[{"date_updated":"2024-10-14T11:18:41Z","oa":1,"volume":3,"license":"https://creativecommons.org/licenses/by/4.0/","article_type":"original","intvolume":" 3","file":[{"file_name":"2020_LifeScienceAlliance_Bersini.pdf","date_updated":"2022-04-08T07:33:01Z","file_size":2653960,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2022-04-08T07:33:01Z","success":1,"relation":"main_file","file_id":"11137","checksum":"3bf33e7e93bef7823287807206b69b38"}],"status":"public","title":"Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling","external_id":{"pmid":["31959624"]},"doi":"10.26508/lsa.201900623","citation":{"short":"S. Bersini, N.K. Lytle, R. Schulte, L. Huang, G.M. Wahl, M. Hetzer, Life Science Alliance 3 (2020).","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,” Life Science Alliance, vol. 3, no. 1. Life Science Alliance, 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. Life Science Alliance. 2020;3(1). doi:10.26508/lsa.201900623","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.","apa":"Bersini, S., Lytle, N. K., Schulte, R., Huang, L., Wahl, G. M., & Hetzer, M. (2020). Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Science Alliance. Life Science Alliance. https://doi.org/10.26508/lsa.201900623","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.” Life Science Alliance. Life Science Alliance, 2020. https://doi.org/10.26508/lsa.201900623.","mla":"Bersini, Simone, et al. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” Life Science Alliance, vol. 3, no. 1, e201900623, Life Science Alliance, 2020, doi:10.26508/lsa.201900623."},"publication":"Life Science Alliance","oa_version":"Published Version","pmid":1,"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","publication_status":"published","keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"quality_controlled":"1","day":"01","type":"journal_article","abstract":[{"lang":"eng","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."}],"has_accepted_license":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Life Science Alliance","author":[{"last_name":"Bersini","first_name":"Simone","full_name":"Bersini, Simone"},{"last_name":"Lytle","first_name":"Nikki K","full_name":"Lytle, Nikki K"},{"full_name":"Schulte, Roberta","first_name":"Roberta","last_name":"Schulte"},{"last_name":"Huang","full_name":"Huang, Ling","first_name":"Ling"},{"last_name":"Wahl","first_name":"Geoffrey M","full_name":"Wahl, Geoffrey M"},{"full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"HETZER"}],"date_published":"2020-01-01T00:00:00Z","scopus_import":"1","article_number":"e201900623","_id":"11058","issue":"1","extern":"1","date_created":"2022-04-07T07:44:18Z","ddc":["570"],"file_date_updated":"2022-04-08T07:33:01Z","publication_identifier":{"issn":["2575-1077"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"oa_version":"None","date_created":"2021-11-21T23:01:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","year":"2020","publication_status":"published","type":"conference","abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","day":"01","publication_identifier":{"isbn":["9-781-5575-2820-9"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Optica Publishing Group","date_updated":"2023-10-18T08:32:34Z","author":[{"last_name":"Lambert","full_name":"Lambert, Nicholas J.","first_name":"Nicholas J."},{"last_name":"Mobassem","full_name":"Mobassem, Sonia","first_name":"Sonia"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R"},{"last_name":"Schwefel","full_name":"Schwefel, Harald G.L.","first_name":"Harald G.L."}],"conference":{"name":"OSA: Optical Society of America","location":"Washington, DC, United States","end_date":"2020-09-17","start_date":"2020-09-14"},"date_published":"2020-01-01T00:00:00Z","alternative_title":["OSA Technical Digest"],"status":"public","title":"New designs and noise channels in electro-optic microwave to optical up-conversion","department":[{"_id":"JoFi"}],"scopus_import":"1","citation":{"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 OSA Quantum 2.0 Conference, Washington, DC, United States, 2020.","short":"N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA Quantum 2.0 Conference, Optica Publishing Group, 2020.","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.","ama":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise channels in electro-optic microwave to optical up-conversion. In: OSA Quantum 2.0 Conference. Optica Publishing Group; 2020. doi:10.1364/QUANTUM.2020.QTu8A.1","mla":"Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” OSA Quantum 2.0 Conference, QTu8A.1, Optica Publishing Group, 2020, doi:10.1364/QUANTUM.2020.QTu8A.1.","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 OSA Quantum 2.0 Conference. Optica Publishing Group, 2020. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1.","apa":"Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., & Schwefel, H. G. L. (2020). New designs and noise channels in electro-optic microwave to optical up-conversion. In OSA Quantum 2.0 Conference. Washington, DC, United States: Optica Publishing Group. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1"},"doi":"10.1364/QUANTUM.2020.QTu8A.1","_id":"10328","publication":"OSA Quantum 2.0 Conference","article_number":"QTu8A.1"},{"status":"public","title":"Physical mechanisms of amyloid nucleation on fluid membranes","external_id":{"pmid":["33328273"]},"doi":"10.1073/pnas.2007694117","citation":{"apa":"Krausser, J., Knowles, T. P. J., & Šarić, A. (2020). Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2007694117","mla":"Krausser, Johannes, et al. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences, vol. 117, no. 52, National Academy of Sciences, 2020, pp. 33090–98, doi:10.1073/pnas.2007694117.","chicago":"Krausser, Johannes, Tuomas P. J. Knowles, and Anđela Šarić. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2007694117.","short":"J. Krausser, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences 117 (2020) 33090–33098.","ieee":"J. Krausser, T. P. J. Knowles, and A. Šarić, “Physical mechanisms of amyloid nucleation on fluid membranes,” Proceedings of the National Academy of Sciences, vol. 117, no. 52. National Academy of Sciences, pp. 33090–33098, 2020.","ama":"Krausser J, Knowles TPJ, Šarić A. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 2020;117(52):33090-33098. doi:10.1073/pnas.2007694117","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."},"publication":"Proceedings of the National Academy of Sciences","article_type":"original","date_updated":"2021-11-25T15:35:58Z","oa":1,"volume":117,"intvolume":" 117","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"12","year":"2020","publication_status":"published","type":"journal_article","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","day":"16","pmid":1,"oa_version":"Published Version","scopus_import":"1","_id":"10336","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"National Academy of Sciences","author":[{"last_name":"Krausser","first_name":"Johannes","full_name":"Krausser, Johannes"},{"full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J.","last_name":"Knowles"},{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"page":"33090-33098","date_published":"2020-12-16T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2"}],"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.","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"extern":"1","issue":"52","date_created":"2021-11-25T15:07:09Z"},{"status":"public","title":"Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes","external_id":{"pmid":["33084724"]},"OA_type":"hybrid","citation":{"apa":"Debets, V. E., Janssen, L. M. C., & Šarić, A. (2020). Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d0sm00712a","chicago":"Debets, V. E., L. M. C. Janssen, and Anđela Šarić. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” Soft Matter. Royal Society of Chemistry, 2020. https://doi.org/10.1039/d0sm00712a.","mla":"Debets, V. E., et al. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” Soft Matter, vol. 16, no. 47, Royal Society of Chemistry, 2020, pp. 10628–39, doi:10.1039/d0sm00712a.","ama":"Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 2020;16(47):10628-10639. doi:10.1039/d0sm00712a","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.","short":"V.E. Debets, L.M.C. Janssen, A. Šarić, Soft Matter 16 (2020) 10628–10639.","ieee":"V. E. Debets, L. M. C. Janssen, and A. Šarić, “Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes,” Soft Matter, vol. 16, no. 47. Royal Society of Chemistry, pp. 10628–10639, 2020."},"doi":"10.1039/d0sm00712a","publication":"Soft Matter","date_updated":"2024-10-16T12:53:17Z","volume":16,"oa":1,"article_type":"original","intvolume":" 16","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","month":"10","year":"2020","publication_status":"published","keyword":["condensed matter physics","general chemistry"],"quality_controlled":"1","day":"06","type":"journal_article","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"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","OA_place":"publisher","_id":"10341","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Royal Society of Chemistry","author":[{"first_name":"V. E.","full_name":"Debets, V. E.","last_name":"Debets"},{"last_name":"Janssen","first_name":"L. M. C.","full_name":"Janssen, L. M. C."},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139"}],"page":"10628-10639","date_published":"2020-10-06T00:00:00Z","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.01.071761v1","open_access":"1"}],"publication_identifier":{"issn":["1744-683X","1744-6848"]},"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.).","issue":"47","extern":"1","date_created":"2021-11-26T06:29:41Z"},{"status":"public","title":"On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias","external_id":{"pmid":["33246953"]},"citation":{"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. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abc4397","mla":"Tian, Xiaohe, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” Science Advances, vol. 6, no. 48, eabc4397, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.abc4397.","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.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.abc4397.","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).","ieee":"X. Tian et al., “On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias,” Science Advances, vol. 6, no. 48. American Association for the Advancement of Science, 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. Science Advances. 2020;6(48). doi:10.1126/sciadv.abc4397","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."},"DOAJ_listed":"1","doi":"10.1126/sciadv.abc4397","publication":"Science Advances","OA_type":"gold","article_type":"original","date_updated":"2024-10-16T12:56:52Z","oa":1,"volume":6,"file":[{"file_name":"2020_SciAdv_Tian.pdf","date_updated":"2021-11-26T06:50:09Z","access_level":"open_access","content_type":"application/pdf","date_created":"2021-11-26T06:50:09Z","creator":"cchlebak","file_size":10381298,"success":1,"relation":"main_file","file_id":"10343","checksum":"3ba2eca975930cdb0b1ce1ae876885a7"}],"intvolume":" 6","year":"2020","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","month":"11","keyword":["multidisciplinary"],"publication_status":"published","type":"journal_article","abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","day":"27","pmid":1,"oa_version":"Published Version","scopus_import":"1","_id":"10342","OA_place":"publisher","article_number":"eabc4397 ","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"American Association for the Advancement of Science","has_accepted_license":"1","author":[{"first_name":"Xiaohe","full_name":"Tian, Xiaohe","last_name":"Tian"},{"last_name":"Leite","full_name":"Leite, Diana M.","first_name":"Diana M."},{"last_name":"Scarpa","full_name":"Scarpa, Edoardo","first_name":"Edoardo"},{"first_name":"Sophie","full_name":"Nyberg, Sophie","last_name":"Nyberg"},{"last_name":"Fullstone","full_name":"Fullstone, Gavin","first_name":"Gavin"},{"last_name":"Forth","first_name":"Joe","full_name":"Forth, Joe"},{"full_name":"Matias, Diana","first_name":"Diana","last_name":"Matias"},{"last_name":"Apriceno","full_name":"Apriceno, Azzurra","first_name":"Azzurra"},{"full_name":"Poma, Alessandro","first_name":"Alessandro","last_name":"Poma"},{"full_name":"Duro-Castano, Aroa","first_name":"Aroa","last_name":"Duro-Castano"},{"first_name":"Manish","full_name":"Vuyyuru, Manish","last_name":"Vuyyuru"},{"first_name":"Lena","full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"},{"first_name":"Zhongping","full_name":"Zhang, Zhongping","last_name":"Zhang"},{"last_name":"Xiang","full_name":"Xiang, Pan","first_name":"Pan"},{"full_name":"Fang, Bin","first_name":"Bin","last_name":"Fang"},{"last_name":"Tian","first_name":"Yupeng","full_name":"Tian, Yupeng"},{"full_name":"Luo, Lei","first_name":"Lei","last_name":"Luo"},{"last_name":"Rizzello","first_name":"Loris","full_name":"Rizzello, Loris"},{"first_name":"Giuseppe","full_name":"Battaglia, Giuseppe","last_name":"Battaglia"}],"date_published":"2020-11-27T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.04.04.025866v1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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.","publication_identifier":{"issn":["2375-2548"]},"extern":"1","issue":"48","file_date_updated":"2021-11-26T06:50:09Z","date_created":"2021-11-26T06:40:28Z","ddc":["611"]},{"file":[{"access_level":"open_access","date_created":"2021-11-26T07:16:49Z","content_type":"application/pdf","creator":"cchlebak","file_size":844353,"date_updated":"2021-11-26T07:16:49Z","file_name":"2020_PhysRevLett_Forster.pdf","checksum":"fbf2e1415e332d6add90222d60401a1d","file_id":"10345","success":1,"relation":"main_file"}],"intvolume":" 125","date_updated":"2024-10-16T12:59:57Z","volume":125,"oa":1,"article_type":"original","OA_type":"hybrid","doi":"10.1103/physrevlett.125.228101","citation":{"apa":"Forster, J. C., Krausser, J., Vuyyuru, M. R., Baum, B., & Šarić, A. (2020). Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.125.228101","mla":"Forster, Joel C., et al. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” Physical Review Letters, vol. 125, no. 22, 228101, American Physical Society, 2020, doi:10.1103/physrevlett.125.228101.","chicago":"Forster, Joel C., Johannes Krausser, Manish R. Vuyyuru, Buzz Baum, and Anđela Šarić. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.125.228101.","ama":"Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 2020;125(22). doi:10.1103/physrevlett.125.228101","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.","short":"J.C. Forster, J. Krausser, M.R. Vuyyuru, B. Baum, A. Šarić, Physical Review Letters 125 (2020).","ieee":"J. C. Forster, J. Krausser, M. R. Vuyyuru, B. Baum, and A. Šarić, “Exploring the design rules for efficient membrane-reshaping nanostructures,” Physical Review Letters, vol. 125, no. 22. American Physical Society, 2020."},"publication":"Physical Review Letters","status":"public","title":"Exploring the design rules for efficient membrane-reshaping nanostructures","external_id":{"pmid":["33315453"]},"oa_version":"Published Version","pmid":1,"quality_controlled":"1","day":"23","type":"journal_article","abstract":[{"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.","lang":"eng"}],"month":"11","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","year":"2020","publication_status":"published","author":[{"first_name":"Joel C.","full_name":"Forster, Joel C.","last_name":"Forster"},{"first_name":"Johannes","full_name":"Krausser, Johannes","last_name":"Krausser"},{"last_name":"Vuyyuru","first_name":"Manish R.","full_name":"Vuyyuru, Manish R."