[{"oa_version":"Published Version","publication_status":"published","ddc":["530"],"abstract":[{"lang":"eng","text":"The process of polymer condensation, i.e., the formation of bonds between reactive end groups, is ubiquitous in both industry and biology. Here we study generic systems undergoing polymer condensation in competition with cyclization. Using a generalized Smoluchowski theory, molecular dynamics simulations and experiments with DNA and ATP-consuming T4 ligase, we find that this system displays a transition, from a ring-dominated regime with finite-length chains at infinite time to a linear-polymers-dominated one with chains that keep growing in time. Finally, we show that fluids prepared close to the transition may have widely different compositions and rheology at large condensation times."}],"has_accepted_license":"1","day":"01","doi":"10.1103/PhysRevResearch.6.023189","article_number":"023189","department":[{"_id":"AnSa"}],"publication":"Physical Review Research","scopus_import":"1","publication_identifier":{"eissn":["2643-1564"]},"status":"public","oa":1,"acknowledgement":"D.M. acknowledges the support of the Royal Society via a University Research Fellowship. This project has received support from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Program (Grant Agreement No. 947918 to D.M. and No. 677532 to M.L.). The authors acknowledge insightful discussions with Daan Noordermeer and Antonio Valdes, who also kindly gifted us with the 1288 plasmid.","date_updated":"2025-05-14T09:32:40Z","author":[{"last_name":"Panoukidou","first_name":"Maria","full_name":"Panoukidou, Maria"},{"last_name":"Weir","full_name":"Weir, Simon","first_name":"Simon"},{"full_name":"Sorichetti, Valerio","first_name":"Valerio","orcid":"0000-0002-9645-6576","last_name":"Sorichetti","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b"},{"last_name":"Fosado","full_name":"Fosado, Yair Gutierrez","first_name":"Yair Gutierrez"},{"last_name":"Lenz","full_name":"Lenz, Martin","first_name":"Martin"},{"full_name":"Michieletto, Davide","first_name":"Davide","last_name":"Michieletto"}],"publisher":"American Physical Society","citation":{"apa":"Panoukidou, M., Weir, S., Sorichetti, V., Fosado, Y. G., Lenz, M., &#38; Michieletto, D. (2024). Runaway transition in irreversible polymer condensation with cyclization. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.023189\">https://doi.org/10.1103/PhysRevResearch.6.023189</a>","short":"M. Panoukidou, S. Weir, V. Sorichetti, Y.G. Fosado, M. Lenz, D. Michieletto, Physical Review Research 6 (2024).","ista":"Panoukidou M, Weir S, Sorichetti V, Fosado YG, Lenz M, Michieletto D. 2024. Runaway transition in irreversible polymer condensation with cyclization. Physical Review Research. 6(2), 023189.","chicago":"Panoukidou, Maria, Simon Weir, Valerio Sorichetti, Yair Gutierrez Fosado, Martin Lenz, and Davide Michieletto. “Runaway Transition in Irreversible Polymer Condensation with Cyclization.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.023189\">https://doi.org/10.1103/PhysRevResearch.6.023189</a>.","ieee":"M. Panoukidou, S. Weir, V. Sorichetti, Y. G. Fosado, M. Lenz, and D. Michieletto, “Runaway transition in irreversible polymer condensation with cyclization,” <i>Physical Review Research</i>, vol. 6, no. 2. American Physical Society, 2024.","mla":"Panoukidou, Maria, et al. “Runaway Transition in Irreversible Polymer Condensation with Cyclization.” <i>Physical Review Research</i>, vol. 6, no. 2, 023189, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.023189\">10.1103/PhysRevResearch.6.023189</a>.","ama":"Panoukidou M, Weir S, Sorichetti V, Fosado YG, Lenz M, Michieletto D. Runaway transition in irreversible polymer condensation with cyclization. <i>Physical Review Research</i>. 2024;6(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.023189\">10.1103/PhysRevResearch.6.023189</a>"},"quality_controlled":"1","type":"journal_article","date_created":"2024-05-26T22:00:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","article_type":"original","file":[{"creator":"dernst","access_level":"open_access","date_created":"2024-05-27T06:37:01Z","file_size":1409416,"content_type":"application/pdf","checksum":"63a962d49ef1e21a3367d265784df14b","success":1,"file_id":"17055","date_updated":"2024-05-27T06:37:01Z","relation":"main_file","file_name":"2024_PhysicalReviewResearch_Panoukidou.pdf"}],"month":"05","issue":"2","volume":6,"intvolume":"         6","language":[{"iso":"eng"}],"_id":"17050","date_published":"2024-05-01T00:00:00Z","DOAJ_listed":"1","file_date_updated":"2024-05-27T06:37:01Z","external_id":{"arxiv":["2210.14010"]},"year":"2024","title":"Runaway transition in irreversible polymer condensation with cyclization","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"arxiv":1},{"citation":{"ista":"Weiner E, Berryman E, Frey FF, Solís AG, Leier A, Lago TM, Šarić A, Otegui MS. 2024. Endosomal membrane budding patterns in plants. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2409407121.","ieee":"E. Weiner <i>et al.</i>, “Endosomal membrane budding patterns in plants,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","chicago":"Weiner, Ethan, Elizabeth Berryman, Felix F Frey, Ariadna González Solís, André Leier, Tatiana Marquez Lago, Anđela Šarić, and Marisa S. Otegui. “Endosomal Membrane Budding Patterns in Plants.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2409407121\">https://doi.org/10.1073/pnas.2409407121</a>.","short":"E. Weiner, E. Berryman, F.F. Frey, A.G. Solís, A. Leier, T.M. Lago, A. Šarić, M.S. Otegui, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","apa":"Weiner, E., Berryman, E., Frey, F. F., Solís, A. G., Leier, A., Lago, T. M., … Otegui, M. S. (2024). Endosomal membrane budding patterns in plants. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2409407121\">https://doi.org/10.1073/pnas.2409407121</a>","ama":"Weiner E, Berryman E, Frey FF, et al. Endosomal membrane budding patterns in plants. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2409407121\">10.1073/pnas.2409407121</a>","mla":"Weiner, Ethan, et al. “Endosomal Membrane Budding Patterns in Plants.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2409407121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2409407121\">10.1073/pnas.2409407121</a>."},"publisher":"National Academy of Sciences","project":[{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"date_updated":"2025-09-08T14:38:35Z","author":[{"full_name":"Weiner, Ethan","first_name":"Ethan","last_name":"Weiner"},{"last_name":"Berryman","first_name":"Elizabeth","full_name":"Berryman, Elizabeth"},{"first_name":"Felix F","full_name":"Frey, Felix F","last_name":"Frey","orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"first_name":"Ariadna González","full_name":"Solís, Ariadna González","last_name":"Solís"},{"last_name":"Leier","full_name":"Leier, André","first_name":"André"},{"last_name":"Lago","first_name":"Tatiana Marquez","full_name":"Lago, Tatiana Marquez"},{"first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139"},{"last_name":"Otegui","first_name":"Marisa S.","full_name":"Otegui, Marisa S."}],"pmid":1,"quality_controlled":"1","ec_funded":1,"scopus_import":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","oa":1,"acknowledgement":"We would like to thank Janice Pennington for her support with electron tomography data collection, Dr. Ingrid Jordon-Thaden, director of the Botany Garden and Greenhouse of University of Wisconsin Madison, for her invaluable assistance collecting plant materials, Dr. Marie Trest for providing Chara specimens, and Dr. Nicholas Keuler for his advice on statistical analyses. We thank Charlie Hamilton for exploring the initial computational model. This work was supported by grant NSF MCB 2114603 and NIH 1S10OD026769-01 to M.S.O. F.F acknowledges support as a NOMIS Fellow from the NOMIS Foundation. A.Š. acknowledges ERC Starting Grant “NEPA” 802960.","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"status":"public","OA_type":"hybrid","doi":"10.1073/pnas.2409407121","article_number":"e2409407121","has_accepted_license":"1","day":"29","department":[{"_id":"AnSa"}],"isi":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Multivesicular endosomes (MVEs) sequester membrane proteins destined for degradation within intralumenal vesicles (ILVs), a process mediated by the membrane-remodeling action of Endosomal Sorting Complex Required for Transport (ESCRT) proteins. In Arabidopsis, endosomal membrane constriction and scission are uncoupled, resulting in the formation of extensive concatenated ILV networks and enhancing cargo sequestration efficiency. Here, we used a combination of electron tomography, computer simulations, and mathematical modeling to address the questions of when concatenated ILV networks evolved in plants and what drives their formation. Through morphometric analyses of tomographic reconstructions of endosomes across yeast, algae, and various land plants, we have found that ILV concatenation is widespread within plant species, but only prevalent in seed plants, especially in flowering plants. Multiple budding sites that require the formation of pores in the limiting membrane were only identified in hornworts and seed plants, suggesting that this mechanism has evolved independently in both plant lineages. To identify the conditions under which these multiple budding sites can arise, we used particle-based molecular dynamics simulations and found that changes in ESCRT filament properties, such as filament curvature and membrane binding energy, can generate the membrane shapes observed in multiple budding sites. To understand the relationship between membrane budding activity and ILV network topology, we performed computational simulations and identified a set of membrane remodeling parameters that can recapitulate our tomographic datasets."