[{"APC_amount":"3041,76 EUR","publisher":"National Academy of Sciences","external_id":{"isi":["001207786500004"],"pmid":["38408249"]},"ec_funded":1,"volume":121,"publication":"Proceedings of the National Academy of Sciences of the United States of America","corr_author":"1","title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","_id":"15083","file_date_updated":"2024-03-12T13:12:22Z","year":"2024","language":[{"iso":"eng"}],"publication_status":"published","day":"05","type":"journal_article","ddc":["000"],"abstract":[{"lang":"eng","text":"Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation."}],"article_number":"e2315558121","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_updated":"2026-09-16T06:58:23Z","issue":"10","doi":"10.1073/pnas.2315558121","citation":{"apa":"Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024). Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2315558121","mla":"Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 10, e2315558121, National Academy of Sciences, 2024, doi:10.1073/pnas.2315558121.","ista":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences of the United States of America. 121(10), e2315558121.","ieee":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency and resilience of cooperation in asymmetric social dilemmas,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 10. National Academy of Sciences, 2024.","chicago":"Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121.","ama":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(10). doi:10.1073/pnas.2315558121","short":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"pmid":1,"intvolume":" 121","has_accepted_license":"1","month":"03","article_type":"original","quality_controlled":"1","OA_type":"hybrid","OA_place":"publisher","department":[{"_id":"KrCh"}],"oa_version":"Published Version","isi":1,"article_processing_charge":"Yes (in subscription journal)","date_created":"2024-03-05T09:18:49Z","related_material":{"record":[{"relation":"research_data","id":"15108","status":"public"},{"id":"19903","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/","relation":"press_release","description":"News on ISTA Website"}]},"oa":1,"file":[{"file_id":"15109","file_name":"2024_PNAS_Huebner.pdf","date_created":"2024-03-12T13:12:22Z","access_level":"open_access","checksum":"068520e3efd4d008bb9177e8aedb7d22","relation":"main_file","date_updated":"2024-03-12T13:12:22Z","success":1,"file_size":2203220,"creator":"dernst","content_type":"application/pdf"}],"date_published":"2024-03-05T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1073/pnas.2315558121","status":"public","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010) (to M.K.).","author":[{"first_name":"Valentin","full_name":"Hübner, Valentin","last_name":"Hübner","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","orcid":"0009-0001-5009-4987"},{"last_name":"Staab","full_name":"Staab, Manuel","first_name":"Manuel"},{"orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Kleshnina, Maria","last_name":"Kleshnina","first_name":"Maria"}],"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"scopus_import":"1"},{"has_accepted_license":"1","month":"12","department":[{"_id":"KrCh"}],"oa_version":"Published Version","OA_type":"hybrid","quality_controlled":"1","OA_place":"publisher","article_type":"original","article_processing_charge":"Yes","isi":1,"file":[{"checksum":"0115e9090b478e0644308c6dab58605b","relation":"main_file","date_created":"2025-01-02T12:14:15Z","access_level":"open_access","file_id":"18721","file_name":"2024_PNAS_Svoboda.pdf","content_type":"application/pdf","creator":"dernst","file_size":2491151,"date_updated":"2025-01-02T12:14:15Z","success":1}],"oa":1,"related_material":{"record":[{"id":"20138","status":"public","relation":"dissertation_contains"}]},"date_created":"2024-12-22T23:01:47Z","status":"public","fulldoi":"https://doi.org/10.1073/pnas.2405605121","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-12-10T00:00:00Z","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"scopus_import":"1","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"author":[{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","orcid":"0000-0002-1419-3267","first_name":"Jakub","last_name":"Svoboda","full_name":"Svoboda, Jakub"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"acknowledgement":"J.S. and K.C. were supported by the European Research Council CoG 863818 (ForM-SMArt) and Austrian Science Fund 10.55776/COE12.","ec_funded":1,"volume":121,"external_id":{"pmid":["39642209"],"isi":["001379596100014"]},"publisher":"National Academy of Sciences","APC_amount":"3143,76 EUR","language":[{"iso":"eng"}],"_id":"18703","year":"2024","file_date_updated":"2025-01-02T12:14:15Z","corr_author":"1","title":"Density amplifiers of cooperation for spatial games","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"10","publication_status":"published","ddc":["000"],"type":"journal_article","abstract":[{"lang":"eng","text":"Spatial games provide a simple and elegant mathematical model to study the evolution of cooperation in networks. In spatial games, individuals reside in vertices, adopt simple strategies, and interact with neighbors to receive a payoff. Depending on their own and neighbors’ payoffs, individuals can change their strategy. The payoff is determined by the Prisoners’ Dilemma, a classical matrix game, where players cooperate or defect. While cooperation is the desired behavior, defection provides a higher payoff for a selfish individual. There are many theoretical and empirical studies related to the role of the network in the evolution of cooperation. However, the fundamental question of whether there exist networks that for low initial cooperation rate ensure a high chance of fixation, i.e., cooperation spreads across the whole population, has remained elusive for spatial games with strong selection. In this work, we answer this fundamental question in the affirmative by presenting network structures that ensure high fixation probability for cooperators in the strong selection regime. Besides, our structures have many desirable properties: (a) they ensure the spread of cooperation even for a low initial density of cooperation and high temptation of defection, (b) they have constant degrees, and (c) the number of steps, until cooperation spreads, is at most quadratic in the size of the network."}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_number":"e2405605121","doi":"10.1073/pnas.2405605121","date_updated":"2026-09-16T06:59:33Z","issue":"50","intvolume":" 121","pmid":1,"citation":{"short":"J. Svoboda, K. Chatterjee, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ama":"Svoboda J, Chatterjee K. Density amplifiers of cooperation for spatial games. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(50). doi:10.1073/pnas.2405605121","ista":"Svoboda J, Chatterjee K. 2024. Density amplifiers of cooperation for spatial games. Proceedings of the National Academy of Sciences of the United States of America. 121(50), e2405605121.","ieee":"J. Svoboda and K. Chatterjee, “Density amplifiers of cooperation for spatial games,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 50. National Academy of Sciences, 2024.","chicago":"Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation for Spatial Games.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2405605121.","mla":"Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation for Spatial Games.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 50, e2405605121, National Academy of Sciences, 2024, doi:10.1073/pnas.2405605121.","apa":"Svoboda, J., & Chatterjee, K. (2024). Density amplifiers of cooperation for spatial games. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2405605121"}},{"article_processing_charge":"Yes","isi":1,"OA_place":"publisher","quality_controlled":"1","OA_type":"hybrid","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"oa_version":"Published Version","article_type":"original","month":"10","has_accepted_license":"1","author":[{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","last_name":"Ruzickova","full_name":"Ruzickova, Natalia","first_name":"Natalia"},{"first_name":"Michal","full_name":"Hledik, Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper"}],"project":[{"name":"Collective behaviour of cells in pancreatic Islets of Langerhans","_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"scopus_import":"1","acknowledgement":"N.R.acknowledges the support of the Austrian Academy of Sciences through the Doctoral Fellowship Programme (DOC) of the Austrian Academy of Sciences 26917. M.H. and G.T. were supported in part by the Human Frontiers Science Program Grant RGP0034/2018. We thank Nicholas H. Barton, Fyodor Kondrashov, and Matthew R. Robinson for fruitful discussions.","status":"public","fulldoi":"https://doi.org/10.1073/pnas.2402340121","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-10-29T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20357"}]},"file":[{"content_type":"application/pdf","creator":"dernst","file_size":25529709,"date_updated":"2024-11-11T09:31:00Z","success":1,"relation":"main_file","checksum":"d930e2ccf9ec900c7d7509a78cfb3564","date_created":"2024-11-11T09:31:00Z","access_level":"open_access","file_id":"18536","file_name":"2024_PNAS_Ruzickova.pdf"}],"oa":1,"date_created":"2024-11-10T23:01:59Z","ddc":["570"],"type":"journal_article","day":"29","publication_status":"published","_id":"18525","file_date_updated":"2024-11-11T09:31:00Z","year":"2024","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","corr_author":"1","title":"Quantitative omnigenic model discovers interpretable genome-wide associations","external_id":{"isi":["001349462600001"],"pmid":["39441639"]},"volume":121,"APC_amount":"3062,93 EUR","publisher":"National Academy of Sciences","pmid":1,"citation":{"mla":"Ruzickova, Natalia, et al. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44, e2402340121, National Academy of Sciences, 2024, doi:10.1073/pnas.2402340121.","apa":"Ruzickova, N., Hledik, M., & Tkačik, G. (2024). Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2402340121","ama":"Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(44). doi:10.1073/pnas.2402340121","short":"N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Ruzickova N, Hledik M, Tkačik G. 2024. Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2402340121.","ieee":"N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers interpretable genome-wide associations,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44. National Academy of Sciences, 2024.","chicago":"Ruzickova, Natalia, Michal Hledik, and Gašper Tkačik. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2402340121."},"intvolume":" 121","doi":"10.1073/pnas.2402340121","issue":"44","date_updated":"2026-09-22T22:30:07Z","article_number":"e2402340121","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"abstract":[{"text":"As their statistical power grows, genome-wide association studies (GWAS) have identified an increasing number of loci underlying quantitative traits of interest. These loci are scattered throughout the genome and are individually responsible only for small fractions of the total heritable trait variance. The recently proposed omnigenic model provides a conceptual framework to explain these observations by postulating that numerous distant loci contribute to each complex trait via effect propagation through intracellular regulatory networks. We formalize this conceptual framework by proposing the “quantitative omnigenic model” (QOM), a statistical model that combines prior knowledge of the regulatory network topology with genomic data. By applying our model to gene expression traits in yeast, we demonstrate that QOM achieves similar gene expression prediction performance to traditional GWAS with hundreds of times less parameters, while simultaneously extracting candidate causal and quantitative chains of effect propagation through the regulatory network for every individual gene. We estimate the fraction of heritable trait variance in cis- and in trans-, break the latter down by effect propagation order, assess the trans- variance not attributable to transcriptional regulation, and show that QOM correctly accounts for the low-dimensional structure of gene expression covariance. We furthermore demonstrate the relevance of QOM for systems biology, by employing it as a statistical test for the quality of regulatory network reconstructions, and linking it to the propagation of nontranscriptional (including environmental) effects.","lang":"eng"}]},{"date_published":"2024-02-20T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1073/pnas.2301449121","status":"public","acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","author":[{"first_name":"Peter","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948"},{"full_name":"Bhandari, Pradeep","last_name":"Bhandari","first_name":"Pradeep","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Önal","full_name":"Önal, Hüseyin C","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011","id":"4659D740-F248-11E8-B48F-1D18A9856A87"},{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","first_name":"Carolina","last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina"},{"id":"3B59276A-F248-11E8-B48F-1D18A9856A87","first_name":"Elodie","last_name":"Le Monnier","full_name":"Le Monnier, Elodie"},{"first_name":"Utsa","last_name":"Roy","full_name":"Roy, Utsa","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2"},{"first_name":"Yukihiro","last_name":"Nakamura","full_name":"Nakamura, Yukihiro"},{"full_name":"Sadakata, Tetsushi","last_name":"Sadakata","first_name":"Tetsushi"},{"full_name":"Sanbo, Makoto","last_name":"Sanbo","first_name":"Makoto"},{"first_name":"Masumi","last_name":"Hirabayashi","full_name":"Hirabayashi, Masumi"},{"first_name":"JeongSeop","last_name":"Rhee","full_name":"Rhee, JeongSeop"},{"full_name":"Brose, Nils","last_name":"Brose","first_name":"Nils"},{"first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"scopus_import":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"date_created":"2024-03-05T09:23:55Z","related_material":{"link":[{"url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/","relation":"press_release","description":"News on ISTA Website"}],"record":[{"id":"13173","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"19271"}]},"file":[{"access_level":"open_access","date_created":"2024-03-12T13:42:42Z","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","relation":"main_file","file_name":"2024_PNAS_Koppensteiner.pdf","file_id":"15110","creator":"dernst","content_type":"application/pdf","success":1,"date_updated":"2024-03-12T13:42:42Z","file_size":13648221}],"oa":1,"article_type":"original","quality_controlled":"1","OA_type":"hybrid","OA_place":"publisher","oa_version":"Published Version","department":[{"_id":"RySh"},{"_id":"PeJo"}],"isi":1,"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","month":"02","issue":"8","date_updated":"2026-09-22T22:30:37Z","doi":"10.1073/pnas.2301449121","citation":{"chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 121(8), e2301449121.","ieee":"P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 8. National Academy of Sciences, 2024.","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(8). doi:10.1073/pnas.2301449121","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121."},"pmid":1,"intvolume":" 121","abstract":[{"lang":"eng","text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals."}],"article_number":"e2301449121","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","day":"20","type":"journal_article","ddc":["570"],"APC_amount":"5887,8 EUR","publisher":"National Academy of Sciences","external_id":{"pmid":["38346189"],"isi":["001208567300006"]},"ec_funded":1,"volume":121,"publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","corr_author":"1","year":"2024","_id":"15084","file_date_updated":"2024-03-12T13:42:42Z","language":[{"iso":"eng"}]},{"article_processing_charge":"Yes (in subscription journal)","keyword":["water permeability","photoelectronic materials","device encapsulation","liquid-infused polymers"],"article_type":"original","oa_version":"Published Version","OA_place":"publisher","quality_controlled":"1","OA_type":"hybrid","month":"08","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2308804120","open_access":"1"}],"has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"scopus_import":"1","author":[{"last_name":"Lemaire","full_name":"Lemaire, Baptiste","first_name":"Baptiste"},{"last_name":"Yu","full_name":"Yu, Yanhao","first_name":"Yanhao"},{"last_name":"Molinari","full_name":"Molinari, Nicola","first_name":"Nicola"},{"last_name":"Wu","full_name":"Wu, Haichao","first_name":"Haichao"},{"first_name":"Zachary A. H.","full_name":"Goodwin, Zachary A. H.","last_name":"Goodwin"},{"id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745","first_name":"Friedrich J","last_name":"Stricker","full_name":"Stricker, Friedrich J"},{"first_name":"Boris","last_name":"Kozinsky","full_name":"Kozinsky, Boris"},{"first_name":"Joanna","last_name":"Aizenberg","full_name":"Aizenberg, Joanna"}],"date_published":"2023-08-14T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","fulldoi":"https://doi.org/10.1073/pnas.2308804120","date_created":"2026-05-06T10:49:51Z","extern":"1","oa":1,"type":"journal_article","ddc":["540"],"publication_status":"published","day":"14","title":"Flexible fluid-based encapsulation platform for water-sensitive materials","publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"year":"2023","_id":"21810","publisher":"National Academy of Sciences","volume":120,"external_id":{"pmid":["37579173"]},"intvolume":" 120","citation":{"apa":"Lemaire, B., Yu, Y., Molinari, N., Wu, H., Goodwin, Z. A. H., Stricker, F. J., … Aizenberg, J. (2023). Flexible fluid-based encapsulation platform for water-sensitive materials. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2308804120","mla":"Lemaire, Baptiste, et al. “Flexible Fluid-Based Encapsulation Platform for Water-Sensitive Materials.” Proceedings of the National Academy of Sciences, vol. 120, no. 34, e2308804120, National Academy of Sciences, 2023, doi:10.1073/pnas.2308804120.","chicago":"Lemaire, Baptiste, Yanhao Yu, Nicola Molinari, Haichao Wu, Zachary A. H. Goodwin, Friedrich J Stricker, Boris Kozinsky, and Joanna Aizenberg. “Flexible Fluid-Based Encapsulation Platform for Water-Sensitive Materials.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2308804120.","ieee":"B. Lemaire et al., “Flexible fluid-based encapsulation platform for water-sensitive materials,” Proceedings of the National Academy of Sciences, vol. 120, no. 34. National Academy of Sciences, 2023.","ista":"Lemaire B, Yu Y, Molinari N, Wu H, Goodwin ZAH, Stricker FJ, Kozinsky B, Aizenberg J. 2023. Flexible fluid-based encapsulation platform for water-sensitive materials. Proceedings of the National Academy of Sciences. 120(34), e2308804120.","short":"B. Lemaire, Y. Yu, N. Molinari, H. Wu, Z.A.H. Goodwin, F.J. Stricker, B. Kozinsky, J. Aizenberg, Proceedings of the National Academy of Sciences 120 (2023).","ama":"Lemaire B, Yu Y, Molinari N, et al. Flexible fluid-based encapsulation platform for water-sensitive materials. Proceedings of the National Academy of Sciences. 2023;120(34). doi:10.1073/pnas.2308804120"},"pmid":1,"date_updated":"2026-05-11T07:26:52Z","issue":"34","doi":"10.1073/pnas.2308804120","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_number":"e2308804120","abstract":[{"lang":"eng","text":"The next-generation semiconductors and devices, such as halide perovskites and flexible electronics, are extremely sensitive to water, thus demanding highly effective protection that not only seals out water in all forms (vapor, droplet, and ice), but simultaneously provides mechanical flexibility, durability, transparency, and self-cleaning. Although various solid-state encapsulation methods have been developed, no strategy is available that can fully meet all the above requirements. Here, we report a bioinspired liquid-based encapsulation strategy that offers protection from water without sacrificing the operational properties of the encapsulated materials. Using halide perovskite as a model system, we show that damage to the perovskite from exposure to water is drastically reduced when it is coated by a polymer matrix with infused hydrophobic oil. With a combination of experimental and simulation studies, we elucidated the fundamental transport mechanisms of ultralow water transmission rate that stem from the ability of the infused liquid to fill-in and reduce defects in the coating layer, thus eliminating the low-energy diffusion pathways, and to cause water molecules to diffuse as clusters, which act together as an excellent water permeation barrier. Importantly, the presence of the liquid, as the central component in this encapsulation method provides a unique possibility of reversing the water transport direction; therefore, the lifetime of enclosed water-sensitive materials could be significantly extended via replenishing the hydrophobic oils regularly. We show that the liquid encapsulation platform presented here has high potential in providing not only water protection of the functional device but also flexibility, optical transparency, and self-healing of the coating layer, which are critical for a variety of applications, such as in perovskite solar cells and bioelectronics."}]},{"abstract":[{"text":"The adiabatic elastocaloric effect measures the temperature change of a given system with strain and provides a thermodynamic probe of the entropic landscape in the temperature-strain space. Here, we demonstrate that the DC bias strain-dependence of AC elastocaloric effect allows decomposition of the latter into symmetric (rotation-symmetry-preserving) and antisymmetric (rotation-symmetry-breaking) strain channels, using a tetragonal \r\n-electron intermetallic DyB2C2—whose antiferroquadrupolar order breaks local fourfold rotational symmetries while globally remaining tetragonal—as a showcase example. We capture the strain evolution of its quadrupolar and magnetic phase transitions using both singularities in the elastocaloric coefficient and its jumps at the transitions, and the latter we show follows a modified Ehrenfest relation. We find that antisymmetric strain couples to the underlying order parameter in a biquadratic (linear-quadratic) manner in the antiferroquadrupolar (canted antiferromagnetic) phase, which are attributed to a preserved (broken) global tetragonal symmetry, respectively. The broken tetragonal symmetry in the magnetic phase is further evidenced by elastocaloric strain-hysteresis and optical birefringence. Additionally, within the staggered quadrupolar order, the observed elastocaloric response reflects a quadratic increase of entropy with antisymmetric strain, analogous to the role magnetic field plays for Ising antiferromagnetic orders by promoting pseudospin flips. Our results demonstrate AC elastocaloric effect as a compact and incisive thermodynamic probe into the coupling between electronic degrees of freedom and strain in free energy, which holds the potential for investigating and understanding the symmetry of a wide variety of ordered phases in broader classes of quantum materials.","lang":"eng"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_number":"e2302800120","doi":"10.1073/pnas.2302800120","issue":"35","date_updated":"2025-06-10T13:13:53Z","intvolume":" 120","pmid":1,"citation":{"short":"L. Ye, Y. Sun, V. Sunko, J.F. Rodriguez-Nieva, M.S. Ikeda, T. Worasaran, M.E. Sorensen, M.D. Bachmann, J. Orenstein, I.R. Fisher, Proceedings of the National Academy of Sciences 120 (2023).","ama":"Ye L, Sun Y, Sunko V, et al. Elastocaloric signatures of symmetric and antisymmetric strain-tuning of quadrupolar and magnetic phases in DyB2C2. Proceedings of the National Academy of Sciences. 