},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139"}],"date_published":"2020-11-23T00:00:00Z","has_accepted_license":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"American Physical Society","article_number":"228101","_id":"10344","OA_place":"publisher","scopus_import":"1","date_created":"2021-11-26T07:10:43Z","ddc":["530"],"file_date_updated":"2021-11-26T07:16:49Z","issue":"22","extern":"1","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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).","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.02.27.968149v1"}]},{"pmid":1,"oa_version":"Published Version","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"}],"type":"journal_article","day":"23","quality_controlled":"1","publication_status":"published","keyword":["biophysics"],"month":"09","year":"2020","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","intvolume":" 119","article_type":"original","volume":119,"oa":1,"date_updated":"2024-10-16T13:05:34Z","publication":"Biophysical Journal","citation":{"mla":"Hafner, Anne E., et al. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” Biophysical Journal, vol. 119, no. 9, Cell Press, 2020, pp. 1791–99, doi:10.1016/j.bpj.2020.09.013.","chicago":"Hafner, Anne E., Noemi G. Gyori, Ciaran A. Bench, Luke K. Davis, and Anđela Šarić. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” Biophysical Journal. Cell Press, 2020. https://doi.org/10.1016/j.bpj.2020.09.013.","apa":"Hafner, A. E., Gyori, N. G., Bench, C. A., Davis, L. K., & Šarić, A. (2020). Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. Cell Press. https://doi.org/10.1016/j.bpj.2020.09.013","ieee":"A. E. Hafner, N. G. Gyori, C. A. Bench, L. K. Davis, and A. Šarić, “Modeling fibrillogenesis of collagen-mimetic molecules,” Biophysical Journal, vol. 119, no. 9. Cell Press, pp. 1791–1799, 2020.","short":"A.E. Hafner, N.G. Gyori, C.A. Bench, L.K. Davis, A. Šarić, Biophysical Journal 119 (2020) 1791–1799.","ista":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. 2020. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 119(9), 1791–1799.","ama":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 2020;119(9):1791-1799. doi:10.1016/j.bpj.2020.09.013"},"doi":"10.1016/j.bpj.2020.09.013","OA_type":"hybrid","title":"Modeling fibrillogenesis of collagen-mimetic molecules","external_id":{"pmid":["33049216"]},"status":"public","date_created":"2021-11-26T07:27:24Z","extern":"1","issue":"9","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).","publication_identifier":{"issn":["0006-3495"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.06.08.140061v1","open_access":"1"}],"date_published":"2020-09-23T00:00:00Z","page":"1791-1799","author":[{"last_name":"Hafner","first_name":"Anne E.","full_name":"Hafner, Anne E."},{"last_name":"Gyori","first_name":"Noemi G.","full_name":"Gyori, Noemi G."},{"last_name":"Bench","first_name":"Ciaran A.","full_name":"Bench, Ciaran A."},{"last_name":"Davis","first_name":"Luke K.","full_name":"Davis, Luke K."},{"orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela"}],"publisher":"Cell Press","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"10346","OA_place":"publisher","scopus_import":"1"},{"date_published":"2020-09-14T00:00:00Z","page":"24251-24257","author":[{"first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T.","last_name":"Michaels"},{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Meisl, Georg","first_name":"Georg","last_name":"Meisl"},{"last_name":"Heller","full_name":"Heller, Gabriella T.","first_name":"Gabriella T."},{"last_name":"Curk","full_name":"Curk, Samo","first_name":"Samo"},{"first_name":"Paolo","full_name":"Arosio, Paolo","last_name":"Arosio"},{"full_name":"Linse, Sara","first_name":"Sara","last_name":"Linse"},{"full_name":"Dobson, Christopher M.","first_name":"Christopher M.","last_name":"Dobson"},{"last_name":"Vendruscolo","full_name":"Vendruscolo, Michele","first_name":"Michele"},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"}],"publisher":"National Academy of Sciences","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"10347","scopus_import":"1","date_created":"2021-11-26T07:48:27Z","issue":"39","extern":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"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).","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.02.22.960716"}],"intvolume":" 117","oa":1,"volume":117,"date_updated":"2021-11-26T08:59:06Z","article_type":"original","publication":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.2006684117","citation":{"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. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2006684117","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.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006684117.","mla":"Michaels, Thomas C. T., et al. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” Proceedings of the National Academy of Sciences, vol. 117, no. 39, National Academy of Sciences, 2020, pp. 24251–57, doi:10.1073/pnas.2006684117.","ama":"Michaels TCT, Šarić A, Meisl G, et al. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 2020;117(39):24251-24257. doi:10.1073/pnas.2006684117","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.","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.","ieee":"T. C. T. Michaels et al., “Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors,” Proceedings of the National Academy of Sciences, vol. 117, no. 39. National Academy of Sciences, pp. 24251–24257, 2020."},"external_id":{"pmid":["32929030"]},"title":"Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors","status":"public","oa_version":"Published Version","pmid":1,"day":"14","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","publication_status":"published","keyword":["multidisciplinary"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2020","month":"09"},{"intvolume":" 182","volume":182,"oa":1,"date_updated":"2021-11-26T08:58:37Z","article_type":"original","publication":"Cell","doi":"10.1016/j.cell.2020.07.021","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.","ieee":"A.-K. Pfitzner et al., “An ESCRT-III polymerization sequence drives membrane deformation and fission,” Cell, vol. 182, no. 5. Elsevier, p. 1140–1155.e18, 2020.","ama":"Pfitzner A-K, Mercier V, Jiang X, et al. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 2020;182(5):1140-1155.e18. doi:10.1016/j.cell.2020.07.021","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., & Roux, A. (2020). An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.07.021","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.” Cell. Elsevier, 2020. https://doi.org/10.1016/j.cell.2020.07.021.","mla":"Pfitzner, Anna-Katharina, et al. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” Cell, vol. 182, no. 5, Elsevier, 2020, p. 1140–1155.e18, doi:10.1016/j.cell.2020.07.021."},"external_id":{"pmid":["32814015"]},"title":"An ESCRT-III polymerization sequence drives membrane deformation and fission","status":"public","oa_version":"Published Version","pmid":1,"day":"18","quality_controlled":"1","abstract":[{"text":"The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity.","lang":"eng"}],"type":"journal_article","publication_status":"published","keyword":["general biochemistry","genetics and molecular biology"],"month":"08","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2020","date_published":"2020-08-18T00:00:00Z","page":"1140-1155.e18","author":[{"last_name":"Pfitzner","full_name":"Pfitzner, Anna-Katharina","first_name":"Anna-Katharina"},{"last_name":"Mercier","first_name":"Vincent","full_name":"Mercier, Vincent"},{"last_name":"Jiang","full_name":"Jiang, Xiuyun","first_name":"Xiuyun"},{"last_name":"Moser von Filseck","first_name":"Joachim","full_name":"Moser von Filseck, Joachim"},{"last_name":"Baum","full_name":"Baum, Buzz","first_name":"Buzz"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"},{"first_name":"Aurélien","full_name":"Roux, Aurélien","last_name":"Roux"}],"publisher":"Elsevier","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"10348","scopus_import":"1","date_created":"2021-11-26T08:02:27Z","issue":"5","extern":"1","publication_identifier":{"issn":["0092-8674"]},"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]).","main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S0092867420309296"}]},{"extern":"1","issue":"6504","date_created":"2021-11-26T08:21:34Z","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/774273v1"}],"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.","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2020-08-07T00:00:00Z","author":[{"full_name":"Tarrason Risa, Gabriel","first_name":"Gabriel","last_name":"Tarrason Risa"},{"last_name":"Hurtig","full_name":"Hurtig, Fredrik","first_name":"Fredrik"},{"last_name":"Bray","first_name":"Sian","full_name":"Bray, Sian"},{"full_name":"Hafner, Anne E.","first_name":"Anne E.","last_name":"Hafner"},{"first_name":"Lena","full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck"},{"full_name":"Faull, Peter","first_name":"Peter","last_name":"Faull"},{"full_name":"Davis, Colin","first_name":"Colin","last_name":"Davis"},{"first_name":"Dimitra","full_name":"Papatziamou, Dimitra","last_name":"Papatziamou"},{"last_name":"Mutavchiev","first_name":"Delyan R.","full_name":"Mutavchiev, Delyan R."