Paolo","last_name":"Arosio","full_name":"Arosio, Paolo"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"first_name":"Christopher M.","last_name":"Dobson","full_name":"Dobson, Christopher M."},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"intvolume":"       117","publication_status":"published","date_published":"2020-09-14T00:00:00Z","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.22.960716","open_access":"1"}]},{"issue":"5","citation":{"short":"A.-K. Pfitzner, V. Mercier, X. Jiang, J. Moser von Filseck, B. Baum, A. Šarić, A. Roux, Cell 182 (2020) 1140–1155.e18.","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>","mla":"Pfitzner, Anna-Katharina, et al. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” <i>Cell</i>, vol. 182, no. 5, Elsevier, 2020, p. 1140–1155.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">10.1016/j.cell.2020.07.021</a>.","ista":"Pfitzner A-K, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux A. 2020. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 182(5), 1140–1155.e18.","apa":"Pfitzner, A.-K., Mercier, V., Jiang, X., Moser von Filseck, J., Baum, B., Šarić, A., &#38; Roux, A. (2020). An ESCRT-III polymerization sequence drives membrane deformation and fission. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">https://doi.org/10.1016/j.cell.2020.07.021</a>","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>."},"date_updated":"2021-11-26T08:58:37Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"type":"journal_article","volume":182,"keyword":["general biochemistry","genetics and molecular biology"],"page":"1140-1155.e18","publisher":"Elsevier","day":"18","extern":"1","article_type":"original","_id":"10348","scopus_import":"1","quality_controlled":"1","title":"An ESCRT-III polymerization sequence drives membrane deformation and fission","doi":"10.1016/j.cell.2020.07.021","external_id":{"pmid":["32814015"]},"oa_version":"Published Version","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]).","pmid":1,"publication":"Cell","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S0092867420309296"}],"date_published":"2020-08-18T00:00:00Z","publication_status":"published","date_created":"2021-11-26T08:02:27Z","publication_identifier":{"issn":["0092-8674"]},"intvolume":"       182","author":[{"full_name":"Pfitzner, Anna-Katharina","last_name":"Pfitzner","first_name":"Anna-Katharina"},{"first_name":"Vincent","last_name":"Mercier","full_name":"Mercier, Vincent"},{"full_name":"Jiang, Xiuyun","last_name":"Jiang","first_name":"Xiuyun"},{"full_name":"Moser von Filseck, Joachim","first_name":"Joachim","last_name":"Moser von Filseck"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Roux","first_name":"Aurélien","full_name":"Roux, Aurélien"}],"year":"2020","month":"08","status":"public"},{"year":"2020","month":"08","status":"public","date_created":"2021-11-26T08:21:34Z","intvolume":"       369","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"author":[{"first_name":"Gabriel","last_name":"Tarrason Risa","full_name":"Tarrason Risa, Gabriel"},{"last_name":"Hurtig","first_name":"Fredrik","full_name":"Hurtig, Fredrik"},{"last_name":"Bray","first_name":"Sian","full_name":"Bray, Sian"},{"last_name":"Hafner","first_name":"Anne E.","full_name":"Hafner, Anne E."},{"full_name":"Harker-Kirschneck, Lena","first_name":"Lena","last_name":"Harker-Kirschneck"},{"full_name":"Faull, Peter","last_name":"Faull","first_name":"Peter"},{"full_name":"Davis, Colin","first_name":"Colin","last_name":"Davis"},{"last_name":"Papatziamou","first_name":"Dimitra","full_name":"Papatziamou, Dimitra"},{"first_name":"Delyan R.","last_name":"Mutavchiev","full_name":"Mutavchiev, Delyan R."},{"last_name":"Fan","first_name":"Catherine","full_name":"Fan, Catherine"},{"last_name":"Meneguello","first_name":"Leticia","full_name":"Meneguello, Leticia"},{"full_name":"Arashiro Pulschen, Andre","last_name":"Arashiro Pulschen","first_name":"Andre"},{"first_name":"Gautam","last_name":"Dey","full_name":"Dey, Gautam"},{"first_name":"Siân","last_name":"Culley","full_name":"Culley, Siân"},{"last_name":"Kilkenny","first_name":"Mairi","full_name":"Kilkenny, Mairi"},{"full_name":"Souza, Diorge P.","first_name":"Diorge P.","last_name":"Souza"},{"first_name":"Luca","last_name":"Pellegrini","full_name":"Pellegrini, Luca"},{"full_name":"de Bruin, Robertus A. M.","last_name":"de Bruin","first_name":"Robertus A. M."