}],"publication_status":"published","ddc":["570"],"external_id":{"pmid":["39441629"],"isi":["001349500800007"]},"file_date_updated":"2024-11-11T09:35:15Z","title":"Endosomal membrane budding patterns in plants","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"year":"2024","date_published":"2024-10-29T00:00:00Z","_id":"18526","issue":"44","OA_place":"publisher","intvolume":"       121","language":[{"iso":"eng"}],"volume":121,"date_created":"2024-11-10T23:01:59Z","type":"journal_article","article_type":"original","month":"10","file":[{"checksum":"21c82d2ab58ff99b2bd0489797be42e5","date_created":"2024-11-11T09:35:15Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_size":5268074,"file_name":"2024_PNAS_Weiner.pdf","file_id":"18538","success":1,"relation":"main_file","date_updated":"2024-11-11T09:35:15Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (in subscription journal)"},{"oa":1,"acknowledgement":"We thank Markus Mund, Aline Tschanz, and Jonas Ries for helpful discussions and a critical reading of the manuscript. We also kindly acknowledge Simon Scheuring for providing the HS-AFM data for the analysis of clathrin coat invagination. We thank the reviewers of previous versions of this manuscript for useful feedback that helped us to improve this work. F.F. acknowledges financial support by the NOMIS foundation. U.S.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Project No. 240245660 (SFB 1129). Moreover, he is a member of the Interdisciplinary Center for Scientific Computing (IWR) at Heidelberg and of the Max Planck School Matter to Life supported by the German Federal Ministry of Education and Research (BMBF) in collaboration with the Max Planck Society.","OA_type":"green","status":"public","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"publication":"Physical Review E","scopus_import":"1","pmid":1,"quality_controlled":"1","publisher":"American Physical Society","citation":{"ama":"Frey FF, Schwarz US. Coat stiffening can explain invagination of clathrin-coated membranes. <i>Physical Review E</i>. 2024;110(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">10.1103/PhysRevE.110.064403</a>","mla":"Frey, Felix F., and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination of Clathrin-Coated Membranes.” <i>Physical Review E</i>, vol. 110, no. 6, 064403, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">10.1103/PhysRevE.110.064403</a>.","ista":"Frey FF, Schwarz US. 2024. Coat stiffening can explain invagination of clathrin-coated membranes. Physical Review E. 110(6), 064403.","ieee":"F. F. Frey and U. S. Schwarz, “Coat stiffening can explain invagination of clathrin-coated membranes,” <i>Physical Review E</i>, vol. 110, no. 6. American Physical Society, 2024.","chicago":"Frey, Felix F, and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination of Clathrin-Coated Membranes.” <i>Physical Review E</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">https://doi.org/10.1103/PhysRevE.110.064403</a>.","short":"F.F. Frey, U.S. Schwarz, Physical Review E 110 (2024).","apa":"Frey, F. F., &#38; Schwarz, U. S. (2024). Coat stiffening can explain invagination of clathrin-coated membranes. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">https://doi.org/10.1103/PhysRevE.110.064403</a>"},"author":[{"full_name":"Frey, Felix F","first_name":"Felix F","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","orcid":"0000-0001-8501-6017"},{"first_name":"Ulrich S.","full_name":"Schwarz, Ulrich S.","last_name":"Schwarz"}],"date_updated":"2025-09-09T11:56:34Z","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the main pathway used by eukaryotic cells to take up extracellular material, but the dominant physical mechanisms driving this process are still elusive. Recently, several high-resolution imaging techniques have been used on different cell lines to measure the geometrical properties of clathrin-coated pits over their whole lifetime. Here, we first show that the combination of all datasets with the recently introduced cooperative curvature model defines a consensus pathway, which is characterized by a flat-to-curved transition at finite area, followed by linear growth and subsequent saturation of curvature. We then apply an energetic model for the composite of the plasma membrane and clathrin coat to this consensus pathway to show that the dominant mechanism for invagination could be coat stiffening, which might originate from cooperative interactions between the different clathrin molecules and progressively drives the system toward its intrinsic curvature. Our theory predicts that two length scales determine the invagination pathway, namely the patch size at which the flat-to-curved transition occurs and the final pit radius."}],"publication_status":"published","oa_version":"Preprint","isi":1,"department":[{"_id":"AnSa"}],"article_number":"064403","doi":"10.1103/PhysRevE.110.064403","day":"10","date_published":"2024-12-10T00:00:00Z","_id":"18704","arxiv":1,"title":"Coat stiffening can explain invagination of clathrin-coated membranes","year":"2024","external_id":{"arxiv":["2405.02820"],"isi":["001379135100004"],"pmid":["39916158"]},"month":"12","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","date_created":"2024-12-22T23:01:48Z","type":"journal_article","intvolume":"       110","language":[{"iso":"eng"}],"volume":110,"issue":"6","OA_place":"repository","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.02820","open_access":"1"}]},{"doi":"10.1021/acsnano.4c03839","day":"16","has_accepted_license":"1","department":[{"_id":"AnSa"}],"isi":1,"oa_version":"Published Version","page":"18485-18492","abstract":[{"lang":"eng","text":"Collagen is the most abundant protein in tissue scaffolds in live organisms. Collagen can self-assemble in vitro, which has led to a number of biotechnological and biomedical applications. To understand the dominant factors that participate in the formation of collagen nanostructures, here we study in real time and with nanoscale resolution the disassembly and reassembly of collagens. We implement a high-speed force microscope, which provides in situ high spatiotemporal resolution images of collagen nanostructures under changing pH conditions. The disassembly and reassembly are dominated by the electrostatic interactions among amino-acid residues of different molecules. Acidic conditions favor disassembly by neutralizing negatively charged residues. The process sets a net repulsive force between collagen molecules. A neutral pH favors the presence of negative and positively charged residues along the collagen molecules, which promotes their electrostatic attraction. Molecular dynamics simulations reproduce the experimental behavior and validate the electrostatic-based model of the disassembly and reassembly processes."}],"publication_status":"published","ddc":["540"],"citation":{"short":"C. Garcia-Sacristan, V.G. Gisbert, K. Klein, A. Šarić, R. Garcia, ACS Nano 18 (2024) 18485–18492.","apa":"Garcia-Sacristan, C., Gisbert, V. G., Klein, K., Šarić, A., &#38; Garcia, R. (2024). In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.4c03839\">https://doi.org/10.1021/acsnano.4c03839</a>","ieee":"C. Garcia-Sacristan, V. G. Gisbert, K. Klein, A. Šarić, and R. Garcia, “In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures,” <i>ACS Nano</i>, vol. 18, no. 28. American Chemical Society, pp. 18485–18492, 2024.","chicago":"Garcia-Sacristan, Clara, Victor G. Gisbert, Kevin Klein, Anđela Šarić, and Ricardo Garcia. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” <i>ACS Nano</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsnano.4c03839\">https://doi.org/10.1021/acsnano.4c03839</a>.","ista":"Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. 2024. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS Nano. 18(28), 18485–18492.","mla":"Garcia-Sacristan, Clara, et al. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” <i>ACS Nano</i>, vol. 18, no. 28, American Chemical Society, 2024, pp. 18485–92, doi:<a href=\"https://doi.org/10.1021/acsnano.4c03839\">10.1021/acsnano.4c03839</a>.","ama":"Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. <i>ACS Nano</i>. 2024;18(28):18485-18492. doi:<a href=\"https://doi.org/10.1021/acsnano.4c03839\">10.1021/acsnano.4c03839</a>"},"publisher":"American Chemical Society","author":[{"first_name":"Clara","full_name":"Garcia-Sacristan, Clara","last_name":"Garcia-Sacristan"},{"full_name":"Gisbert, Victor G.","first_name":"Victor G.","last_name":"Gisbert"},{"first_name":"Kevin","full_name":"Klein, Kevin","id":"1e7ede04-9e54-11f0-9ec4-8d4d5563c398","last_name":"Klein"},{"full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Ricardo","full_name":"Garcia, Ricardo","last_name":"Garcia"}],"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"}],"date_updated":"2025-12-16T09:01:10Z","pmid":1,"quality_controlled":"1","ec_funded":1,"scopus_import":"1","publication":"ACS Nano","oa":1,"acknowledgement":"We are grateful to Nancy Forde (Simon Fraser University) for her motivating comments. Financial support from the Ministerio de Ciencia, Innovación y Universidades (PID2019-106801GB-I00 and PID2022-136851NB-I00) is acknowledged. A.