},{"last_name":"Fan","full_name":"Fan, Catherine","first_name":"Catherine"},{"full_name":"Meneguello, Leticia","first_name":"Leticia","last_name":"Meneguello"},{"last_name":"Arashiro Pulschen","first_name":"Andre","full_name":"Arashiro Pulschen, Andre"},{"last_name":"Dey","full_name":"Dey, Gautam","first_name":"Gautam"},{"full_name":"Culley, Siân","first_name":"Siân","last_name":"Culley"},{"last_name":"Kilkenny","first_name":"Mairi","full_name":"Kilkenny, Mairi"},{"first_name":"Diorge P.","full_name":"Souza, Diorge P.","last_name":"Souza"},{"full_name":"Pellegrini, Luca","first_name":"Luca","last_name":"Pellegrini"},{"first_name":"Robertus A. M.","full_name":"de Bruin, Robertus A. M.","last_name":"de Bruin"},{"full_name":"Henriques, Ricardo","first_name":"Ricardo","last_name":"Henriques"},{"first_name":"Ambrosius P.","full_name":"Snijders, Ambrosius P.","last_name":"Snijders"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"},{"last_name":"Lindås","first_name":"Ann-Christin","full_name":"Lindås, Ann-Christin"},{"last_name":"Robinson","full_name":"Robinson, Nicholas P.","first_name":"Nicholas P."},{"full_name":"Baum, Buzz","first_name":"Buzz","last_name":"Baum"}],"scopus_import":"1","_id":"10349","pmid":1,"oa_version":"Preprint","publication_status":"published","keyword":["multidisciplinary"],"month":"08","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2020","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"}],"type":"journal_article","day":"07","quality_controlled":"1","article_type":"original","oa":1,"volume":369,"date_updated":"2021-11-26T08:58:33Z","intvolume":" 369","external_id":{"pmid":["32764038"]},"title":"The proteasome controls ESCRT-III–mediated cell division in an archaeon","status":"public","publication":"Science","doi":"10.1126/science.aaz2532","citation":{"ama":"Tarrason Risa G, Hurtig F, Bray S, et al. The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. 2020;369(6504). doi:10.1126/science.aaz2532","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).","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).","ieee":"G. Tarrason Risa et al., “The proteasome controls ESCRT-III–mediated cell division in an archaeon,” Science, vol. 369, no. 6504. American Association for the Advancement of Science, 2020.","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. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaz2532","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.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aaz2532.","mla":"Tarrason Risa, Gabriel, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” Science, vol. 369, no. 6504, American Association for the Advancement of Science, 2020, doi:10.1126/science.aaz2532."}},{"issue":"24","extern":"1","date_created":"2021-11-26T09:08:19Z","main_file_link":[{"open_access":"1","url":"https://pubs.rsc.org/en/content/articlehtml/2020/sc/c9sc06501f"}],"publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)"},"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).","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Royal Society of Chemistry","author":[{"full_name":"Dear, Alexander J.","first_name":"Alexander J.","last_name":"Dear"},{"full_name":"Meisl, Georg","first_name":"Georg","last_name":"Meisl"},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139"},{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"last_name":"Kjaergaard","first_name":"Magnus","full_name":"Kjaergaard, Magnus"},{"last_name":"Linse","first_name":"Sara","full_name":"Linse, Sara"},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"}],"page":"6236-6247","date_published":"2020-06-08T00:00:00Z","scopus_import":"1","_id":"10350","oa_version":"Published Version","pmid":1,"month":"06","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2020","keyword":["general chemistry"],"publication_status":"published","quality_controlled":"1","day":"08","type":"journal_article","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","oa":1,"volume":11,"license":"https://creativecommons.org/licenses/by-nc/3.0/","article_type":"original","intvolume":" 11","status":"public","title":"Identification of on- and off-pathway oligomers in amyloid fibril formation","external_id":{"pmid":["32953019"]},"citation":{"mla":"Dear, Alexander J., et al. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” Chemical Science, vol. 11, no. 24, Royal Society of Chemistry, 2020, pp. 6236–47, doi:10.1039/c9sc06501f.","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.” Chemical Science. Royal Society of Chemistry, 2020. https://doi.org/10.1039/c9sc06501f.","apa":"Dear, A. J., Meisl, G., Šarić, A., Michaels, T. C. T., Kjaergaard, M., Linse, S., & Knowles, T. P. J. (2020). Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/c9sc06501f","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.","ama":"Dear AJ, Meisl G, Šarić A, et al. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. 2020;11(24):6236-6247. doi:10.1039/c9sc06501f","ieee":"A. J. Dear et al., “Identification of on- and off-pathway oligomers in amyloid fibril formation,” Chemical Science, vol. 11, no. 24. Royal Society of Chemistry, pp. 6236–6247, 2020.","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."},"doi":"10.1039/c9sc06501f","publication":"Chemical Science"},{"page":"445-451","author":[{"first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T.","last_name":"Michaels"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela"},{"last_name":"Curk","full_name":"Curk, Samo","first_name":"Samo"},{"full_name":"Bernfur, Katja","first_name":"Katja","last_name":"Bernfur"},{"full_name":"Arosio, Paolo","first_name":"Paolo","last_name":"Arosio"},{"full_name":"Meisl, Georg","first_name":"Georg","last_name":"Meisl"},{"full_name":"Dear, Alexander J.","first_name":"Alexander J.","last_name":"Dear"},{"first_name":"Samuel I. A.","full_name":"Cohen, Samuel I. A.","last_name":"Cohen"},{"first_name":"Christopher M.","full_name":"Dobson, Christopher M.","last_name":"Dobson"},{"last_name":"Vendruscolo","full_name":"Vendruscolo, Michele","first_name":"Michele"},{"full_name":"Linse, Sara","first_name":"Sara","last_name":"Linse"},{"full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J.","last_name":"Knowles"}],"date_published":"2020-04-13T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Springer Nature","_id":"10351","scopus_import":"1","date_created":"2021-11-26T09:15:13Z","issue":"5","extern":"1","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"acknowledgement":"We acknowledge support from Peterhouse (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the UCL Institute for the Physics of Living Systems (S.C.), Sidney Sussex College (G.M.), the Wellcome Trust (A.Š., M.V., C.M.D. and T.P.J.K.), the Schiff Foundation (A.J.D.), the Cambridge Centre for Misfolding Diseases (M.V., C.M.D. and T.P.J.K.), the BBSRC (C.M.D. and T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Swedish Research Council (S.L.) and the ERC grant MAMBA (S.L., agreement no. 340890). The research that led to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969).","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.01.08.897488","open_access":"1"}],"intvolume":" 12","date_updated":"2021-11-26T11:21:08Z","oa":1,"volume":12,"article_type":"original","doi":"10.1038/s41557-020-0452-1","citation":{"apa":"Michaels, T. C. T., Šarić, A., Curk, S., Bernfur, K., Arosio, P., Meisl, G., … Knowles, T. P. J. (2020). Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-020-0452-1","mla":"Michaels, Thomas C. T., et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” Nature Chemistry, vol. 12, no. 5, Springer Nature, 2020, pp. 445–51, doi:10.1038/s41557-020-0452-1.","chicago":"Michaels, Thomas C. T., Anđela Šarić, Samo Curk, Katja Bernfur, Paolo Arosio, Georg Meisl, Alexander J. Dear, et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” Nature Chemistry. Springer Nature, 2020. https://doi.org/10.1038/s41557-020-0452-1.","ama":"Michaels TCT, Šarić A, Curk S, et al. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 2020;12(5):445-451. doi:10.1038/s41557-020-0452-1","ista":"Michaels TCT, Šarić A, Curk S, Bernfur K, Arosio P, Meisl G, Dear AJ, Cohen SIA, Dobson CM, Vendruscolo M, Linse S, Knowles TPJ. 2020. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 12(5), 445–451.","short":"T.C.T. Michaels, A. Šarić, S. Curk, K. Bernfur, P. Arosio, G. Meisl, A.J. Dear, S.I.A. Cohen, C.M. Dobson, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Chemistry 12 (2020) 445–451.","ieee":"T. C. T. Michaels et al., “Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide,” Nature Chemistry, vol. 12, no. 5. Springer Nature, pp. 445–451, 2020."},"publication":"Nature Chemistry","status":"public","external_id":{"pmid":["32303714"]},"title":"Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide","oa_version":"None","pmid":1,"quality_controlled":"1","day":"13","type":"journal_article","abstract":[{"lang":"eng","text":"Oligomeric species populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach that combines theory, experiment and simulation, we reveal, in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we found that most Aβ42 oligomers dissociate into their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar structures. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to those of aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41557-020-0468-6"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2020","month":"04","publication_status":"published","keyword":["general chemical engineering","general chemistry"]},{"author":[{"last_name":"Davis","full_name":"Davis, Luke K.","first_name":"Luke K."},{"last_name":"Ford","first_name":"Ian J.","full_name":"Ford, Ian J."},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139"},{"full_name":"Hoogenboom, Bart W.","first_name":"Bart W.","last_name":"Hoogenboom"}],"date_published":"2020-02-28T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"American Physical Society","_id":"10352","article_number":"022420","scopus_import":"1","date_created":"2021-11-26T09:41:04Z","extern":"1","issue":"2","acknowledgement":"We thank Dino Osmanović (MIT), Roy Beck (Tel-Aviv), Larissa Kapinos (Basel), Roderick Lim (Basel), Ralf Richter (Leeds), and Anton Zilman (Toronto) for discussions. This work was funded by the Royal Society (A.Š.) and the UK Engineering and Physical Sciences Research Council (EP/L504889/1, B.W.H.).","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/571687"}],"intvolume":" 101","article_type":"original","date_updated":"2021-11-26T11:21:16Z","oa":1,"volume":101,"doi":"10.1103/physreve.101.022420","citation":{"chicago":"Davis, Luke K., Ian J. Ford, Anđela Šarić, and Bart W. Hoogenboom. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” Physical Review E. American Physical Society, 2020. https://doi.org/10.1103/physreve.101.022420.","mla":"Davis, Luke K., et al. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” Physical Review E, vol. 101, no. 2, 022420, American Physical Society, 2020, doi:10.1103/physreve.101.022420.","apa":"Davis, L. K., Ford, I. J., Šarić, A., & Hoogenboom, B. W. (2020). Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.101.022420","ieee":"L. K. Davis, I. J. Ford, A. Šarić, and B. W. Hoogenboom, “Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics,” Physical Review E, vol. 101, no. 2. American Physical Society, 2020.","short":"L.K. Davis, I.J. Ford, A. Šarić, B.W. Hoogenboom, Physical Review E 101 (2020).","ista":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. 2020. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 101(2), 022420.","ama":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 2020;101(2). doi:10.1103/physreve.101.022420"},"publication":"Physical Review E","status":"public","external_id":{"pmid":["32168597"]},"title":"Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics","pmid":1,"oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events."}],"quality_controlled":"1","day":"28","month":"02","year":"2020","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published"},{"acknowledgement":"We thank Samantha Miller, Bert Poolman, and the members of Šarić and Pilizota laboratories for useful discussion. We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute for the Physics of Living Systems (A.P. and A.Š.), Darwin Trust of University of Edinburgh (H.S.), Industrial Biotechnology Innovation Centre (H.S. and T.P.), BBSRC Council Crossing Biological Membrane Network (H.S. and T.P.), BBSRC/EPSRC/MRC Synthetic Biology Research Centre (T.P.), and the Royal Society (A.Š.).","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/553248","open_access":"1"}],"date_created":"2021-11-26T09:57:01Z","extern":"1","issue":"4","_id":"10353","article_number":"048102","scopus_import":"1","date_published":"2020-01-31T00:00:00Z","author":[{"last_name":"Paraschiv","first_name":"Alexandru","full_name":"Paraschiv, Alexandru"},{"last_name":"Hegde","full_name":"Hegde, Smitha","first_name":"Smitha"},{"first_name":"Raman","full_name":"Ganti, Raman","last_name":"Ganti"},{"first_name":"Teuta","full_name":"Pilizota, Teuta","last_name":"Pilizota"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"}],"publisher":"American Physical Society","article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Experiments have suggested that bacterial mechanosensitive channels separate into 2D clusters, the role of which is unclear. By developing a coarse-grained computer model we find that clustering promotes the channel closure, which is highly dependent on the channel concentration and membrane stress. This behaviour yields a tightly regulated gating system, whereby at high tensions channels gate individually, and at lower tensions the channels spontaneously aggregate and inactivate. We implement this positive feedback into the model for cell volume regulation, and find that the channel clustering protects the cell against excessive loss of cytoplasmic content."}],"type":"journal_article","day":"31","quality_controlled":"1","keyword":["general physics and astronomy"],"publication_status":"published","month":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2020","pmid":1,"oa_version":"Preprint","publication":"Physical Review Letters","citation":{"mla":"Paraschiv, Alexandru, et al. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” Physical Review Letters, vol. 124, no. 4, 048102, American Physical Society, 2020, doi:10.1103/physrevlett.124.048102.","chicago":"Paraschiv, Alexandru, Smitha Hegde, Raman Ganti, Teuta Pilizota, and Anđela Šarić. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.124.048102.","apa":"Paraschiv, A., Hegde, S., Ganti, R., Pilizota, T., & Šarić, A. (2020). Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.124.048102","ieee":"A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, and A. Šarić, “Dynamic clustering regulates activity of mechanosensitive membrane channels,” Physical Review Letters, vol. 124, no. 4. American Physical Society, 2020.","short":"A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, A. Šarić, Physical Review Letters 124 (2020).","ista":"Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. 2020. Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. 124(4), 048102.","ama":"Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. 