2023;120(35). doi:10.1073/pnas.2302800120","ista":"Ye L, Sun Y, Sunko V, Rodriguez-Nieva JF, Ikeda MS, Worasaran T, Sorensen ME, Bachmann MD, Orenstein J, Fisher IR. 2023. Elastocaloric signatures of symmetric and antisymmetric strain-tuning of quadrupolar and magnetic phases in DyB2C2. Proceedings of the National Academy of Sciences. 120(35), e2302800120.","ieee":"L. Ye et al., “Elastocaloric signatures of symmetric and antisymmetric strain-tuning of quadrupolar and magnetic phases in DyB2C2,” Proceedings of the National Academy of Sciences, vol. 120, no. 35. National Academy of Sciences, 2023.","chicago":"Ye, Linda, Yue Sun, Veronika Sunko, Joaquin F. Rodriguez-Nieva, Matthias S. Ikeda, Thanapat Worasaran, Matthew E. Sorensen, Maja D. Bachmann, Joseph Orenstein, and Ian R. Fisher. “Elastocaloric Signatures of Symmetric and Antisymmetric Strain-Tuning of Quadrupolar and Magnetic Phases in DyB2C2.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2302800120.","mla":"Ye, Linda, et al. “Elastocaloric Signatures of Symmetric and Antisymmetric Strain-Tuning of Quadrupolar and Magnetic Phases in DyB2C2.” Proceedings of the National Academy of Sciences, vol. 120, no. 35, e2302800120, National Academy of Sciences, 2023, doi:10.1073/pnas.2302800120.","apa":"Ye, L., Sun, Y., Sunko, V., Rodriguez-Nieva, J. F., Ikeda, M. S., Worasaran, T., … Fisher, I. R. (2023). Elastocaloric signatures of symmetric and antisymmetric strain-tuning of quadrupolar and magnetic phases in DyB2C2. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2302800120"},"volume":120,"external_id":{"pmid":["37607225"]},"publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"_id":"19821","year":"2023","title":"Elastocaloric signatures of symmetric and antisymmetric strain-tuning of quadrupolar and magnetic phases in DyB2C2","publication":"Proceedings of the National Academy of Sciences","day":"29","publication_status":"published","ddc":["530"],"type":"journal_article","oa":1,"date_created":"2025-06-10T09:20:12Z","extern":"1","fulldoi":"https://doi.org/10.1073/pnas.2302800120","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-08-29T00:00:00Z","scopus_import":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"author":[{"first_name":"Linda","full_name":"Ye, Linda","last_name":"Ye"},{"last_name":"Sun","full_name":"Sun, Yue","first_name":"Yue"},{"id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","orcid":"0000-0003-2724-3523","first_name":"Veronika","last_name":"Sunko","full_name":"Sunko, Veronika"},{"first_name":"Joaquin F.","last_name":"Rodriguez-Nieva","full_name":"Rodriguez-Nieva, Joaquin F."},{"full_name":"Ikeda, Matthias S.","last_name":"Ikeda","first_name":"Matthias S."},{"first_name":"Thanapat","full_name":"Worasaran, Thanapat","last_name":"Worasaran"},{"first_name":"Matthew E.","full_name":"Sorensen, Matthew E.","last_name":"Sorensen"},{"first_name":"Maja D.","last_name":"Bachmann","full_name":"Bachmann, Maja D."},{"last_name":"Orenstein","full_name":"Orenstein, Joseph","first_name":"Joseph"},{"last_name":"Fisher","full_name":"Fisher, Ian R.","first_name":"Ian R."}],"has_accepted_license":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2302800120"}],"month":"08","oa_version":"Published Version","quality_controlled":"1","OA_place":"publisher","OA_type":"hybrid","article_type":"original","article_processing_charge":"No"},{"article_processing_charge":"Yes (in subscription journal)","article_type":"original","quality_controlled":"1","oa_version":"Published Version","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2301064120"}],"author":[{"full_name":"Rosenberg, Aviv A.","last_name":"Rosenberg","first_name":"Aviv A."},{"full_name":"Yehishalom, Nitsan","last_name":"Yehishalom","first_name":"Nitsan"},{"last_name":"Marx","full_name":"Marx, Ailie","first_name":"Ailie"},{"orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander","last_name":"Bronstein","first_name":"Alexander"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-10-25T00:00:00Z","fulldoi":"https://doi.org/10.1073/pnas.2301064120","status":"public","extern":"1","date_created":"2024-10-08T12:50:36Z","oa":1,"type":"journal_article","publication_status":"published","day":"25","publication":"Proceedings of the National Academy of Sciences","title":"An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units","_id":"18216","year":"2023","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","external_id":{"pmid":["37878722"]},"volume":120,"citation":{"short":"A.A. Rosenberg, N. Yehishalom, A. Marx, A.M. Bronstein, Proceedings of the National Academy of Sciences 120 (2023).","ama":"Rosenberg AA, Yehishalom N, Marx A, Bronstein AM. An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units. Proceedings of the National Academy of Sciences. 2023;120(44). doi:10.1073/pnas.2301064120","ista":"Rosenberg AA, Yehishalom N, Marx A, Bronstein AM. 2023. An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units. Proceedings of the National Academy of Sciences. 120(44), e2301064120.","ieee":"A. A. Rosenberg, N. Yehishalom, A. Marx, and A. M. Bronstein, “An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units,” Proceedings of the National Academy of Sciences, vol. 120, no. 44. National Academy of Sciences, 2023.","chicago":"Rosenberg, Aviv A., Nitsan Yehishalom, Ailie Marx, and Alex M. Bronstein. “An Amino-Domino Model Described by a Cross-Peptide-Bond Ramachandran Plot Defines Amino Acid Pairs as Local Structural Units.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2301064120.","mla":"Rosenberg, Aviv A., et al. “An Amino-Domino Model Described by a Cross-Peptide-Bond Ramachandran Plot Defines Amino Acid Pairs as Local Structural Units.” Proceedings of the National Academy of Sciences, vol. 120, no. 44, e2301064120, National Academy of Sciences, 2023, doi:10.1073/pnas.2301064120.","apa":"Rosenberg, A. A., Yehishalom, N., Marx, A., & Bronstein, A. M. (2023). An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2301064120"},"pmid":1,"intvolume":" 120","issue":"44","date_updated":"2024-10-09T11:55:12Z","doi":"10.1073/pnas.2301064120","article_number":"e2301064120","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"abstract":[{"text":"Protein structure, both at the global and local level, dictates function. Proteins fold from chains of amino acids, forming secondary structures, α-helices and β-strands, that, at least for globular proteins, subsequently fold into a three-dimensional structure. Here, we show that a Ramachandran-type plot focusing on the two dihedral angles separated by the peptide bond, and entirely contained within an amino acid pair, defines a local structural unit. We further demonstrate the usefulness of this cross-peptide-bond Ramachandran plot by showing that it captures β-turn conformations in coil regions, that traditional Ramachandran plot outliers fall into occupied regions of our plot, and that thermophilic proteins prefer specific amino acid pair conformations. Further, we demonstrate experimentally that the effect of a point mutation on backbone conformation and protein stability depends on the amino acid pair context, i.e., the identity of the adjacent amino acid, in a manner predictable by our method.","lang":"eng"}]},{"month":"11","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","isi":1,"OA_place":"publisher","quality_controlled":"1","OA_type":"hybrid","department":[{"_id":"TiVo"}],"oa_version":"Published Version","article_type":"original","related_material":{"link":[{"url":"https://github.com/ccluri/metabolic_spiking","relation":"software"}]},"oa":1,"file":[{"content_type":"application/pdf","creator":"dernst","file_size":16891602,"date_updated":"2023-12-11T12:45:12Z","success":1,"relation":"main_file","checksum":"bf4ec38602a70dae4338077a5a4d497f","date_created":"2023-12-11T12:45:12Z","access_level":"open_access","file_id":"14678","file_name":"2023_PNAS_Chintaluri.pdf"}],"date_created":"2023-12-10T23:01:00Z","author":[{"orcid":"0000-0003-4252-1608","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","full_name":"Chintaluri, Chaitanya","last_name":"Chintaluri","first_name":"Chaitanya"},{"orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","full_name":"Vogels, Tim P","first_name":"Tim P"}],"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"project":[{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."