Š. and K.K. acknowledge support from the Royal Society University Research Fellowship and ERC the European Union’s Horizon 2020584 Research and Innovation Programme (Grant No. 585 80296).","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"OA_type":"hybrid","status":"public","issue":"28","OA_place":"publisher","intvolume":"        18","language":[{"iso":"eng"}],"volume":18,"date_created":"2024-07-14T22:01:12Z","type":"journal_article","month":"07","file":[{"date_created":"2025-01-09T12:06:48Z","access_level":"open_access","creator":"dernst","file_size":10036838,"content_type":"application/pdf","checksum":"b7e9ce718e92f568bcb3810e8e28e458","file_id":"18808","success":1,"date_updated":"2025-01-09T12:06:48Z","relation":"main_file","file_name":"2024_ACSNano_GarciaSacristan.pdf"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38958189"],"isi":["001263155500001"]},"file_date_updated":"2025-01-09T12:06:48Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures","year":"2024","date_published":"2024-07-16T00:00:00Z","_id":"17239"},{"OA_place":"publisher","volume":20,"language":[{"iso":"eng"}],"intvolume":"        20","type":"journal_article","APC_amount":"12348 EUR","date_created":"2024-08-25T22:01:08Z","article_processing_charge":"Yes (in subscription journal)","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"10","article_type":"original","file":[{"file_name":"2024_NaturePhysics_VanhilleCampos.pdf","file_id":"19556","success":1,"relation":"main_file","date_updated":"2025-04-14T06:06:35Z","checksum":"c4842152e2b90d67f48ea8c9ed7c473b","date_created":"2025-04-14T06:06:35Z","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":8058249}],"file_date_updated":"2025-04-14T06:06:35Z","external_id":{"isi":["001289394500005"],"pmid":["39416851"]},"year":"2024","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Self-organization of mortal filaments and its role in bacterial division ring formation","_id":"17460","date_published":"2024-10-01T00:00:00Z","has_accepted_license":"1","day":"01","doi":"10.1038/s41567-024-02597-8","isi":1,"department":[{"_id":"AnSa"},{"_id":"MaLo"}],"oa_version":"Published Version","ddc":["570"],"publication_status":"published","corr_author":"1","abstract":[{"text":"Filaments in the cell commonly treadmill. Driven by energy consumption, they grow on one end while shrinking on the other, causing filaments to appear motile even though individual proteins remain static. This process is characteristic of cytoskeletal filaments and leads to collective filament self-organization. Here we show that treadmilling drives filament nematic ordering by dissolving misaligned filaments. Taking the bacterial FtsZ protein involved in cell division as an example, we show that this mechanism aligns FtsZ filaments in vitro and drives the organization of the division ring in living Bacillus subtilis cells. We find that ordering via local dissolution also allows the system to quickly respond to chemical and geometrical biases in the cell, enabling us to quantitatively explain the ring formation dynamics in vivo. Beyond FtsZ and other cytoskeletal filaments, our study identifies a mechanism for self-organization via constant birth and death of energy-consuming filaments.","lang":"eng"}],"page":"1670-1678","project":[{"name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"date_updated":"2025-09-08T09:02:20Z","author":[{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo","first_name":"Christian Eduardo"},{"first_name":"Kevin D.","full_name":"Whitley, Kevin D.","last_name":"Whitley"},{"first_name":"Philipp","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler"},{"first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"},{"full_name":"Holden, Séamus","first_name":"Séamus","last_name":"Holden"},{"first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139"}],"citation":{"ista":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. 2024. Self-organization of mortal filaments and its role in bacterial division ring formation. Nature Physics. 20, 1670–1678.","ieee":"C. E. Vanhille-Campos, K. D. Whitley, P. Radler, M. Loose, S. Holden, and A. Šarić, “Self-organization of mortal filaments and its role in bacterial division ring formation,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1670–1678, 2024.","chicago":"Vanhille-Campos, Christian Eduardo, Kevin D. Whitley, Philipp Radler, Martin Loose, Séamus Holden, and Anđela Šarić. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02597-8\">https://doi.org/10.1038/s41567-024-02597-8</a>.","short":"C.E. Vanhille-Campos, K.D. Whitley, P. Radler, M. Loose, S. Holden, A. Šarić, Nature Physics 20 (2024) 1670–1678.","apa":"Vanhille-Campos, C. E., Whitley, K. D., Radler, P., Loose, M., Holden, S., &#38; Šarić, A. (2024). Self-organization of mortal filaments and its role in bacterial division ring formation. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02597-8\">https://doi.org/10.1038/s41567-024-02597-8</a>","ama":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. Self-organization of mortal filaments and its role in bacterial division ring formation. <i>Nature Physics</i>. 2024;20:1670-1678. doi:<a href=\"https://doi.org/10.1038/s41567-024-02597-8\">10.1038/s41567-024-02597-8</a>","mla":"Vanhille-Campos, Christian Eduardo, et al. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1670–78, doi:<a href=\"https://doi.org/10.1038/s41567-024-02597-8\">10.1038/s41567-024-02597-8</a>."},"publisher":"Springer Nature","quality_controlled":"1","ec_funded":1,"pmid":1,"scopus_import":"1","publication":"Nature Physics","OA_type":"hybrid","status":"public","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"acknowledgement":"We thank I. Palaia (ISTA) for useful discussions and K. Lim and R. W. Wong (WPI-Nano Life Science Institute, Kanazawa University) for providing access to HS-AFM. We would like to thank B. Prats Mateu (MSD Austria, Vienna) for providing the HS-AFM data. This work was supported by the Royal Society (grant no. UF160266; C.V.-C. and A.Š.), the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960; A.Š.), the Austrian Science Fund (FWF) Stand-Alone P34607 (M.L.) and a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (grant no. 206670/Z/17/Z; S.H. and K.D.W.).","oa":1},{"language":[{"iso":"eng"}],"intvolume":"        84","volume":84,"issue":"17","file":[{"access_level":"open_access","creator":"dernst","date_created":"2024-09-16T07:38:38Z","content_type":"application/pdf","file_size":11654644,"checksum":"3f360e0287b8ec79fb2b8b02b5070360","success":1,"file_id":"18075","relation":"main_file","date_updated":"2024-09-16T07:38:38Z","file_name":"2024_MolecularCell_HernandezArmendariz.pdf"}],"month":"09","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (in subscription journal)","date_created":"2024-09-15T22:01:41Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"A liquid-like coat mediates chromosome clustering during mitotic exit","year":"2024","external_id":{"pmid":["39153474"],"isi":["001309051100001"]},"file_date_updated":"2024-09-16T07:38:38Z","date_published":"2024-09-05T00:00:00Z","_id":"18072","isi":1,"department":[{"_id":"AnSa"}],"doi":"10.1016/j.molcel.2024.07.022","has_accepted_license":"1","day":"05","abstract":[{"text":"The individualization of chromosomes during early mitosis and their clustering upon exit from cell division are two key transitions that ensure efficient segregation of eukaryotic chromosomes. Both processes are regulated by the surfactant-like protein Ki-67, but how Ki-67 achieves these diametric functions has remained unknown. Here, we report that Ki-67 radically switches from a chromosome repellent to a chromosome attractant during anaphase in human cells. We show that Ki-67 dephosphorylation during mitotic exit and the simultaneous exposure of a conserved basic patch induce the RNA-dependent formation of a liquid-like condensed phase on the chromosome surface. Experiments and coarse-grained simulations support a model in which the coalescence of chromosome surfaces, driven by co-condensation of Ki-67 and RNA, promotes clustering of chromosomes. Our study reveals how the switch of Ki-67 from a surfactant to a liquid-like condensed phase can generate mechanical forces during genome segregation that are required for re-establishing nuclear-cytoplasmic compartmentalization after mitosis.","lang":"eng"}],"page":"P3254-3270.E9","ddc":["570"],"publication_status":"published","oa_version":"Published Version","pmid":1,"quality_controlled":"1","ec_funded":1,"citation":{"short":"A. Hernandez-Armendariz, V. Sorichetti, Y. Hayashi, Z. Koskova, A. Brunner, J. Ellenberg, A. Šarić, S. Cuylen-Haering, Molecular Cell 84 (2024) P3254–3270.E9.","apa":"Hernandez-Armendariz, A., Sorichetti, V., Hayashi, Y., Koskova, Z., Brunner, A., Ellenberg, J., … Cuylen-Haering, S. (2024). A liquid-like coat mediates chromosome clustering during mitotic exit. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2024.07.022\">https://doi.org/10.1016/j.molcel.2024.07.022</a>","ista":"Hernandez-Armendariz A, Sorichetti V, Hayashi Y, Koskova Z, Brunner A, Ellenberg J, Šarić A, Cuylen-Haering S. 2024. A liquid-like coat mediates chromosome clustering during mitotic exit. Molecular Cell. 84(17), P3254–3270.E9.","ieee":"A. Hernandez-Armendariz <i>et al.</i>, “A liquid-like coat mediates chromosome clustering during mitotic exit,” <i>Molecular Cell</i>, vol. 84, no. 17. Cell Press, p. P3254–3270.E9, 2024.","chicago":"Hernandez-Armendariz, Alberto, Valerio Sorichetti, Yuki Hayashi, Zuzana Koskova, Andreas Brunner, Jan Ellenberg, Anđela Šarić, and Sara Cuylen-Haering. “A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit.” <i>Molecular Cell</i>. Cell Press, 2024. <a href=\"https://doi.org/10.1016/j.molcel.2024.07.022\">https://doi.org/10.1016/j.molcel.2024.07.022</a>.","mla":"Hernandez-Armendariz, Alberto, et al. “A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit.” <i>Molecular Cell</i>, vol. 84, no. 17, Cell Press, 2024, p. P3254–3270.E9, doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.07.022\">10.1016/j.molcel.2024.07.022</a>.","ama":"Hernandez-Armendariz A, Sorichetti V, Hayashi Y, et al. A liquid-like coat mediates chromosome clustering during mitotic exit. <i>Molecular Cell</i>. 2024;84(17):P3254-3270.E9. doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.07.022\">10.1016/j.molcel.2024.07.022</a>"},"publisher":"Cell Press","date_updated":"2025-09-08T09:23:02Z","project":[{"call_identifier":"H2020","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"author":[{"first_name":"Alberto","full_name":"Hernandez-Armendariz, Alberto","last_name":"Hernandez-Armendariz"},{"full_name":"Sorichetti, Valerio","first_name":"Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","orcid":"0000-0002-9645-6576","last_name":"Sorichetti"},{"last_name":"Hayashi","first_name":"Yuki","full_name":"Hayashi, Yuki"},{"last_name":"Koskova","full_name":"Koskova, Zuzana","first_name":"Zuzana"},{"first_name":"Andreas","full_name":"Brunner, Andreas","last_name":"Brunner"},{"last_name":"Ellenberg","first_name":"Jan","full_name":"Ellenberg, Jan"},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"last_name":"Cuylen-Haering","first_name":"Sara","full_name":"Cuylen-Haering, Sara"}],"acknowledgement":"We thank Daniel W. Gerlich for providing cell lines, the EMBL Advanced Light Microscopy Facility (ALMF) for support, Christian H. Haering and Thomas Quail for input on the manuscript, and Martina Dees for cloning several Ki-67 constructs. This work was supported by the German Research Foundation (DFG project number 402723784) and the Human Frontier Science Program (CDA00045/2019). A.H.