2020;124(4). doi:10.1103/physrevlett.124.048102"},"doi":"10.1103/physrevlett.124.048102","title":"Dynamic clustering regulates activity of mechanosensitive membrane channels","external_id":{"pmid":["32058787"]},"status":"public","intvolume":" 124","article_type":"original","volume":124,"oa":1,"date_updated":"2021-11-26T11:21:12Z"},{"date_updated":"2026-02-20T06:53:53Z","oa":1,"volume":26,"license":"https://creativecommons.org/licenses/by-nc/4.0/","article_type":"original","intvolume":" 26","status":"public","title":"Aromatic foldamer helices as α‐helix extended surface mimetics","OA_type":"hybrid","doi":"10.1002/chem.202004064","citation":{"apa":"Zwillinger, M., Reddy, P. S., Wicher, B., Mandal, P. K., Csékei, M., Fischer, L., … Huc, I. (2020). Aromatic foldamer helices as α‐helix extended surface mimetics. Chemistry – A European Journal. Wiley. https://doi.org/10.1002/chem.202004064","chicago":"Zwillinger, Márton, Post Sai Reddy, Barbara Wicher, Pradeep K Mandal, Márton Csékei, Lucile Fischer, András Kotschy, and Ivan Huc. “Aromatic Foldamer Helices as Α‐helix Extended Surface Mimetics.” Chemistry – A European Journal. Wiley, 2020. https://doi.org/10.1002/chem.202004064.","mla":"Zwillinger, Márton, et al. “Aromatic Foldamer Helices as Α‐helix Extended Surface Mimetics.” Chemistry – A European Journal, vol. 26, no. 72, Wiley, 2020, pp. 17366–70, doi:10.1002/chem.202004064.","short":"M. Zwillinger, P.S. Reddy, B. Wicher, P.K. Mandal, M. Csékei, L. Fischer, A. Kotschy, I. Huc, Chemistry – A European Journal 26 (2020) 17366–17370.","ieee":"M. Zwillinger et al., “Aromatic foldamer helices as α‐helix extended surface mimetics,” Chemistry – A European Journal, vol. 26, no. 72. Wiley, pp. 17366–17370, 2020.","ama":"Zwillinger M, Reddy PS, Wicher B, et al. Aromatic foldamer helices as α‐helix extended surface mimetics. Chemistry – A European Journal. 2020;26(72):17366-17370. doi:10.1002/chem.202004064","ista":"Zwillinger M, Reddy PS, Wicher B, Mandal PK, Csékei M, Fischer L, Kotschy A, Huc I. 2020. Aromatic foldamer helices as α‐helix extended surface mimetics. Chemistry – A European Journal. 26(72), 17366–17370."},"publication":"Chemistry – A European Journal","oa_version":"Published Version","month":"09","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","quality_controlled":"1","day":"10","type":"journal_article","abstract":[{"text":"Helically folded aromatic oligoamide foldamers have a size and geometrical parameters very distinct from those of α‐helices and are not obvious candidates for α‐helix mimicry. Nevertheless, they offer multiple sites for attaching side chains. It was found that some arrays of side chains at the surface of an aromatic helix make it possible to mimic extended α‐helical surfaces. Synthetic methods were developed to produce quinoline monomers suitably functionalized for solid phase synthesis. A dodecamer was prepared. Its crystal structure validated the initial design and showed helix bundling involving the α‐helix‐like interface. These results open up new uses of aromatic helices to recognize protein surfaces and to program helix bundling in water.","lang":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Wiley","author":[{"last_name":"Zwillinger","first_name":"Márton","full_name":"Zwillinger, Márton"},{"full_name":"Reddy, Post Sai","first_name":"Post Sai","last_name":"Reddy"},{"last_name":"Wicher","first_name":"Barbara","full_name":"Wicher, Barbara"},{"id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","orcid":"0000-0001-5996-956X","last_name":"Mandal","full_name":"Mandal, Pradeep K","first_name":"Pradeep K"},{"last_name":"Csékei","full_name":"Csékei, Márton","first_name":"Márton"},{"first_name":"Lucile","full_name":"Fischer, Lucile","last_name":"Fischer"},{"first_name":"András","full_name":"Kotschy, András","last_name":"Kotschy"},{"last_name":"Huc","full_name":"Huc, Ivan","first_name":"Ivan"}],"page":"17366-17370","date_published":"2020-09-10T00:00:00Z","OA_place":"publisher","_id":"21083","issue":"72","extern":"1","date_created":"2026-01-29T15:31:13Z","ddc":["540"],"main_file_link":[{"url":"https://doi.org/10.1002/chem.202004064","open_access":"1"}],"publication_identifier":{"eissn":["1521-3765"],"issn":["0947-6539"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"}},{"pmid":1,"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","month":"11","publication_status":"published","type":"journal_article","abstract":[{"text":"Self-assembly is a powerful method to obtain large discrete functional molecular architectures. When using a single building block, self-assembly generally yields symmetrical objects in which all the subunits relate similarly to their neighbours. Here we report the discovery of a family of self-constructing cyclic macromolecules with stable folded conformations of low symmetry, which include some with a prime number (13, 17 and 23) of units, despite being formed from a single component. The formation of these objects amounts to the production of polymers with a perfectly uniform length. Design rules for the spontaneous emergence of such macromolecules include endowing monomers with a strong potential for non-covalent interactions that remain frustrated in competing entropically favoured yet conformationally restrained smaller cycles. The process can also be templated by a guest molecule that itself has an asymmetrical structure, which paves the way to molecular imprinting techniques at the level of single polymer chains.","lang":"eng"}],"quality_controlled":"1","day":"20","article_type":"original","date_updated":"2026-02-23T11:46:11Z","volume":12,"oa":1,"intvolume":" 12","status":"public","external_id":{"pmid":["33219361 "]},"title":"Emergence of low-symmetry foldamers from single monomers","citation":{"ista":"Pappas CG, Mandal PK, Liu B, Kauffmann B, Miao X, Komáromy D, Hoffmann W, Manz C, Chang R, Liu K, Pagel K, Huc I, Otto S. 2020. Emergence of low-symmetry foldamers from single monomers. Nature Chemistry. 12(12), 1180–1186.","ama":"Pappas CG, Mandal PK, Liu B, et al. Emergence of low-symmetry foldamers from single monomers. Nature Chemistry. 2020;12(12):1180-1186. doi:10.1038/s41557-020-00565-2","ieee":"C. G. Pappas et al., “Emergence of low-symmetry foldamers from single monomers,” Nature Chemistry, vol. 12, no. 12. Springer Nature, pp. 1180–1186, 2020.","short":"C.G. Pappas, P.K. Mandal, B. Liu, B. Kauffmann, X. Miao, D. Komáromy, W. Hoffmann, C. Manz, R. Chang, K. Liu, K. Pagel, I. Huc, S. Otto, Nature Chemistry 12 (2020) 1180–1186.","mla":"Pappas, Charalampos G., et al. “Emergence of Low-Symmetry Foldamers from Single Monomers.” Nature Chemistry, vol. 12, no. 12, Springer Nature, 2020, pp. 1180–86, doi:10.1038/s41557-020-00565-2.","chicago":"Pappas, Charalampos G., Pradeep K Mandal, Bin Liu, Brice Kauffmann, Xiaoming Miao, Dávid Komáromy, Waldemar Hoffmann, et al. “Emergence of Low-Symmetry Foldamers from Single Monomers.” Nature Chemistry. Springer Nature, 2020. https://doi.org/10.1038/s41557-020-00565-2.","apa":"Pappas, C. G., Mandal, P. K., Liu, B., Kauffmann, B., Miao, X., Komáromy, D., … Otto, S. (2020). Emergence of low-symmetry foldamers from single monomers. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-020-00565-2"},"doi":"10.1038/s41557-020-00565-2","publication":"Nature Chemistry","OA_type":"green","extern":"1","issue":"12","date_created":"2026-01-29T15:32:38Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv.10079186"}],"publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","page":"1180-1186","author":[{"last_name":"Pappas","full_name":"Pappas, Charalampos G.","first_name":"Charalampos G."