}],"acknowledgement":"We thank Prof. C. Nazaret and Prof. J.-P. Mazat for sharing the code of their mitochondrial model. We also thank G. Miesenböck, E. Marder, L. Abbott, A. Kempf, P. Hasenhuetl, W. Podlaski, F. Zenke, E. Agnes, P. Bozelos, J. Watson, B. Confavreux, and G. Christodoulou, and the rest of the Vogels Lab for their feedback. This work was funded by Wellcome Trust and Royal Society Sir Henry Dale Research Fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council grant (UKRI-BBSRC BB/N019512/1).","fulldoi":"https://doi.org/10.1073/pnas.2306525120","status":"public","date_published":"2023-11-21T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","_id":"14666","file_date_updated":"2023-12-11T12:45:12Z","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species","corr_author":"1","external_id":{"pmid":["37988463"],"isi":["001157389000005"]},"volume":120,"publisher":"National Academy of Sciences","ddc":["570"],"type":"journal_article","day":"21","publication_status":"published","article_number":"e2306525120","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"das_tickbox":"1","abstract":[{"lang":"eng","text":"So-called spontaneous activity is a central hallmark of most nervous systems. Such non-causal firing is contrary to the tenet of spikes as a means of communication, and its purpose remains unclear. We propose that self-initiated firing can serve as a release valve to protect neurons from the toxic conditions arising in mitochondria from lower-than-baseline energy consumption. To demonstrate the viability of our hypothesis, we built a set of models that incorporate recent experimental results indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP), adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing. We explore the relationship of metabolic cost of spiking with its effect on the temporal patterning of spikes and reproduce experimentally observed changes in intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with ROS-modulated potassium channels. We also show that metabolic spiking homeostasis can produce indefinitely sustained avalanche dynamics in cortical circuits. Our theory can account for key features of neuronal activity observed in many studies ranging from ion channel function all the way to resting state dynamics. We finish with a set of experimental predictions that would confirm an integrated, crucial role for metabolically regulated spiking and firmly link metabolic homeostasis and neuronal function."}],"citation":{"short":"C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ama":"Chintaluri C, Vogels TP. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(48). doi:10.1073/pnas.2306525120","ieee":"C. Chintaluri and T. P. Vogels, “Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48. National Academy of Sciences, 2023.","ista":"Chintaluri C, Vogels TP. 2023. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 120(48), e2306525120.","chicago":"Chintaluri, Chaitanya, and Tim P Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2306525120.","mla":"Chintaluri, Chaitanya, and Tim P. Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48, e2306525120, National Academy of Sciences, 2023, doi:10.1073/pnas.2306525120.","apa":"Chintaluri, C., & Vogels, T. P. (2023). Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2306525120"},"pmid":1,"intvolume":" 120","doi":"10.1073/pnas.2306525120","issue":"48","date_updated":"2026-07-13T12:30:49Z"},{"status":"public","fulldoi":"https://doi.org/10.1073/pnas.2221313120","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2023-06-12T00:00:00Z","scopus_import":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"author":[{"first_name":"Yalu","last_name":"Wang","full_name":"Wang, Yalu"},{"first_name":"Zhi","full_name":"Yuan, Zhi","last_name":"Yuan"},{"first_name":"Jinyi","full_name":"Wang, Jinyi","last_name":"Wang"},{"last_name":"Xiao","full_name":"Xiao, Huixin","first_name":"Huixin"},{"full_name":"Wan, Lu","last_name":"Wan","first_name":"Lu"},{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yan","full_name":"Guo, Yan","last_name":"Guo"},{"first_name":"Zhizhong","full_name":"Gong, Zhizhong","last_name":"Gong"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"full_name":"Zhang, Jing","last_name":"Zhang","first_name":"Jing"}],"acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), Hainan Provincial Natural Science Foundation of China (323CXTD379), Chinese Universities Scientific Fund (2023TC019), Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, and China Postdoctoral Science Foundation (BH2020259460).","oa":1,"file":[{"file_size":5244581,"date_updated":"2023-12-13T23:30:03Z","content_type":"application/pdf","creator":"alisjak","embargo":"2023-12-12","file_id":"13204","file_name":"2023_PNAS_Wang.pdf","checksum":"d800e06252eaefba28531fa9440f23f0","relation":"main_file","date_created":"2023-07-10T08:48:40Z","access_level":"open_access"}],"date_created":"2023-07-09T22:01:12Z","department":[{"_id":"JiFr"}],"oa_version":"Published Version","quality_controlled":"1","article_type":"original","article_processing_charge":"No","isi":1,"has_accepted_license":"1","month":"06","doi":"10.1073/pnas.2221313120","issue":"25","date_updated":"2023-12-13T23:30:04Z","intvolume":" 120","pmid":1,"citation":{"mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:10.1073/pnas.2221313120.","apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2221313120","ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(25). doi:10.1073/pnas.2221313120","short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120.","ieee":"Y. Wang et al., “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25. National Academy of Sciences, 2023.","chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2221313120."},"abstract":[{"lang":"eng","text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability."}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_number":"e2221313120","day":"12","publication_status":"published","ddc":["570"],"type":"journal_article","volume":120,"external_id":{"pmid":["37307446"],"isi":["001030689600003"]},"publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"_id":"13201","file_date_updated":"2023-12-13T23:30:03Z","year":"2023","title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"30","date_updated":"2025-05-14T11:01:10Z","doi":"10.1073/pnas.2122147119","citation":{"mla":"Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 30, e2122147119, National Academy of Sciences, 2022, doi:10.1073/pnas.2122147119.","apa":"Barton, N. H. (2022). The “New Synthesis.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2122147119","ama":"Barton NH. The “New Synthesis.” Proceedings of the National Academy of Sciences of the United States of America. 2022;119(30). doi:10.1073/pnas.2122147119","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ieee":"N. H. Barton, “The ‘New Synthesis,’” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 30. National Academy of Sciences, 2022.","chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122147119.","ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119."