-A. and A.B. have received PhD fellowships from the Boehringer Ingelheim Fonds, V.S. and A.Š. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960), and Y.H. was supported by a fellowship from the EMBL interdisciplinary Postdoc (EIPOD) program (Marie Sklodowska-Curie Actions, COFUND grant agreement 664726).","oa":1,"status":"public","publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"publication":"Molecular Cell","scopus_import":"1"},{"oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-046-6"]},"status":"public","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","citation":{"apa":"Santana de Freitas Amaral, M. (2024). <i>Archaeal membranes : In silico modelling and design</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>","short":"M. Santana de Freitas Amaral, Archaeal Membranes : In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.","ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria.","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes : In silico modelling and design,” Institute of Science and Technology Austria, 2024.","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal Membranes : In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>.","mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal Membranes : In Silico Modelling and Design</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>.","ama":"Santana de Freitas Amaral M. Archaeal membranes : In silico modelling and design. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>"},"related_material":{"record":[{"relation":"part_of_dissertation","id":"18670","status":"public"}]},"author":[{"full_name":"Santana de Freitas Amaral, Miguel","first_name":"Miguel","last_name":"Santana de Freitas Amaral","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501"}],"date_updated":"2026-04-07T13:22:29Z","page":"57","supervisor":[{"first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Across the tree of life, distinct designs of cellular membranes have evolved that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed, monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile archaea to survive harsh environments. Here, through the creation of a\r\nminimal computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those found in archaea at higher temperatures,\r\npreferentially take on a straight conformation to self-assemble into liquid membranes that are\r\nstable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever, our analysis reveals that it is possible to achieve the best of both worlds – membranes\r\nthat are fluid, stable at high temperatures and flexible enough to be reshaped without leaking –\r\nthrough the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking the membrane effectively a plastic material. Taken together, our study compares the\r\ndifferent membrane designs across the tree of life and indicates how combining lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological applications.\r\n"}],"publication_status":"published","ddc":["572","530"],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"AnSa"}],"doi":"10.15479/at:ista:18661","has_accepted_license":"1","day":"17","date_published":"2024-12-17T00:00:00Z","_id":"18661","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"title":"Archaeal membranes : In silico modelling and design","year":"2024","file_date_updated":"2025-06-18T22:30:03Z","month":"12","file":[{"file_name":"2024_msfa_thesis.zip","file_id":"18671","date_updated":"2025-06-18T22:30:03Z","relation":"source_file","checksum":"eca06497a29078558395455c890a32d9","embargo_to":"open_access","date_created":"2024-12-18T12:27:01Z","creator":"mamaral","access_level":"closed","file_size":19161387,"content_type":"application/zip"},{"content_type":"application/pdf","file_size":16530084,"access_level":"open_access","date_created":"2024-12-18T12:26:30Z","creator":"mamaral","checksum":"2dc30ea46c5daf48d07e4cccb3c3de00","relation":"main_file","date_updated":"2025-06-18T22:30:03Z","file_id":"18672","embargo":"2025-06-18","file_name":"2024_msfa_thesis.pdf"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","date_created":"2024-12-16T10:53:39Z","license":"https://creativecommons.org/licenses/by-sa/4.0/","type":"dissertation","degree_awarded":"PhD","language":[{"iso":"eng"}],"OA_place":"publisher"},{"_id":"18670","date_published":"2024-11-27T00:00:00Z","publication":"bioRxiv","status":"public","oa":1,"acknowledgement":"MA, BB, and AŠ acknowledge funding by the\r\nVolkswagen Foundation Grant Az 96727. FF\r\nacknowledges fnancial support by the NOMIS\r\nfoundation. AŠ acknowledges funding by ERC\r\nStarting Grant “NEPA” 802960. We thank\r\nClaudia Flandoli for help with illustrations.","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"}],"date_updated":"2026-07-04T22:30:26Z","author":[{"full_name":"Santana de Freitas Amaral, Miguel","first_name":"Miguel","last_name":"Santana de Freitas Amaral","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501"},{"first_name":"Felix F","full_name":"Frey, Felix F","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","orcid":"0000-0001-8501-6017"},{"last_name":"Jiang","full_name":"Jiang, Xiuyun","first_name":"Xiuyun"},{"full_name":"Baum, Buzz","first_name":"Buzz","last_name":"Baum"},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić"}],"related_material":{"record":[{"status":"public","id":"18661","relation":"dissertation_contains"}]},"citation":{"apa":"Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., &#38; Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>","short":"M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.).","ista":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, <a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","ieee":"M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” <i>bioRxiv</i>. .","chicago":"Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>.","mla":"Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","ama":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>"},"ec_funded":1,"year":"2024","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"title":"Stability vs flexibility: Reshaping archaeal membranes in silico","type":"preprint","oa_version":"Preprint","date_created":"2024-12-18T10:07:45Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_status":"draft","corr_author":"1","abstract":[{"text":"Across the tree of life, distinct designs of cellular membranes have evolved. In bacteria and eukaryotes single-headed lipids self-assemble into flexible bilayer membranes. By contrast, archaea often possess double-headed, monolayer spanning bolalipids, mixed with bilayer lipids, enabling them to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we discover trade-offs when forming membranes. We find that membranes made out of flexible bolalipids resemble bilayer membranes as bolalipids exhibit conformational switch into U-shaped conformations to enable higher curvatures. Conversely, stiffer bolalipids, resembling those in extremophile archaea, take on straight conformations and form liquid membranes that are stiff, and prone to pore formation during membrane reshaping. Strikingly, we show how to achieve fluid bolalipid membranes that are both stable and flexible – by including small amounts of bilayer lipids, as archaea do. Our study explains how different organisms resolve trade-offs when generating membranes of desired material properties.","lang":"eng"}],"month":"11","main_file_link":[{"url":"https://doi.org/10.1101/2024.10.18.619072","open_access":"1"}],"day":"27","doi":"10.1101/2024.10.18.619072","OA_place":"repository","language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}]},{"external_id":{"pmid":["36813705"],"arxiv":["2211.04810"],"isi":["000936943800002"]},"year":"2023","arxiv":1,"title":"Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks","_id":"12705","date_published":"2023-02-21T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04810","open_access":"1"}],"issue":"7","volume":158,"language":[{"iso":"eng"}],"intvolume":"       158","type":"journal_article","date_created":"2023-03-05T23:01:05Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","article_type":"original","author":[{"orcid":"0000-0002-9645-6576","last_name":"Sorichetti","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","full_name":"Sorichetti, Valerio","first_name":"Valerio"},{"last_name":"Ninarello","full_name":"Ninarello, Andrea","first_name":"Andrea"},{"last_name":"Ruiz-Franco","first_name":"José","full_name":"Ruiz-Franco, José"},{"last_name":"Hugouvieux","full_name":"Hugouvieux, Virginie","first_name":"Virginie"},{"last_name":"Zaccarelli","first_name":"Emanuela","full_name":"Zaccarelli, Emanuela"},{"first_name":"Cristian","full_name":"Micheletti, Cristian","last_name":"Micheletti"},{"last_name":"Kob","full_name":"Kob, Walter","first_name":"Walter"},{"first_name":"Lorenzo","full_name":"Rovigatti, Lorenzo","last_name":"Rovigatti"}],"date_updated":"2023-10-03T11:31:51Z","citation":{"ama":"Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. <i>Journal of Chemical Physics</i>. 2023;158(7). doi:<a href=\"https://doi.org/10.1063/5.0134271\">10.1063/5.0134271</a>","mla":"Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” <i>Journal of Chemical Physics</i>, vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:<a href=\"https://doi.org/10.1063/5.0134271\">10.1063/5.0134271</a>.","ieee":"V. Sorichetti <i>et al.</i>, “Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks,” <i>Journal of Chemical Physics</i>, vol. 158, no. 7. American Institute of Physics, 2023.","chicago":"Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux, Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” <i>Journal of Chemical Physics</i>. American Institute of Physics, 2023. <a href=\"https://doi.org/10.1063/5.0134271\">https://doi.org/10.1063/5.0134271</a>.","ista":"Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905.","apa":"Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli, E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. <i>Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0134271\">https://doi.org/10.1063/5.0134271</a>","short":"V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023)."