},{"first_name":"Pradeep K","full_name":"Mandal, Pradeep K","orcid":"0000-0001-5996-956X","last_name":"Mandal","id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3"},{"last_name":"Liu","full_name":"Liu, Bin","first_name":"Bin"},{"full_name":"Kauffmann, Brice","first_name":"Brice","last_name":"Kauffmann"},{"first_name":"Xiaoming","full_name":"Miao, Xiaoming","last_name":"Miao"},{"first_name":"Dávid","full_name":"Komáromy, Dávid","last_name":"Komáromy"},{"last_name":"Hoffmann","full_name":"Hoffmann, Waldemar","first_name":"Waldemar"},{"last_name":"Manz","full_name":"Manz, Christian","first_name":"Christian"},{"last_name":"Chang","full_name":"Chang, Rayoon","first_name":"Rayoon"},{"last_name":"Liu","first_name":"Kai","full_name":"Liu, Kai"},{"full_name":"Pagel, Kevin","first_name":"Kevin","last_name":"Pagel"},{"last_name":"Huc","first_name":"Ivan","full_name":"Huc, Ivan"},{"first_name":"Sijbren","full_name":"Otto, Sijbren","last_name":"Otto"}],"date_published":"2020-11-20T00:00:00Z","_id":"21084","OA_place":"repository"},{"day":"06","quality_controlled":"1","abstract":[{"lang":"eng","text":"Foldamers combining aliphatic and aromatic main-chain units often produce atypical structures that cannot easily be accessed from purely aromatic or aliphatic sequences. We report solid-state evidence that sequences comprising α-amino acids and quinoline-based monomers adopt conformations that combine the folding propensities of both components. Foldamers 2 and 3 having an XQQ repeat motif (X=α-amino acid, Q=quinoline) were synthesized. Crystals of 2 (X=Phe, Q with an anionic side chain) obtained from water revealed an aromatic helix where amide groups belonging to the α-amino acids created a hydrogen-bond array typical of peptidic helices. Crystals of 3 (X=Ser, Q with a lipophilic side chain) obtained from organic solvents revealed a helix-turn-helix structure in which α-amino acid side chains interfere with main-chain hydrogen bonding. High sequence-dependency of the conformation is typical of peptides but is shown here to include aromatic folding features."}],"type":"journal_article","publication_status":"published","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","oa_version":"Published Version","pmid":1,"OA_type":"hybrid","publication":"ChemPlusChem","doi":"10.1002/cplu.202000416","citation":{"apa":"Hu, X., Mandal, P. K., Kauffmann, B., & Huc, I. (2020). Hybrid sequences that express both aromatic amide and α‐peptidic folding features. ChemPlusChem. Wiley. https://doi.org/10.1002/cplu.202000416","mla":"Hu, Xiaobo, et al. “Hybrid Sequences That Express Both Aromatic Amide and Α‐peptidic Folding Features.” ChemPlusChem, vol. 85, no. 7, Wiley, 2020, pp. 1580–86, doi:10.1002/cplu.202000416.","chicago":"Hu, Xiaobo, Pradeep K Mandal, Brice Kauffmann, and Ivan Huc. “Hybrid Sequences That Express Both Aromatic Amide and Α‐peptidic Folding Features.” ChemPlusChem. Wiley, 2020. https://doi.org/10.1002/cplu.202000416.","short":"X. Hu, P.K. Mandal, B. Kauffmann, I. Huc, ChemPlusChem 85 (2020) 1580–1586.","ieee":"X. Hu, P. K. Mandal, B. Kauffmann, and I. Huc, “Hybrid sequences that express both aromatic amide and α‐peptidic folding features,” ChemPlusChem, vol. 85, no. 7. Wiley, pp. 1580–1586, 2020.","ama":"Hu X, Mandal PK, Kauffmann B, Huc I. Hybrid sequences that express both aromatic amide and α‐peptidic folding features. ChemPlusChem. 2020;85(7):1580-1586. doi:10.1002/cplu.202000416","ista":"Hu X, Mandal PK, Kauffmann B, Huc I. 2020. Hybrid sequences that express both aromatic amide and α‐peptidic folding features. ChemPlusChem. 85(7), 1580–1586."},"external_id":{"pmid":["32729681"]},"title":"Hybrid sequences that express both aromatic amide and α‐peptidic folding features","status":"public","intvolume":" 85","volume":85,"oa":1,"date_updated":"2026-02-20T06:51:31Z","article_type":"original","publication_identifier":{"eissn":["2192-6506"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"main_file_link":[{"url":"https://doi.org/10.1002/cplu.202000416","open_access":"1"}],"date_created":"2026-01-29T15:34:50Z","issue":"7","extern":"1","_id":"21085","OA_place":"publisher","scopus_import":"1","date_published":"2020-07-06T00:00:00Z","page":"1580-1586","author":[{"first_name":"Xiaobo","full_name":"Hu, Xiaobo","last_name":"Hu"},{"id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","last_name":"Mandal","orcid":"0000-0001-5996-956X","full_name":"Mandal, Pradeep K","first_name":"Pradeep K"},{"full_name":"Kauffmann, Brice","first_name":"Brice","last_name":"Kauffmann"},{"full_name":"Huc, Ivan","first_name":"Ivan","last_name":"Huc"}],"has_accepted_license":"1","publisher":"Wiley","article_processing_charge":"No","language":[{"iso":"eng"}]},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","month":"04","day":"23","quality_controlled":"1","related_material":{"record":[{"status":"public","relation":"other","id":"7541"}]},"abstract":[{"lang":"eng","text":"The first wafer-scale growth of site-controlled Ge/Si nanowires is reported by Georgios Katsaros, Jian-Jun Zhang, and co-workers in article number 1906523. They are highly uniform and their position, distance, length, and even square- or L-shaped structures can all be precisely controlled. The electrically tunable spin-orbit coupling demonstrated by transport measurements and the charge sensing between quantum dots in closely spaced wires open a path toward scalable qubit devices using nanowires on silicon."}],"type":"other_academic_publication","oa_version":"Published Version","department":[{"_id":"GeKa"}],"title":"Nanowires: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling (Adv. Mater. 16/2020)","status":"public","publication":"Advanced Materials","citation":{"ista":"Gao F, Wang J, Watzinger H, Hu H, Rančić MJ, Zhang J, Wang T, Yao Y, Wang G, Kukucka J, Vukušić L, Kloeffel C, Loss D, Liu F, Katsaros G, Zhang J. 2020. Nanowires: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling (Adv. Mater. 16/2020), Wiley,p.","ama":"Gao F, Wang J, Watzinger H, et al. Nanowires: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling (Adv. Mater. 16/2020). Vol 32. Wiley; 2020. doi:10.1002/adma.202070122","ieee":"F. Gao et al., Nanowires: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling (Adv. Mater. 16/2020), vol. 32, no. 16. Wiley, 2020.","short":"F. Gao, J. Wang, H. Watzinger, H. Hu, M.J. Rančić, J. Zhang, T. Wang, Y. Yao, G. Wang, J. Kukucka, L. Vukušić, C. Kloeffel, D. Loss, F. Liu, G. Katsaros, J. Zhang, Nanowires: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling (Adv. Mater. 16/2020), Wiley, 2020.","mla":"Gao, Fei, et al. “Nanowires: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling (Adv. Mater. 16/2020).” Advanced Materials, vol. 32, no. 16, 2070122, Wiley, 2020, doi:10.1002/adma.202070122.","chicago":"Gao, Fei, Jian‐Huan Wang, Hannes Watzinger, Hao Hu, Marko J. Rančić, Jie‐Yin Zhang, Ting Wang, et al. Nanowires: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling (Adv. Mater. 16/2020). Advanced Materials. Vol. 32. Wiley, 2020. https://doi.org/10.1002/adma.202070122.","apa":"Gao, F., Wang, J., Watzinger, H., Hu, H., Rančić, M. J., Zhang, J., … Zhang, J. (2020). Nanowires: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling (Adv. Mater. 16/2020). Advanced Materials (Vol. 32). Wiley. https://doi.org/10.1002/adma.202070122"},"doi":"10.1002/adma.202070122","oa":1,"volume":32,"date_updated":"2025-06-12T07:16:21Z","intvolume":" 32","main_file_link":[{"url":"https://doi.org/10.1002/adma.202070122","open_access":"1"}],"publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"issue":"16","date_created":"2024-08-20T08:22:42Z","article_number":"2070122","_id":"17444","publisher":"Wiley","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2020-04-23T00:00:00Z","author":[{"first_name":"Fei","full_name":"Gao, Fei","last_name":"Gao"},{"last_name":"Wang","first_name":"Jian‐Huan","full_name":"Wang, Jian‐Huan"},{"last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","full_name":"Watzinger, Hannes"},{"last_name":"Hu","full_name":"Hu, Hao","first_name":"Hao"},{"last_name":"Rančić","full_name":"Rančić, Marko J.","first_name":"Marko J."