},{"last_name":"Henriques","first_name":"Ricardo","full_name":"Henriques, Ricardo"},{"full_name":"Snijders, Ambrosius P.","last_name":"Snijders","first_name":"Ambrosius P."},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"},{"first_name":"Ann-Christin","last_name":"Lindås","full_name":"Lindås, Ann-Christin"},{"last_name":"Robinson","first_name":"Nicholas P.","full_name":"Robinson, Nicholas P."},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"}],"publication_status":"published","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/774273v1","open_access":"1"}],"date_published":"2020-08-07T00:00:00Z","article_processing_charge":"No","acknowledgement":"We thank the MRC LMCB at UCL for their support; the flow cytometry STP at the Francis Crick Institute for assistance, with special thanks to S. Purewal and D. Davis; C. Bertoli for mentorship\r\nand advice; J. M. Garcia-Arcos for help early on in this project; the entire Baum lab for their input throughout the project; the Albers lab for advice and reagents, with special thanks to M. Van Wolferen and S. Albers; the members of the Wellcome consortium for archaeal cytoskeleton studies for advice and comments; and J. Löwe, S. Oliferenko, M. Balasubramanian, and D. Gerlich for discussions and advice on the manuscript. N.P.R. and S.B. would like to thank N. Rzechorzek, A. Simon, and S. Anjum for discussion and advice.","pmid":1,"publication":"Science","doi":"10.1126/science.aaz2532","oa_version":"Preprint","external_id":{"pmid":["32764038"]},"scopus_import":"1","quality_controlled":"1","title":"The proteasome controls ESCRT-III–mediated cell division in an archaeon","_id":"10349","article_type":"original","day":"07","publisher":"American Association for the Advancement of Science","extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"volume":369,"type":"journal_article","keyword":["multidisciplinary"],"date_updated":"2021-11-26T08:58:33Z","language":[{"iso":"eng"}],"abstract":[{"text":"Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III–mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control.","lang":"eng"}],"citation":{"ama":"Tarrason Risa G, Hurtig F, Bray S, et al. The proteasome controls ESCRT-III–mediated cell division in an archaeon. <i>Science</i>. 2020;369(6504). doi:<a href=\"https://doi.org/10.1126/science.aaz2532\">10.1126/science.aaz2532</a>","short":"G. Tarrason Risa, F. Hurtig, S. Bray, A.E. Hafner, L. Harker-Kirschneck, P. Faull, C. Davis, D. Papatziamou, D.R. Mutavchiev, C. Fan, L. Meneguello, A. Arashiro Pulschen, G. Dey, S. Culley, M. Kilkenny, D.P. Souza, L. Pellegrini, R.A.M. de Bruin, R. Henriques, A.P. Snijders, A. Šarić, A.-C. Lindås, N.P. Robinson, B. Baum, Science 369 (2020).","mla":"Tarrason Risa, Gabriel, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” <i>Science</i>, vol. 369, no. 6504, American Association for the Advancement of Science, 2020, doi:<a href=\"https://doi.org/10.1126/science.aaz2532\">10.1126/science.aaz2532</a>.","ista":"Tarrason Risa G, Hurtig F, Bray S, Hafner AE, Harker-Kirschneck L, Faull P, Davis C, Papatziamou D, Mutavchiev DR, Fan C, Meneguello L, Arashiro Pulschen A, Dey G, Culley S, Kilkenny M, Souza DP, Pellegrini L, de Bruin RAM, Henriques R, Snijders AP, Šarić A, Lindås A-C, Robinson NP, Baum B. 2020. The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. 369(6504).","ieee":"G. Tarrason Risa <i>et al.</i>, “The proteasome controls ESCRT-III–mediated cell division in an archaeon,” <i>Science</i>, vol. 369, no. 6504. American Association for the Advancement of Science, 2020.","chicago":"Tarrason Risa, Gabriel, Fredrik Hurtig, Sian Bray, Anne E. Hafner, Lena Harker-Kirschneck, Peter Faull, Colin Davis, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” <i>Science</i>. American Association for the Advancement of Science, 2020. <a href=\"https://doi.org/10.1126/science.aaz2532\">https://doi.org/10.1126/science.aaz2532</a>.","apa":"Tarrason Risa, G., Hurtig, F., Bray, S., Hafner, A. E., Harker-Kirschneck, L., Faull, P., … Baum, B. (2020). The proteasome controls ESCRT-III–mediated cell division in an archaeon. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaz2532\">https://doi.org/10.1126/science.aaz2532</a>"},"issue":"6504"},{"publication_status":"published","date_published":"2020-06-08T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://pubs.rsc.org/en/content/articlehtml/2020/sc/c9sc06501f"}],"month":"06","status":"public","year":"2020","intvolume":"        11","publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"author":[{"full_name":"Dear, Alexander J.","first_name":"Alexander J.","last_name":"Dear"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"},{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"full_name":"Kjaergaard, Magnus","first_name":"Magnus","last_name":"Kjaergaard"},{"full_name":"Linse, Sara","first_name":"Sara","last_name":"Linse"},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."}],"date_created":"2021-11-26T09:08:19Z","oa_version":"Published Version","doi":"10.1039/c9sc06501f","external_id":{"pmid":["32953019"]},"quality_controlled":"1","title":"Identification of on- and off-pathway oligomers in amyloid fibril formation","scopus_import":"1","article_processing_charge":"No","pmid":1,"publication":"Chemical Science","acknowledgement":"We are grateful to the Schiff Foundation (AJD), Peterhouse, Cambridge (TCTM), the Swiss National Science foundation (TCTM), Ramon Jenkins Fellowship, Sidney Sussex, Cambridge (GM), the Royal Society (AŠ), the Academy of Medical Sciences and Wellcome Trust (AŠ), the Danish Research Council (MK), the Lundbeck Foundation (MK), the Swedish Research Council (SL), the Wellcome Trust (TPJK), the Cambridge Centre for Misfolding Diseases (TPJK), the BBSRC (TPJK), the Frances and Augustus Newman Foundation (TPJK) for financial support. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) through the ERC grants PhysProt (agreement no. 337969), MAMBA (agreement no. 340890) and NovoNordiskFonden (SL).","page":"6236-6247","_id":"10350","article_type":"original","extern":"1","publisher":"Royal Society of Chemistry","day":"08","citation":{"mla":"Dear, Alexander J., et al. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” <i>Chemical Science</i>, vol. 11, no. 24, Royal Society of Chemistry, 2020, pp. 6236–47, doi:<a href=\"https://doi.org/10.1039/c9sc06501f\">10.1039/c9sc06501f</a>.","short":"A.J. Dear, G. Meisl, A. Šarić, T.C.T. Michaels, M. Kjaergaard, S. Linse, T.P.J. Knowles, Chemical Science 11 (2020) 6236–6247.","ama":"Dear AJ, Meisl G, Šarić A, et al. Identification of on- and off-pathway oligomers in amyloid fibril formation. <i>Chemical Science</i>. 2020;11(24):6236-6247. doi:<a href=\"https://doi.org/10.1039/c9sc06501f\">10.1039/c9sc06501f</a>","apa":"Dear, A. J., Meisl, G., Šarić, A., Michaels, T. C. T., Kjaergaard, M., Linse, S., &#38; Knowles, T. P. J. (2020). Identification of on- and off-pathway oligomers in amyloid fibril formation. <i>Chemical Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c9sc06501f\">https://doi.org/10.1039/c9sc06501f</a>","chicago":"Dear, Alexander J., Georg Meisl, Anđela Šarić, Thomas C. T. Michaels, Magnus Kjaergaard, Sara Linse, and Tuomas P. J. Knowles. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” <i>Chemical Science</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/c9sc06501f\">https://doi.org/10.1039/c9sc06501f</a>.","ieee":"A. J. Dear <i>et al.</i>, “Identification of on- and off-pathway oligomers in amyloid fibril formation,” <i>Chemical Science</i>, vol. 11, no. 24. Royal Society of Chemistry, pp. 6236–6247, 2020.","ista":"Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ. 2020. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. 11(24), 6236–6247."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","short":"CC BY-NC (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","image":"/images/cc_by_nc.png"},"license":"https://creativecommons.org/licenses/by-nc/3.0/","issue":"24","volume":11,"type":"journal_article","keyword":["general chemistry"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation."}],"date_updated":"2021-11-26T11:21:20Z"}]