},"publisher":"American Institute of Physics","quality_controlled":"1","pmid":1,"publication":"Journal of Chemical Physics","scopus_import":"1","status":"public","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"oa":1,"acknowledgement":"We thank Michael Lang for helpful discussions. We acknowledge financial support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC) and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir” French Government program, managed by the French National Research Agency (ANR). W.K. is a senior member of the Institut Universitaire de France.","day":"21","article_number":"074905","doi":"10.1063/5.0134271","isi":1,"department":[{"_id":"AnSa"}],"oa_version":"Preprint","publication_status":"published","abstract":[{"text":"The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system.","lang":"eng"}]},{"date_created":"2023-03-05T23:01:06Z","type":"journal_article","month":"02","article_type":"original","file":[{"success":1,"file_id":"12711","date_updated":"2023-03-07T09:19:41Z","relation":"main_file","file_name":"2023_SoftMatter_Araujo.pdf","date_created":"2023-03-07T09:19:41Z","creator":"cchlebak","access_level":"open_access","file_size":3581939,"content_type":"application/pdf","checksum":"af95aa18b9b01e32fb8f13477c0e2687"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"intvolume":"        19","volume":19,"date_published":"2023-02-06T00:00:00Z","_id":"12708","external_id":{"pmid":["36779972"],"isi":["000940388100001"],"arxiv":["2204.10059"]},"file_date_updated":"2023-03-07T09:19:41Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Steering self-organisation through confinement","arxiv":1,"year":"2023","oa_version":"Published Version","page":"1695-1704","abstract":[{"lang":"eng","text":"Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter."}],"publication_status":"published","ddc":["540"],"doi":"10.1039/d2sm01562e","has_accepted_license":"1","day":"06","department":[{"_id":"AnSa"}],"isi":1,"scopus_import":"1","publication":"Soft Matter","acknowledgement":"All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).","oa":1,"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"status":"public","citation":{"mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” <i>Soft Matter</i>, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>.","ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. <i>Soft Matter</i>. 2023;19:1695-1704. doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>","apa":"Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>","short":"N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.","chicago":"Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” <i>Soft Matter</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>.","ieee":"N. A. M. Araújo <i>et al.</i>, “Steering self-organisation through confinement,” <i>Soft Matter</i>, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","ista":"Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704."},"publisher":"Royal Society of Chemistry","project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"date_updated":"2025-04-23T08:48:51Z","author":[{"first_name":"Nuno A.M.","full_name":"Araújo, Nuno A.M.","last_name":"Araújo"},{"full_name":"Janssen, Liesbeth M.C.","first_name":"Liesbeth M.C.","last_name":"Janssen"},{"last_name":"Barois","first_name":"Thomas","full_name":"Barois, Thomas"},{"first_name":"Guido","full_name":"Boffetta, Guido","last_name":"Boffetta"},{"full_name":"Cohen, Itai","first_name":"Itai","last_name":"Cohen"},{"full_name":"Corbetta, Alessandro","first_name":"Alessandro","last_name":"Corbetta"},{"last_name":"Dauchot","first_name":"Olivier","full_name":"Dauchot, Olivier"},{"first_name":"Marjolein","full_name":"Dijkstra, Marjolein","last_name":"Dijkstra"},{"first_name":"William M.","full_name":"Durham, William M.","last_name":"Durham"},{"last_name":"Dussutour","full_name":"Dussutour, Audrey","first_name":"Audrey"},{"last_name":"Garnier","first_name":"Simon","full_name":"Garnier, Simon"},{"last_name":"Gelderblom","full_name":"Gelderblom, Hanneke","first_name":"Hanneke"},{"first_name":"Ramin","full_name":"Golestanian, Ramin","last_name":"Golestanian"},{"full_name":"Isa, Lucio","first_name":"Lucio","last_name":"Isa"},{"first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H.","last_name":"Koenderink"},{"last_name":"Löwen","full_name":"Löwen, Hartmut","first_name":"Hartmut"},{"first_name":"Ralf","full_name":"Metzler, Ralf","last_name":"Metzler"},{"first_name":"Marco","full_name":"Polin, Marco","last_name":"Polin"},{"full_name":"Royall, C. Patrick","first_name":"C. Patrick","last_name":"Royall"},{"first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Sengupta","full_name":"Sengupta, Anupam","first_name":"Anupam"},{"last_name":"Sykes","full_name":"Sykes, Cécile","first_name":"Cécile"},{"full_name":"Trianni, Vito","first_name":"Vito","last_name":"Trianni"},{"last_name":"Tuval","full_name":"Tuval, Idan","first_name":"Idan"},{"last_name":"Vogel","full_name":"Vogel, Nicolas","first_name":"Nicolas"},{"last_name":"Yeomans","full_name":"Yeomans, Julia M.","first_name":"Julia M."},{"last_name":"Zuriguel","full_name":"Zuriguel, Iker","first_name":"Iker"},{"last_name":"Marin","first_name":"Alvaro","full_name":"Marin, Alvaro"},{"last_name":"Volpe","full_name":"Volpe, Giorgio","first_name":"Giorgio"}],"pmid":1,"ec_funded":1,"quality_controlled":"1"},{"issue":"11","volume":9,"language":[{"iso":"eng"}],"intvolume":"         9","type":"journal_article","date_created":"2023-03-26T22:01:06Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","file":[{"checksum":"6d7dbe9ed86a116c8a002d62971202c5","file_size":1826471,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","date_created":"2023-03-27T06:24:49Z","file_name":"2023_ScienceAdvances_Hurtig.pdf","date_updated":"2023-03-27T06:24:49Z","relation":"main_file","success":1,"file_id":"12768"}],"month":"03","file_date_updated":"2023-03-27T06:24:49Z","external_id":{"pmid":["36921039"],"isi":["000968083500010"]},"year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","_id":"12756","date_published":"2023-03-17T00:00:00Z","day":"17","has_accepted_license":"1","doi":"10.1126/sciadv.ade5224","article_number":"eade5224","department":[{"_id":"AnSa"}],"isi":1,"oa_version":"Published Version","publication_status":"published","ddc":["570"],"corr_author":"1","abstract":[{"lang":"eng","text":"ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling."}],"date_updated":"2025-04-23T08:50:02Z","project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"}],"author":[{"first_name":"Fredrik","full_name":"Hurtig, Fredrik","last_name":"Hurtig"},{"last_name":"Burgers","full_name":"Burgers, Thomas C.Q.","first_name":"Thomas C.Q."},{"last_name":"Cezanne","full_name":"Cezanne, Alice","first_name":"Alice"},{"last_name":"Jiang","first_name":"Xiuyun","full_name":"Jiang, Xiuyun"},{"last_name":"Mol","first_name":"Frank N.","full_name":"Mol, Frank N."},{"first_name":"Jovan","full_name":"Traparić, Jovan","last_name":"Traparić"},{"full_name":"Pulschen, Andre Arashiro","first_name":"Andre Arashiro","last_name":"Pulschen"},{"last_name":"Nierhaus","full_name":"Nierhaus, Tim","first_name":"Tim"},{"last_name":"Tarrason-Risa","first_name":"Gabriel","full_name":"Tarrason-Risa, Gabriel"},{"last_name":"Harker-Kirschneck","first_name":"Lena","full_name":"Harker-Kirschneck, Lena"},{"full_name":"Löwe, Jan","first_name":"Jan","last_name":"Löwe"},{"full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"first_name":"Rifka","full_name":"Vlijm, Rifka","last_name":"Vlijm"},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"}],"citation":{"short":"F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023).","apa":"Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>","ieee":"F. Hurtig <i>et al.</i>, “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” <i>Science Advances</i>, vol. 9, no. 11. American Association for the Advancement of Science, 2023.","chicago":"Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>.","ista":"Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>.","ama":"Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. 2023;9(11). doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>"},"publisher":"American Association for the Advancement of Science","quality_controlled":"1","ec_funded":1,"pmid":1,"scopus_import":"1","publication":"Science Advances","publication_identifier":{"eissn":["2375-2548"]},"status":"public","oa":1,"acknowledgement":"We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z)."},{"scopus_import":"1","publication":"Nano Letters","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"status":"public","acknowledgement":"We sincerely thank Casper van der Wel for providing open-source packages for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation and Rachel Doherty for her assistance with particle functionalization. We are grateful to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC Starting Grant No. 802960).","oa":1,"project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"date_updated":"2025-04-14T07:59:30Z","author":[{"full_name":"Azadbakht, Ali","first_name":"Ali","last_name":"Azadbakht"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","orcid":"0000-0003-3441-1337","last_name":"Meadowcroft","first_name":"Billie","full_name":"Meadowcroft, Billie"},{"last_name":"Varkevisser","full_name":"Varkevisser, Thijs","first_name":"Thijs"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"},{"full_name":"Kraft, Daniela J.","first_name":"Daniela J.","last_name":"Kraft"}],"citation":{"ista":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 23(10), 4267–4273.","chicago":"Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” <i>Nano Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">https://doi.org/10.1021/acs.nanolett.3c00375</a>.","ieee":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” <i>Nano Letters</i>, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.","apa":"Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., &#38; Kraft, D. J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">https://doi.org/10.1021/acs.nanolett.3c00375</a>","short":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273.","ama":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. <i>Nano Letters</i>. 