},{"full_name":"Zhang, Jie‐Yin","first_name":"Jie‐Yin","last_name":"Zhang"},{"full_name":"Wang, Ting","first_name":"Ting","last_name":"Wang"},{"full_name":"Yao, Yuan","first_name":"Yuan","last_name":"Yao"},{"first_name":"Gui‐Lei","full_name":"Wang, Gui‐Lei","last_name":"Wang"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","full_name":"Kukucka, Josip","first_name":"Josip"},{"full_name":"Vukušić, Lada","first_name":"Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukušić","orcid":"0000-0003-2424-8636"},{"last_name":"Kloeffel","full_name":"Kloeffel, Christoph","first_name":"Christoph"},{"first_name":"Daniel","full_name":"Loss, Daniel","last_name":"Loss"},{"first_name":"Feng","full_name":"Liu, Feng","last_name":"Liu"},{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios"},{"last_name":"Zhang","full_name":"Zhang, Jian‐Jun","first_name":"Jian‐Jun"}]},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/mnras/staa1258"}],"publication_identifier":{"issn":["0035-8711","1365-2966"]},"issue":"1","extern":"1","date_created":"2024-09-05T09:27:32Z","scopus_import":"1","_id":"17524","publisher":"Oxford University Press","language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2020-05-07T00:00:00Z","page":"1403-1413","author":[{"full_name":"Xin, Chengcheng","first_name":"Chengcheng","last_name":"Xin"},{"last_name":"Charisi","full_name":"Charisi, Maria","first_name":"Maria"},{"id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","last_name":"Haiman","full_name":"Haiman, Zoltán","first_name":"Zoltán"},{"last_name":"Schiminovich","full_name":"Schiminovich, David","first_name":"David"}],"publication_status":"published","month":"05","year":"2020","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"07","quality_controlled":"1","abstract":[{"lang":"eng","text":"The variability of quasars across multiple wavelengths is a useful probe of physical conditions in active galactic nuclei. In particular, variable accretion rates, instabilities, and reverberation effects in the accretion disc of a supermassive black hole are expected to produce correlated flux variations in ultraviolet (UV) and optical bands. Recent work has further argued that binary quasars should exhibit strongly correlated UV and optical periodicities. Strong UV–optical correlations have indeed been established in small samples of (N ≲ 30) quasars with well-sampled light curves, and have extended the ‘bluer-when-brighter’ trend previously found within the optical bands. Here, we further test the nature of quasar variability by examining the observed-frame UV–optical correlations among bright quasars extracted from the Half Million Quasars (HMQ) catalogue. We identified a large sample of 1315 quasars in HMQ with overlapping UV and optical light curves from the Galaxy Evolution Explorer and the Catalina Real-time Transient Survey, respectively. We find that strong correlations exist in this much larger sample, but we rule out, at ∼95 per cent confidence, the simple hypothesis that the intrinsic UV and optical variations of all quasars are fully correlated. Our results therefore imply the existence of physical mechanism(s) that can generate uncorrelated optical and UV flux variations."}],"type":"journal_article","oa_version":"Published Version","title":"Correlation between optical and UV variability of a large sample of quasars","status":"public","publication":"Monthly Notices of the Royal Astronomical Society","doi":"10.1093/mnras/staa1258","citation":{"ista":"Xin C, Charisi M, Haiman Z, Schiminovich D. 2020. Correlation between optical and UV variability of a large sample of quasars. Monthly Notices of the Royal Astronomical Society. 495(1), 1403–1413.","ama":"Xin C, Charisi M, Haiman Z, Schiminovich D. Correlation between optical and UV variability of a large sample of quasars. Monthly Notices of the Royal Astronomical Society. 2020;495(1):1403-1413. doi:10.1093/mnras/staa1258","ieee":"C. Xin, M. Charisi, Z. Haiman, and D. Schiminovich, “Correlation between optical and UV variability of a large sample of quasars,” Monthly Notices of the Royal Astronomical Society, vol. 495, no. 1. Oxford University Press, pp. 1403–1413, 2020.","short":"C. Xin, M. Charisi, Z. Haiman, D. Schiminovich, Monthly Notices of the Royal Astronomical Society 495 (2020) 1403–1413.","chicago":"Xin, Chengcheng, Maria Charisi, Zoltán Haiman, and David Schiminovich. “Correlation between Optical and UV Variability of a Large Sample of Quasars.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa1258.","mla":"Xin, Chengcheng, et al. “Correlation between Optical and UV Variability of a Large Sample of Quasars.” Monthly Notices of the Royal Astronomical Society, vol. 495, no. 1, Oxford University Press, 2020, pp. 1403–13, doi:10.1093/mnras/staa1258.","apa":"Xin, C., Charisi, M., Haiman, Z., & Schiminovich, D. (2020). Correlation between optical and UV variability of a large sample of quasars. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa1258"},"volume":495,"oa":1,"date_updated":"2024-09-11T08:08:21Z","article_type":"original","intvolume":" 495"},{"citation":{"apa":"Matilla, J. M. Z., Waterval, S., & Haiman, Z. (2020). Optimizing simulation parameters for weak lensing analyses involving non-Gaussian observables. The Astronomical Journal. American Astronomical Society. https://doi.org/10.3847/1538-3881/ab8f8c","mla":"Matilla, José Manuel Zorrilla, et al. “Optimizing Simulation Parameters for Weak Lensing Analyses Involving Non-Gaussian Observables.” The Astronomical Journal, vol. 159, no. 6, 284, American Astronomical Society, 2020, doi:10.3847/1538-3881/ab8f8c.","chicago":"Matilla, José Manuel Zorrilla, Stefan Waterval, and Zoltán Haiman. “Optimizing Simulation Parameters for Weak Lensing Analyses Involving Non-Gaussian Observables.” The Astronomical Journal. American Astronomical Society, 2020. https://doi.org/10.3847/1538-3881/ab8f8c.","short":"J.M.Z. Matilla, S. Waterval, Z. Haiman, The Astronomical Journal 159 (2020).","ieee":"J. M. Z. Matilla, S. Waterval, and Z. Haiman, “Optimizing simulation parameters for weak lensing analyses involving non-Gaussian observables,” The Astronomical Journal, vol. 159, no. 6. American Astronomical Society, 2020.","ama":"Matilla JMZ, Waterval S, Haiman Z. Optimizing simulation parameters for weak lensing analyses involving non-Gaussian observables. The Astronomical Journal. 2020;159(6). doi:10.3847/1538-3881/ab8f8c","ista":"Matilla JMZ, Waterval S, Haiman Z. 2020. Optimizing simulation parameters for weak lensing analyses involving non-Gaussian observables. The Astronomical Journal. 159(6), 284."},"doi":"10.3847/1538-3881/ab8f8c","publication":"The Astronomical Journal","status":"public","title":"Optimizing simulation parameters for weak lensing analyses involving non-Gaussian observables","intvolume":" 159","date_updated":"2024-09-11T09:03:15Z","volume":159,"oa":1,"article_type":"original","quality_controlled":"1","day":"29","type":"journal_article","abstract":[{"text":"We performed a series of numerical experiments to quantify the sensitivity of the predictions for weak lensing statistics obtained in ray-tracing dark matter (DM)-only simulations, to two hyper-parameters that influence the accuracy as well as the computational cost of the predictions: the thickness of the lens planes used to build past light cones and the mass resolution of the underlying DM simulation. The statistics considered are the power spectrum (PS) and a series of non-Gaussian observables, including the one-point probability density function, lensing peaks, and Minkowski functionals. Counterintuitively, we find that using thin lens planes (< 60 h−1 Mpc on a 240 h−1 Mpc simulation box) suppresses the PS over a broad range of scales beyond what would be acceptable for a survey comparable to the Large Synoptic Survey Telescope (LSST). A mass resolution of 7.2 × 1011 h−1 M⊙ per DM particle (or 2563 particles in a (240 h−1 Mpc)3 box) is sufficient to extract information using the PS and non-Gaussian statistics from weak lensing data at angular scales down to 1' with LSST-like levels of shape noise.","lang":"eng"}],"month":"05","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2020","publication_status":"published","oa_version":"Published Version","article_number":"284","_id":"17528","scopus_import":"1","author":[{"full_name":"Matilla, José Manuel Zorrilla","first_name":"José Manuel Zorrilla","last_name":"Matilla"},{"last_name":"Waterval","first_name":"Stefan","full_name":"Waterval, Stefan"},{"first_name":"Zoltán","full_name":"Haiman, Zoltán","last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36"}],"date_published":"2020-05-29T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"American Astronomical Society","publication_identifier":{"issn":["0004-6256","1538-3881"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.3847/1538-3881/ab8f8c"}],"date_created":"2024-09-05T09:35:49Z","issue":"6","extern":"1"}]