2023;23(10):4267–4273. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">10.1021/acs.nanolett.3c00375</a>","mla":"Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” <i>Nano Letters</i>, vol. 23, no. 10, American Chemical Society, 2023, pp. 4267–4273, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">10.1021/acs.nanolett.3c00375</a>."},"publisher":"American Chemical Society","quality_controlled":"1","ec_funded":1,"pmid":1,"oa_version":"Published Version","publication_status":"published","ddc":["540"],"page":"4267–4273","abstract":[{"lang":"eng","text":"Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states."}],"has_accepted_license":"1","day":"04","doi":"10.1021/acs.nanolett.3c00375","department":[{"_id":"AnSa"}],"isi":1,"_id":"13094","date_published":"2023-05-04T00:00:00Z","file_date_updated":"2023-05-30T07:55:31Z","external_id":{"isi":["000985481400001"],"pmid":["37141427"]},"year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","type":"journal_article","date_created":"2023-05-28T22:01:03Z","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"05","file":[{"file_name":"2023_NanoLetters_Azadbakht.pdf","file_id":"13100","success":1,"relation":"main_file","date_updated":"2023-05-30T07:55:31Z","checksum":"9734d4c617bab3578ef62916b764547a","creator":"dernst","date_created":"2023-05-30T07:55:31Z","access_level":"open_access","content_type":"application/pdf","file_size":3654910}],"article_type":"letter_note","issue":"10","volume":23,"intvolume":"        23","language":[{"iso":"eng"}]},{"publication":"Nature Reviews Physics","scopus_import":"1","acknowledgement":"The authors acknowledge support from the Institute for the Physics of Living Systems, University College London (T.C.T.M.), the Swedish Research Council (2015-00143) (S.L.), the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C. Flandoli for help with illustrations.","status":"public","publication_identifier":{"eissn":["2522-5820"]},"citation":{"short":"T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Reviews Physics 5 (2023) 379–397.","apa":"Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., &#38; Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. <i>Nature Reviews Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42254-023-00598-9\">https://doi.org/10.1038/s42254-023-00598-9</a>","ieee":"T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P. J. Knowles, “Amyloid formation as a protein phase transition,” <i>Nature Reviews Physics</i>, vol. 5. Springer Nature, pp. 379–397, 2023.","chicago":"Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo, Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.” <i>Nature Reviews Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42254-023-00598-9\">https://doi.org/10.1038/s42254-023-00598-9</a>.","ista":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023. Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397.","mla":"Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.” <i>Nature Reviews Physics</i>, vol. 5, Springer Nature, 2023, pp. 379–397, doi:<a href=\"https://doi.org/10.1038/s42254-023-00598-9\">10.1038/s42254-023-00598-9</a>.","ama":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid formation as a protein phase transition. <i>Nature Reviews Physics</i>. 2023;5:379–397. doi:<a href=\"https://doi.org/10.1038/s42254-023-00598-9\">10.1038/s42254-023-00598-9</a>"},"publisher":"Springer Nature","author":[{"full_name":"Michaels, Thomas C.T.","first_name":"Thomas C.T.","last_name":"Michaels"},{"last_name":"Qian","full_name":"Qian, Daoyuan","first_name":"Daoyuan"},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"first_name":"Michele","full_name":"Vendruscolo, Michele","last_name":"Vendruscolo"},{"first_name":"Sara","full_name":"Linse, Sara","last_name":"Linse"},{"last_name":"Knowles","first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J."}],"date_updated":"2023-08-02T06:28:38Z","quality_controlled":"1","oa_version":"None","abstract":[{"text":"The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases.","lang":"eng"}],"page":"379–397","publication_status":"published","doi":"10.1038/s42254-023-00598-9","day":"01","isi":1,"department":[{"_id":"AnSa"}],"date_published":"2023-07-01T00:00:00Z","_id":"13237","external_id":{"isi":["001017539800001"]},"title":"Amyloid formation as a protein phase transition","year":"2023","date_created":"2023-07-16T22:01:12Z","type":"journal_article","article_type":"original","month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","language":[{"iso":"eng"}],"intvolume":"         5","volume":5},{"publication_status":"published","ddc":["530"],"page":"1680-1688","abstract":[{"lang":"eng","text":"When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases."}],"corr_author":"1","oa_version":"Published Version","department":[{"_id":"EdHa"},{"_id":"AnSa"},{"_id":"JePa"}],"isi":1,"day":"01","has_accepted_license":"1","doi":"10.1038/s41567-023-02136-x","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"status":"public","acknowledgement":"D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa for providing the E. coli strains. This material is based upon work supported by the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 754411.","oa":1,"publication":"Nature Physics","scopus_import":"1","ec_funded":1,"quality_controlled":"1","date_updated":"2025-04-14T07:43:56Z","project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"},{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"author":[{"id":"abdfc56f-34fb-11ee-bd33-fd766fce5a99","last_name":"Grober","first_name":"Daniel","full_name":"Grober, Daniel"},{"first_name":"Ivan","full_name":"Palaia, Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","orcid":" 0000-0002-8843-9485 ","last_name":"Palaia"},{"first_name":"Mehmet C","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","last_name":"Ucar"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","last_name":"Palacci","first_name":"Jérémie A","full_name":"Palacci, Jérémie A"}],"citation":{"ama":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional colloidal aggregation in chiral bacterial baths. <i>Nature Physics</i>. 2023;19:1680-1688. doi:<a href=\"https://doi.org/10.1038/s41567-023-02136-x\">10.1038/s41567-023-02136-x</a>","mla":"Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:<a href=\"https://doi.org/10.1038/s41567-023-02136-x\">10.1038/s41567-023-02136-x</a>.","ieee":"D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci, “Unconventional colloidal aggregation in chiral bacterial baths,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1680–1688, 2023.","chicago":"Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić, and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02136-x\">https://doi.org/10.1038/s41567-023-02136-x</a>.","ista":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.","apa":"Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., &#38; Palacci, J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02136-x\">https://doi.org/10.1038/s41567-023-02136-x</a>","short":"D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature Physics 19 (2023) 1680–1688."},"publisher":"Springer Nature","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"7e282c2ebc0ac82125a04f6b4742d4c1","content_type":"application/pdf","file_size":6365607,"access_level":"open_access","date_created":"2024-01-30T12:26:08Z","creator":"dernst","file_name":"2023_NaturePhysics_Grober.pdf","relation":"main_file","date_updated":"2024-01-30T12:26:08Z","success":1,"file_id":"14906"}],"month":"11","article_type":"original","type":"journal_article","date_created":"2023-08-06T22:01:11Z","volume":19,"intvolume":"        19","language":[{"iso":"eng"}],"_id":"13971","date_published":"2023-11-01T00:00:00Z","year":"2023","title":"Unconventional colloidal aggregation in chiral bacterial baths","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file_date_updated":"2024-01-30T12:26:08Z","external_id":{"isi":["001037346400005"]}},{"date_published":"2023-10-01T00:00:00Z","_id":"14442","external_id":{"isi":["001187541900001"],"arxiv":["2111.05952"],"pmid":["37819444"]},"arxiv":1,"title":"Mixtures of self-propelled particles interacting with asymmetric obstacles","year":"2023","date_created":"2023-10-22T22:01:13Z","type":"journal_article","article_type":"original","month":"10","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"10","OA_place":"repository","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2111.05952","open_access":"1"}],"intvolume":"        46","language":[{"iso":"eng"}],"volume":46,"scopus_import":"1","publication":"The European Physical Journal E","oa":1,"acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and Millennium Science Initiative Program NCN19_170D of ANID, Chile. P.d.C. was supported by Scholarships Nos. 2021/10139-2 and 2022/13872-5 and ICTP-SAIFR Grant No. 2021/14335-0, all granted by São Paulo Research Foundation (FAPESP), Brazil.","status":"public","OA_type":"green","publication_identifier":{"eissn":["1292-895X"],"issn":["1292-8941"]},"citation":{"ama":"Rojas Vega MN, De Castro P, Soto R. Mixtures of self-propelled particles interacting with asymmetric obstacles. <i>The European Physical Journal E</i>. 2023;46(10). doi:<a href=\"https://doi.org/10.1140/epje/s10189-023-00354-y\">10.1140/epje/s10189-023-00354-y</a>","mla":"Rojas Vega, Mauricio Nicolas, et al. “Mixtures of Self-Propelled Particles Interacting with Asymmetric Obstacles.” <i>The European Physical Journal E</i>, vol. 46, no. 10, 95, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1140/epje/s10189-023-00354-y\">10.1140/epje/s10189-023-00354-y</a>.","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Mixtures of self-propelled particles interacting with asymmetric obstacles,” <i>The European Physical Journal E</i>, vol. 46, no. 10. Springer Nature, 2023.","chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Mixtures of Self-Propelled Particles Interacting with Asymmetric Obstacles.” <i>The European Physical Journal E</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1140/epje/s10189-023-00354-y\">https://doi.org/10.1140/epje/s10189-023-00354-y</a>.","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Mixtures of self-propelled particles interacting with asymmetric obstacles. The European Physical Journal E. 46(10), 95.","apa":"Rojas Vega, M. N., De Castro, P., &#38; Soto, R. (2023). Mixtures of self-propelled particles interacting with asymmetric obstacles. <i>The European Physical Journal E</i>. Springer Nature. <a href=\"https://doi.org/10.1140/epje/s10189-023-00354-y\">https://doi.org/10.1140/epje/s10189-023-00354-y</a>","short":"M.N. Rojas Vega, P. De Castro, R. Soto, The European Physical Journal E 46 (2023)."},"publisher":"Springer Nature","date_updated":"2025-09-09T13:08:14Z","author":[{"full_name":"Rojas Vega, Mauricio Nicolas","first_name":"Mauricio Nicolas","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","last_name":"Rojas Vega"},{"first_name":"Pablo","full_name":"De Castro, Pablo","last_name":"De Castro"},{"full_name":"Soto, Rodrigo","first_name":"Rodrigo","last_name":"Soto"}],"pmid":1,"quality_controlled":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"In the presence of an obstacle, active particles condensate into a surface “wetting” layer due to persistent motion. If the obstacle is asymmetric, a rectification current arises in addition to wetting. Asymmetric geometries are therefore commonly used to concentrate microorganisms like bacteria and sperms. However, most studies neglect the fact that biological active matter is diverse, composed of individuals with distinct self-propulsions. Using simulations, we study a mixture of “fast” and “slow” active Brownian disks in two dimensions interacting with large half-disk obstacles. With this prototypical obstacle geometry, we analyze how the stationary collective behavior depends on the degree of self-propulsion “diversity,” defined as proportional to the difference between the self-propulsion speeds, while keeping the average self-propulsion speed fixed. A wetting layer rich in fast particles arises. The rectification current is amplified by speed diversity due to a superlinear dependence of rectification on self-propulsion speed, which arises from cooperative effects. Thus, the total rectification current cannot be obtained from an effective one-component active fluid with the same average self-propulsion speed, highlighting the importance of considering diversity in active matter."}],"corr_author":"1","publication_status":"published","article_number":"95","doi":"10.1140/epje/s10189-023-00354-y","day":"01","isi":1,"department":[{"_id":"AnSa"}]},{"type":"research_data","license":"https://creativecommons.org/publicdomain/zero/1.0/","oa_version":"Published Version","date_created":"2023-10-30T16:38:32Z","ddc":["570"],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","abstract":[{"text":"Data related to the following paper:\r\n\"Stress granules plug and stabilize damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract: \r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in \"Stress granules plug and stabilize damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w.","lang":"eng"}],"file":[{"relation":"main_file","date_updated":"2023-10-30T16:31:08Z","file_id":"14473","success":1,"file_name":"SGporecondensation-main.zip","content_type":"application/zip","file_size":62821432,"access_level":"open_access","date_created":"2023-10-30T16:31:08Z","creator":"ipalaia","checksum":"a18706e952e8660c51ede52a167270b7"},{"file_name":"README.txt","date_updated":"2023-10-31T08:57:50Z","relation":"main_file","file_id":"14474","success":1,"checksum":"389eab31c6509dbc05795017fb618758","file_size":1697,"content_type":"text/plain","access_level":"open_access","date_created":"2023-10-31T08:57:50Z","creator":"dernst"}],"month":"10","has_accepted_license":"1","day":"31","doi":"10.15479/AT:ISTA:14472","department":[{"_id":"AnSa"}],"_id":"14472","date_published":"2023-10-31T00:00:00Z","status":"public","oa":1,"file_date_updated":"2023-10-31T08:57:50Z","author":[{"last_name":"Vanhille-Campos","id":"3adeca52-9313-11ed-b1ac-c170b2505714","first_name":"Christian Eduardo","full_name":"Vanhille-Campos, Christian Eduardo"},{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"date_updated":"2025-09-09T13:30:33Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14610"}]},"citation":{"mla":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. <i>Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14472\">10.15479/AT:ISTA:14472</a>.","ama":"Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal membranes. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14472\">10.15479/AT:ISTA:14472</a>","apa":"Vanhille-Campos, C. E., &#38; Šarić, A. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14472\">https://doi.org/10.15479/AT:ISTA:14472</a>","short":"C.E. Vanhille-Campos, A. Šarić, (2023).","chicago":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14472\">https://doi.org/10.15479/AT:ISTA:14472</a>.","ista":"Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged endolysosomal membranes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14472\">10.15479/AT:ISTA:14472</a>.","ieee":"C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged endolysosomal membranes.” Institute of Science and Technology Austria, 2023."},"publisher":"Institute of Science and Technology Austria","year":"2023","title":"Stress granules plug and stabilize damaged endolysosomal membranes","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"}},{"year":"2023","title":"Stress granules plug and stabilize damaged endolysosomal membranes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file_date_updated":"2024-07-16T07:41:39Z","external_id":{"pmid":["37968398"],"isi":["001105882300018"]},"_id":"14610","date_published":"2023-11-30T00:00:00Z","volume":623,"language":[{"iso":"eng"}],"intvolume":"       623","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (via OA deal)","month":"11","file":[{"file_id":"17248","success":1,"relation":"main_file","date_updated":"2024-07-16T07:41:39Z","file_name":"2023_Nature_Bussi.pdf","date_created":"2024-07-16T07:41:39Z","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":17047711,"checksum":"b939a19e4c228fbf3beca298ac2ac014"}],"article_type":"original","type":"journal_article","date_created":"2023-11-27T07:56:37Z","quality_controlled":"1","pmid":1,"date_updated":"2025-09-09T13:30:34Z","author":[{"last_name":"Bussi","full_name":"Bussi, Claudio","first_name":"Claudio"},{"last_name":"Mangiarotti","full_name":"Mangiarotti, Agustín","first_name":"Agustín"},{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo","first_name":"Christian Eduardo"},{"full_name":"Aylan, Beren","first_name":"Beren","last_name":"Aylan"},{"full_name":"Pellegrino, Enrica","first_name":"Enrica","last_name":"Pellegrino"},{"first_name":"Natalia","full_name":"Athanasiadi, Natalia","last_name":"Athanasiadi"},{"full_name":"Fearns, Antony","first_name":"Antony","last_name":"Fearns"},{"full_name":"Rodgers, Angela","first_name":"Angela","last_name":"Rodgers"},{"first_name":"Titus M.","full_name":"Franzmann, Titus M.","last_name":"Franzmann"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"},{"first_name":"Rumiana","full_name":"Dimova, Rumiana","last_name":"Dimova"},{"last_name":"Gutierrez","full_name":"Gutierrez, Maximiliano G.","first_name":"Maximiliano G."}],"publisher":"Springer Nature","related_material":{"record":[{"relation":"research_data","status":"public","id":"14472"}],"link":[{"url":"https://doi.org/10.1038/s41586-023-06882-z","relation":"erratum"}]},"citation":{"short":"C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino, N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G. Gutierrez, Nature 623 (2023) 1062–1069.","apa":"Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino, E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>","chicago":"Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos, Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>.","ista":"Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress granules plug and stabilize damaged endolysosomal membranes. Nature. 623, 1062–1069.","ieee":"C. Bussi <i>et al.</i>, “Stress granules plug and stabilize damaged endolysosomal membranes,” <i>Nature</i>, vol. 623. Springer Nature, pp. 1062–1069, 2023.","mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>, vol. 623, Springer Nature, 2023, pp. 1062–69, doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>.","ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. 2023;623:1062-1069. doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>"},"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"status":"public","acknowledgement":"We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy and High-throughput Screening facilities at the Crick for their support in various aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO U2OS cells. The authors thank N. Chen for providing the purified glycinin protein; Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for helpful discussions and valuable input regarding analysis methods. This work was supported by the Francis Crick Institute (to M.G.G.), which receives its core funding from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and the Wellcome Trust (FC001092). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from the European Respiratory Society and the European Union’s H2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding by the Royal Society and the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations were carried out on the high-performance computing cluster at the Institute of Science and Technology Austria. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.\r\nOpen Access funding provided by The Francis Crick Institute.","oa":1,"scopus_import":"1","publication":"Nature","department":[{"_id":"AnSa"}],"isi":1,"day":"30","has_accepted_license":"1","doi":"10.1038/s41586-023-06726-w","publication_status":"published","ddc":["570"],"page":"1062-1069","abstract":[{"text":"Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells<jats:sup>1,2</jats:sup>. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis<jats:sup>3–7</jats:sup>. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for <jats:italic>Mycobacterium tuberculosis</jats:italic>, a human pathogen that exploits endomembrane damage to survive within the host.","lang":"eng"}],"oa_version":"Published Version"},{"date_published":"2023-12-01T00:00:00Z","_id":"14655","external_id":{"pmid":["38101392"],"isi":["001163810200008"],"arxiv":["2303.03088"]},"title":"Transverse fluctuations control the assembly of semiflexible filaments","arxiv":1,"year":"2023","date_created":"2023-12-10T23:00:57Z","type":"journal_article","article_type":"original","month":"12","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"22","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.03088"}],"language":[{"iso":"eng"}],"intvolume":"       131","volume":131,"scopus_import":"1","publication":"Physical Review Letters","oa":1,"acknowledgement":"The authors thank C´ecile Leduc and Duc-Quang Tran for invaluable help with understanding the experimental behavior of intermediate filaments, and Raphael Voituriez, Nicolas Levernier, and Alexander Grosberg for fruitful discussion on the theoretical model. V. S. also thanks Davide Michieletto, Maria Panoukidou, and Lorenzo Rovigatti for very helpful suggestions on the simulation model. M. L. was supported by Marie Curie Integration Grant No. PCIG12-GA-2012-334053, “Investissements d’Avenir” LabEx PALM (ANR-10-LABX- 0039-PALM), ANR Grants No. ANR-15-CE13-0004-03, No. ANR-21-CE11-0004-02 and No. ANR-22-CE30-0024, as well as ERC Starting Grant No. 677532. M.L.’s group belongs to the CNRS consortium AQV. Part of this work was performed using HPC resources from GENCI–IDRIS (Grants No. 2020-A0090712066 and No. 2021-A0110712066).","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"status":"public","publisher":"American Physical Society","citation":{"short":"V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023).","apa":"Sorichetti, V., &#38; Lenz, M. (2023). Transverse fluctuations control the assembly of semiflexible filaments. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">https://doi.org/10.1103/PhysRevLett.131.228401</a>","ieee":"V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of semiflexible filaments,” <i>Physical Review Letters</i>, vol. 131, no. 22. American Physical Society, 2023.","ista":"Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 131(22), 228401.","chicago":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">https://doi.org/10.1103/PhysRevLett.131.228401</a>.","mla":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” <i>Physical Review Letters</i>, vol. 131, no. 22, 228401, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">10.1103/PhysRevLett.131.228401</a>.","ama":"Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible filaments. <i>Physical Review Letters</i>. 2023;131(22). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">10.1103/PhysRevLett.131.228401</a>"},"author":[{"id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","last_name":"Sorichetti","orcid":"0000-0002-9645-6576","full_name":"Sorichetti, Valerio","first_name":"Valerio"},{"first_name":"Martin","full_name":"Lenz, Martin","last_name":"Lenz"}],"date_updated":"2025-09-09T13:35:06Z","pmid":1,"quality_controlled":"1","oa_version":"Preprint","corr_author":"1","abstract":[{"lang":"eng","text":"The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division."}],"publication_status":"published","doi":"10.1103/PhysRevLett.131.228401","article_number":"228401","day":"01","department":[{"_id":"AnSa"}],"isi":1},{"_id":"14782","date_published":"2023-06-06T00:00:00Z","year":"2023","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","file_date_updated":"2024-01-16T09:09:29Z","external_id":{"isi":["001016792600001"],"pmid":["36806830"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","file":[{"file_size":3285810,"content_type":"application/pdf","access_level":"open_access","date_created":"2024-01-16T09:09:29Z","creator":"dernst","checksum":"70566e54cd95ea6df340909ad44c5cd5","date_updated":"2024-01-16T09:09:29Z","relation":"main_file","success":1,"file_id":"14807","file_name":"2023_BiophysicalJournal_Baldauf.pdf"}],"month":"06","article_type":"original","type":"journal_article","date_created":"2024-01-10T09:45:48Z","volume":122,"intvolume":"       122","language":[{"iso":"eng"}],"issue":"11","publication_identifier":{"issn":["0006-3495"]},"status":"public","acknowledgement":"We thank Jeffrey den Haan for protein purification, Kristina Ganzinger (AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago) for the CP constructs, and Michael Way (Crick Institute) for providing purified human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation experiments that formed the basis for establishing the eDICE method, to Federico Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE, and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling. Lennard van Buren is thanked for his help with image analysis to quantify actin concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher for insightful and inspiring discussions. We acknowledge financial support from The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.","oa":1,"publication":"Biophysical Journal","quality_controlled":"1","pmid":1,"date_updated":"2024-01-16T09:20:03Z","author":[{"last_name":"Baldauf","first_name":"Lucia","full_name":"Baldauf, Lucia"},{"last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F","first_name":"Felix F"},{"first_name":"Marcos","full_name":"Arribas Perez, Marcos","last_name":"Arribas Perez"},{"first_name":"Timon","full_name":"Idema, Timon","last_name":"Idema"},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."}],"related_material":{"link":[{"url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing","relation":"software"}]},"citation":{"ieee":"L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink, “Branched actin cortices reconstituted in vesicles sense membrane curvature,” <i>Biophysical Journal</i>, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.","ista":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 122(11), 2311–2324.","chicago":"Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>.","apa":"Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., &#38; Koenderink, G. H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>","short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 2311–2324.","ama":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. 2023;122(11):2311-2324. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>","mla":"Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>, vol. 122, no. 11, Elsevier, 2023, pp. 2311–24, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>."},"publisher":"Elsevier","publication_status":"published","ddc":["570"],"keyword":["Biophysics"],"page":"2311-2324","abstract":[{"lang":"eng","text":"The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration."}],"oa_version":"Published Version","department":[{"_id":"AnSa"}],"isi":1,"has_accepted_license":"1","day":"06","doi":"10.1016/j.bpj.2023.02.018"},{"doi":"10.1083/jcb.202206038","article_number":"e202206038","day":"03","has_accepted_license":"1","department":[{"_id":"AnSa"}],"isi":1,"oa_version":"Published Version","abstract":[{"text":"Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane.","lang":"eng"}],"publication_status":"published","ddc":["570"],"keyword":["Cell Biology"],"citation":{"ista":"Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 222(3), e202206038.","chicago":"Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2023. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>.","ieee":"M. Mund <i>et al.</i>, “Clathrin coats partially preassemble and subsequently bend during endocytosis,” <i>Journal of Cell Biology</i>, vol. 222, no. 3. Rockefeller University Press, 2023.","apa":"Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., … Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>","short":"M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).","ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. 2023;222(3). doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>","mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>."},"publisher":"Rockefeller University Press","date_updated":"2024-01-16T10:17:05Z","author":[{"last_name":"Mund","first_name":"Markus","full_name":"Mund, Markus"},{"last_name":"Tschanz","first_name":"Aline","full_name":"Tschanz, Aline"},{"first_name":"Yu-Le","full_name":"Wu, Yu-Le","last_name":"Wu"},{"first_name":"Felix F","full_name":"Frey, Felix F","last_name":"Frey","orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"full_name":"Mehl, Johanna L.","first_name":"Johanna L.","last_name":"Mehl"},{"full_name":"Kaksonen, Marko","first_name":"Marko","last_name":"Kaksonen"},{"first_name":"Ori","full_name":"Avinoam, Ori","last_name":"Avinoam"},{"last_name":"Schwarz","first_name":"Ulrich S.","full_name":"Schwarz, Ulrich S."},{"full_name":"Ries, Jonas","first_name":"Jonas","last_name":"Ries"}],"pmid":1,"quality_controlled":"1","publication":"Journal of Cell Biology","oa":1,"acknowledgement":"We thank the entire Ries and Kaksonen labs for fruitful discussions and support. This work was supported by the European Research Council (ERC CoG-724489 to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND (Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund, A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant 310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent of the Miriam Berman Presidential Development Chair.","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"status":"public","issue":"3","intvolume":"       222","language":[{"iso":"eng"}],"volume":222,"date_created":"2024-01-10T10:45:55Z","type":"journal_article","file":[{"content_type":"application/pdf","file_size":5678069,"access_level":"open_access","date_created":"2024-01-16T10:15:09Z","creator":"dernst","checksum":"505d5cac36c14b073b68c7fed1a92bd3","relation":"main_file","date_updated":"2024-01-16T10:15:09Z","file_id":"14811","success":1,"file_name":"2023_JCB_Mund.pdf"}],"month":"02","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["36734980"],"isi":["000978065000001"]},"file_date_updated":"2024-01-16T10:15:09Z","title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2023","date_published":"2023-02-03T00:00:00Z","_id":"14788"}]