},"pmid":1,"intvolume":" 119","abstract":[{"text":"When Mendel’s work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin’s theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher, Haldane, and Wright established a century ago, Mendelian inheritance is exactly what is needed for natural selection to work efficiently. Yet, the synthesis remains unfinished. We do not understand why sexual reproduction and a fair meiosis predominate in eukaryotes, or how far these are responsible for their diversity and complexity. Moreover, although quantitative geneticists have long known that adaptive variation is highly polygenic, and that this is essential for efficient selection, this is only now becoming appreciated by molecular biologists—and we still do not have a good framework for understanding polygenic variation or diffuse function.","lang":"eng"}],"article_number":"e2122147119","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","day":"18","type":"journal_article","ddc":["570"],"publisher":"National Academy of Sciences","external_id":{"pmid":["35858408"]},"volume":119,"publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"The \"New Synthesis\"","corr_author":"1","_id":"11702","year":"2022","file_date_updated":"2022-08-01T10:58:28Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-07-18T00:00:00Z","status":"public","fulldoi":"https://doi.org/10.1073/pnas.2122147119","acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","date_created":"2022-07-31T22:01:47Z","file":[{"file_id":"11716","file_name":"2022_PNAS_Barton.pdf","checksum":"06c866196a8957f0c37b8a121771c885","relation":"main_file","date_created":"2022-08-01T10:58:28Z","access_level":"open_access","file_size":848511,"date_updated":"2022-08-01T10:58:28Z","success":1,"content_type":"application/pdf","creator":"dernst"}],"oa":1,"article_type":"original","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"NiBa"}],"article_processing_charge":"No","has_accepted_license":"1","month":"07"},{"article_number":"e2121058119","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"abstract":[{"lang":"eng","text":"Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term."}],"citation":{"apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., & Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2121058119","mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31, e2121058119, National Academy of Sciences, 2022, doi:10.1073/pnas.2121058119.","ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121058119.","ieee":"L. Li et al., “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31. National Academy of Sciences, 2022.","chicago":"Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2121058119.","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(31). doi:10.1073/pnas.2121058119","short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 119 (2022)."},"pmid":1,"intvolume":" 119","issue":"31","date_updated":"2025-05-14T11:01:00Z","doi":"10.1073/pnas.2121058119","publication":"Proceedings of the National Academy of Sciences of the United States of America","corr_author":"1","title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","_id":"11723","file_date_updated":"2022-08-08T07:42:09Z","year":"2022","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"volume":119,"type":"journal_article","ddc":["580"],"publication_status":"published","day":"25","date_created":"2022-08-04T20:06:49Z","file":[{"file_size":2506262,"date_updated":"2022-08-08T07:42:09Z","success":1,"content_type":"application/pdf","creator":"dernst","file_id":"11747","file_name":"2022_PNAS_Li.pdf","relation":"main_file","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","date_created":"2022-08-08T07:42:09Z","access_level":"open_access"}],"oa":1,"acknowledgement":"We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for kindly sharing seeds; Matyáš Fendrych for initiating this project and providing constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and Arseny Savin for contributing to genotyping. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”","author":[{"orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin"},{"full_name":"Chen, Huihuang","last_name":"Chen","first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f"},{"first_name":"Saqer S.","last_name":"Alotaibi","full_name":"Alotaibi, Saqer S."},{"last_name":"Pěnčík","full_name":"Pěnčík, Aleš","first_name":"Aleš"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski","full_name":"Adamowski, Maciek"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"scopus_import":"1","project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"date_published":"2022-07-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1073/pnas.2121058119","status":"public","month":"07","has_accepted_license":"1","isi":1,"article_processing_charge":"No","keyword":["Multidisciplinary"],"article_type":"original","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"JiFr"}]},{"ddc":["570"],"type":"journal_article","day":"28","publication_status":"published","language":[{"iso":"eng"}],"file_date_updated":"2023-10-04T09:05:44Z","_id":"11841","year":"2022","title":"Adsorption free energy predicts amyloid protein nucleation rates","publication":"Proceedings of the National Academy of Sciences of the United States of America","ec_funded":1,"volume":119,"external_id":{"pmid":["35901206"],"isi":["000903753500002"]},"publisher":"National Academy of Sciences","intvolume":" 119","pmid":1,"citation":{"ista":"Toprakcioglu Z, Kamada A, Michaels TCT, Xie M, Krausser J, Wei J, Šarić A, Vendruscolo M, Knowles TPJ. 2022. Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2109718119.","ieee":"Z. Toprakcioglu et al., “Adsorption free energy predicts amyloid protein nucleation rates,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31. National Academy of Sciences, 2022.","chicago":"Toprakcioglu, Zenon, Ayaka Kamada, Thomas C.T. Michaels, Mengqi Xie, Johannes Krausser, Jiapeng Wei, Anđela Šarić, Michele Vendruscolo, and Tuomas P.J. Knowles. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2109718119.","ama":"Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(31). doi:10.1073/pnas.2109718119","short":"Z. Toprakcioglu, A. Kamada, T.C.T. Michaels, M. Xie, J. Krausser, J. Wei, A. Šarić, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","apa":"Toprakcioglu, Z., Kamada, A., Michaels, T. C. T., Xie, M., Krausser, J., Wei, J., … Knowles, T. P. J. (2022). Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2109718119","mla":"Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31, e2109718119, National Academy of Sciences, 2022, doi:10.1073/pnas.2109718119."},"doi":"10.1073/pnas.2109718119","issue":"31","date_updated":"2025-06-12T06:21:34Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_number":"e2109718119","abstract":[{"lang":"eng","text":"Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process."}],"article_processing_charge":"No","isi":1,"department":[{"_id":"AnSa"}],"oa_version":"Published Version","quality_controlled":"1","article_type":"original","month":"07","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"scopus_import":"1","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"}],"author":[{"first_name":"Zenon","full_name":"Toprakcioglu, Zenon","last_name":"Toprakcioglu"},{"first_name":"Ayaka","last_name":"Kamada","full_name":"Kamada, Ayaka"},{"first_name":"Thomas C.T.","last_name":"Michaels","full_name":"Michaels, Thomas C.T."},{"full_name":"Xie, Mengqi","last_name":"Xie","first_name":"Mengqi"},{"first_name":"Johannes","full_name":"Krausser, Johannes","last_name":"Krausser"},{"last_name":"Wei","full_name":"Wei, Jiapeng","first_name":"Jiapeng"},{"last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Michele","full_name":"Vendruscolo, Michele","last_name":"Vendruscolo"},{"first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J.","last_name":"Knowles"}],"acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt\r\n(agreement 337969). We are grateful for financial support from the Biotechnology and Biological Sciences Research Council (BBSRC) (T.P.J.K.), the Newman\r\nFoundation (T.P.J.K.), the Wellcome Trust (T.P.J.K. and M.V.), Peterhouse College\r\nCambridge (T.C.T.M.), the ERC Starting Grant (StG) Non-Equilibrium Protein Assembly (NEPA) (A.S.), the Royal Society (A.S.), the Academy of Medical Sciences\r\n(A.S. and J.K.), and the Cambridge Centre for Misfolding Diseases (CMD).","fulldoi":"https://doi.org/10.1073/pnas.2109718119","status":"public","date_published":"2022-07-28T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file":[{"file_id":"14386","file_name":"2022_PNAS_Toprakcioglu.pdf","relation":"main_file","checksum":"0fe3878896cbeb6c44e29222ec2f336a","date_created":"2023-10-04T09:05:44Z","access_level":"open_access","file_size":2476021,"date_updated":"2023-10-04T09:05:44Z","success":1,"content_type":"application/pdf","creator":"dernst"}],"date_created":"2022-08-14T22:01:45Z"},{"fulldoi":"https://doi.org/10.1073/pnas.2123152119","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-08-29T00:00:00Z","author":[{"first_name":"Michal","full_name":"Hledik, Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper"}],"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"15020"}]},"oa":1,"file":[{"content_type":"application/pdf","creator":"dernst","file_size":2165752,"success":1,"date_updated":"2022-09-12T08:08:12Z","relation":"main_file","checksum":"6dec51f6567da9039982a571508a8e4d","access_level":"open_access","date_created":"2022-09-12T08:08:12Z","file_name":"2022_PNAS_Hledik.pdf","file_id":"12091"}],"date_created":"2022-09-11T22:01:55Z","quality_controlled":"1","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"oa_version":"Published Version","article_type":"original","article_processing_charge":"No","isi":1,"has_accepted_license":"1","month":"08","doi":"10.1073/pnas.2123152119","date_updated":"2026-04-07T12:59:24Z","issue":"36","pmid":1,"citation":{"apa":"Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119","mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 36, e2123152119, National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 36. National Academy of Sciences, 2022.","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences of the United States of America. 119(36), e2123152119.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(36). doi:10.1073/pnas.2123152119"},"intvolume":" 119","abstract":[{"text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.","lang":"eng"}],"article_number":"e2123152119","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"day":"29","publication_status":"published","ddc":["570"],"type":"journal_article","external_id":{"pmid":["36037343"],"isi":["000889278400014"]},"ec_funded":1,"volume":119,"publisher":"National Academy of Sciences","_id":"12081","file_date_updated":"2022-09-12T08:08:12Z","year":"2022","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"Accumulation and maintenance of information in evolution","corr_author":"1"},{"month":"09","oa_version":"None","quality_controlled":"1","article_type":"original","article_processing_charge":"No","keyword":["Multidisciplinary"],"date_created":"2023-02-20T08:10:02Z","extern":"1","fulldoi":"https://doi.org/10.1073/pnas.2109796119","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-09-06T00:00:00Z","scopus_import":"1","author":[{"first_name":"Achille","last_name":"Jouberton","full_name":"Jouberton, Achille"},{"last_name":"Shaw","full_name":"Shaw, Thomas E.","first_name":"Thomas E."},{"first_name":"Evan","last_name":"Miles","full_name":"Miles, Evan"},{"last_name":"McCarthy","full_name":"McCarthy, Michael","first_name":"Michael"},{"first_name":"Stefan","full_name":"Fugger, Stefan","last_name":"Fugger"},{"full_name":"Ren, Shaoting","last_name":"Ren","first_name":"Shaoting"},{"full_name":"Dehecq, Amaury","last_name":"Dehecq","first_name":"Amaury"},{"first_name":"Wei","full_name":"Yang, Wei","last_name":"Yang"},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"}],"volume":119,"publisher":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"year":"2022","_id":"12577","title":"Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau","publication":"PNAS","day":"06","publication_status":"published","type":"journal_article","abstract":[{"text":"Glaciers are key components of the mountain water towers of Asia and are vital for downstream domestic, agricultural, and industrial uses. The glacier mass loss rate over the southeastern Tibetan Plateau is among the highest in Asia and has accelerated in recent decades. This acceleration has been attributed to increased warming, but the mechanisms behind these glaciers’ high sensitivity to warming remain unclear, while the influence of changes in precipitation over the past decades is poorly quantified. Here, we reconstruct glacier mass changes and catchment runoff since 1975 at a benchmark glacier, Parlung No. 4, to shed light on the drivers of recent mass losses for the monsoonal, spring-accumulation glaciers of the Tibetan Plateau. Our modeling demonstrates how a temperature increase (mean of 0.39∘C ⋅dec−1since 1990) has accelerated mass loss rates by altering both the ablation and accumulation regimes in a complex manner. The majority of the post-2000 mass loss occurred during the monsoon months, caused by simultaneous decreases in the solid precipitation ratio (from 0.70 to 0.56) and precipitation amount (–10%), leading to reduced monsoon accumulation (–26%). Higher solid precipitation in spring (+18%) during the last two decades was increasingly important in mitigating glacier mass loss by providing mass to the glacier and protecting it from melting in the early monsoon. With bare ice exposed to warmer temperatures for longer periods, icemelt and catchment discharge have unsustainably intensified since the start of the 21st century, raising concerns for long-term water supply and hazard occurrence in the region.","lang":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_number":"e2109796119","doi":"10.1073/pnas.2109796119","issue":"37","date_updated":"2023-02-28T13:50:37Z","intvolume":" 119","citation":{"apa":"Jouberton, A., Shaw, T. E., Miles, E., McCarthy, M., Fugger, S., Ren, S., … Pellicciotti, F. (2022). Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2109796119","mla":"Jouberton, Achille, et al. “Warming-Induced Monsoon Precipitation Phase Change Intensifies Glacier Mass Loss in the Southeastern Tibetan Plateau.” PNAS, vol. 119, no. 37, e2109796119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2109796119.","ista":"Jouberton A, Shaw TE, Miles E, McCarthy M, Fugger S, Ren S, Dehecq A, Yang W, Pellicciotti F. 2022. Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau. PNAS. 119(37), e2109796119.","ieee":"A. Jouberton et al., “Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau,” PNAS, vol. 119, no. 37. Proceedings of the National Academy of Sciences, 2022.","chicago":"Jouberton, Achille, Thomas E. Shaw, Evan Miles, Michael McCarthy, Stefan Fugger, Shaoting Ren, Amaury Dehecq, Wei Yang, and Francesca Pellicciotti. “Warming-Induced Monsoon Precipitation Phase Change Intensifies Glacier Mass Loss in the Southeastern Tibetan Plateau.” PNAS. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2109796119.","short":"A. Jouberton, T.E. Shaw, E. Miles, M. McCarthy, S. Fugger, S. Ren, A. Dehecq, W. Yang, F. Pellicciotti, PNAS 119 (2022).","ama":"Jouberton A, Shaw TE, Miles E, et al. Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau. PNAS. 2022;119(37). doi:10.1073/pnas.2109796119"}},{"day":"10","publication_status":"published","ddc":["570"],"type":"journal_article","external_id":{"pmid":["34341109"]},"volume":118,"publisher":"Proceedings of the National Academy of Sciences","file_date_updated":"2023-02-23T10:42:07Z","_id":"12667","year":"2021","language":[{"iso":"eng"}],"publication":"PNAS","title":"Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals","doi":"10.1073/pnas.2107588118","date_updated":"2023-02-23T10:45:44Z","issue":"32","citation":{"mla":"Li, Ling, et al. “Microscopic Origins of the Crystallographically Preferred Growth in Evaporation-Induced Colloidal Crystals.” PNAS, vol. 118, no. 32, e2107588118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2107588118.","apa":"Li, L., Goodrich, C. P., Yang, H., Phillips, K. R., Jia, Z., Chen, H., … Aizenberg, J. (2021). Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2107588118","ama":"Li L, Goodrich CP, Yang H, et al. Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. PNAS. 2021;118(32). doi:10.1073/pnas.2107588118","short":"L. Li, C.P. Goodrich, H. Yang, K.R. Phillips, Z. Jia, H. Chen, L. Wang, J. Zhong, A. Liu, J. Lu, J. Shuai, M.P. Brenner, F. Spaepen, J. Aizenberg, PNAS 118 (2021).","ieee":"L. Li et al., “Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals,” PNAS, vol. 118, no. 32. Proceedings of the National Academy of Sciences, 2021.","chicago":"Li, Ling, Carl Peter Goodrich, Haizhao Yang, Katherine R. Phillips, Zian Jia, Hongshun Chen, Lifeng Wang, et al. “Microscopic Origins of the Crystallographically Preferred Growth in Evaporation-Induced Colloidal Crystals.” PNAS. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2107588118.","ista":"Li L, Goodrich CP, Yang H, Phillips KR, Jia Z, Chen H, Wang L, Zhong J, Liu A, Lu J, Shuai J, Brenner MP, Spaepen F, Aizenberg J. 2021. Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. PNAS. 118(32), e2107588118."},"pmid":1,"intvolume":" 118","abstract":[{"lang":"eng","text":"Unlike crystalline atomic and ionic solids, texture development due to crystallographically preferred growth in colloidal crystals is less studied. Here we investigate the underlying mechanisms of the texture evolution in an evaporation-induced colloidal assembly process through experiments, modeling, and theoretical analysis. In this widely used approach to obtain large-area colloidal crystals, the colloidal particles are driven to the meniscus via the evaporation of a solvent or matrix precursor solution where they close-pack to form a face-centered cubic colloidal assembly. Via two-dimensional large-area crystallographic mapping, we show that the initial crystal orientation is dominated by the interaction of particles with the meniscus, resulting in the expected coalignment of the close-packed direction with the local meniscus geometry. By combining with crystal structure analysis at a single-particle level, we further reveal that, at the later stage of self-assembly, however, the colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary dislocations (GNDs) and achieves a large-area uniform crystallographic orientation with the close-packed direction perpendicular to the meniscus and parallel to the growth direction. Classical slip analysis, finite element-based mechanical simulation, computational colloidal assembly modeling, and continuum theory unequivocally show that these GNDs result from the tensile stress field along the meniscus direction due to the constrained shrinkage of the colloidal crystal during drying. The generation of GNDs with specific slip systems within individual grains leads to crystallographic rotation to accommodate the mechanical stress. The mechanistic understanding reported here can be utilized to control crystallographic features of colloidal assemblies, and may provide further insights into crystallographically preferred growth in synthetic, biological, and geological crystals."}],"article_number":"e2107588118","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"quality_controlled":"1","oa_version":"Published Version","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","month":"08","status":"public","fulldoi":"https://doi.org/10.1073/pnas.2107588118","date_published":"2021-08-10T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Li","full_name":"Li, Ling","first_name":"Ling"},{"first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"first_name":"Haizhao","last_name":"Yang","full_name":"Yang, Haizhao"},{"full_name":"Phillips, Katherine R.","last_name":"Phillips","first_name":"Katherine R."},{"full_name":"Jia, Zian","last_name":"Jia","first_name":"Zian"},{"last_name":"Chen","full_name":"Chen, Hongshun","first_name":"Hongshun"},{"first_name":"Lifeng","last_name":"Wang","full_name":"Wang, Lifeng"},{"first_name":"Jinjin","full_name":"Zhong, Jinjin","last_name":"Zhong"},{"first_name":"Anhua","full_name":"Liu, Anhua","last_name":"Liu"},{"first_name":"Jianfeng","full_name":"Lu, Jianfeng","last_name":"Lu"},{"full_name":"Shuai, Jianwei","last_name":"Shuai","first_name":"Jianwei"},{"full_name":"Brenner, Michael P.","last_name":"Brenner","first_name":"Michael P."},{"full_name":"Spaepen, Frans","last_name":"Spaepen","first_name":"Frans"},{"full_name":"Aizenberg, Joanna","last_name":"Aizenberg","first_name":"Joanna"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"scopus_import":"1","file":[{"file_name":"2021_PNAS_Li.pdf","file_id":"12674","checksum":"702f7ec60ce6f2815104ab649dc661a4","relation":"main_file","access_level":"open_access","date_created":"2023-02-23T10:42:07Z","file_size":3275944,"success":1,"date_updated":"2023-02-23T10:42:07Z","content_type":"application/pdf","creator":"dernst"}],"oa":1,"extern":"1","date_created":"2023-02-21T08:51:04Z"},{"article_number":"e2100198118","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"abstract":[{"lang":"eng","text":"Rotavirus genomes are distributed between 11 distinct RNA molecules, all of which must be selectively copackaged during virus assembly. This likely occurs through sequence-specific RNA interactions facilitated by the RNA chaperone NSP2. Here, we report that NSP2 autoregulates its chaperone activity through its C-terminal region (CTR) that promotes RNA–RNA interactions by limiting its helix-unwinding activity. Unexpectedly, structural proteomics data revealed that the CTR does not directly interact with RNA, while accelerating RNA release from NSP2. Cryo–electron microscopy reconstructions of an NSP2–RNA complex reveal a highly conserved acidic patch on the CTR, which is poised toward the bound RNA. Virus replication was abrogated by charge-disrupting mutations within the acidic patch but completely restored by charge-preserving mutations. Mechanistic similarities between NSP2 and the unrelated bacterial RNA chaperone Hfq suggest that accelerating RNA dissociation while promoting intermolecular RNA interactions may be a widespread strategy of RNA chaperone recycling."}],"pmid":1,"citation":{"mla":"Bravo, Jack Peter Kelly, et al. “Structural Basis of Rotavirus RNA Chaperone Displacement and RNA Annealing.” Proceedings of the National Academy of Sciences, vol. 118, no. 41, e2100198118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2100198118.","apa":"Bravo, J. P. K., Bartnik, K., Venditti, L., Acker, J., Gail, E. H., Colyer, A., … Borodavka, A. (2021). Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2100198118","short":"J.P.K. Bravo, K. Bartnik, L. Venditti, J. Acker, E.H. Gail, A. Colyer, C. Davidovich, D.C. Lamb, R. Tuma, A.N. Calabrese, A. Borodavka, Proceedings of the National Academy of Sciences 118 (2021).","ama":"Bravo JPK, Bartnik K, Venditti L, et al. Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proceedings of the National Academy of Sciences. 2021;118(41). doi:10.1073/pnas.2100198118","ista":"Bravo JPK, Bartnik K, Venditti L, Acker J, Gail EH, Colyer A, Davidovich C, Lamb DC, Tuma R, Calabrese AN, Borodavka A. 2021. Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proceedings of the National Academy of Sciences. 118(41), e2100198118.","chicago":"Bravo, Jack Peter Kelly, Kira Bartnik, Luca Venditti, Julia Acker, Emma H. Gail, Alice Colyer, Chen Davidovich, et al. “Structural Basis of Rotavirus RNA Chaperone Displacement and RNA Annealing.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2100198118.","ieee":"J. P. K. Bravo et al., “Structural basis of rotavirus RNA chaperone displacement and RNA annealing,” Proceedings of the National Academy of Sciences, vol. 118, no. 41. Proceedings of the National Academy of Sciences, 2021."},"intvolume":" 118","date_updated":"2024-06-04T06:04:07Z","issue":"41","doi":"10.1073/pnas.2100198118","publication":"Proceedings of the National Academy of Sciences","title":"Structural basis of rotavirus RNA chaperone displacement and RNA annealing","_id":"15139","year":"2021","language":[{"iso":"eng"}],"publisher":"Proceedings of the National Academy of Sciences","external_id":{"pmid":["34615715"]},"volume":118,"type":"journal_article","publication_status":"published","day":"06","extern":"1","date_created":"2024-03-20T10:42:45Z","oa":1,"author":[{"id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo"},{"last_name":"Bartnik","full_name":"Bartnik, Kira","first_name":"Kira"},{"first_name":"Luca","last_name":"Venditti","full_name":"Venditti, Luca"},{"last_name":"Acker","full_name":"Acker, Julia","first_name":"Julia"},{"last_name":"Gail","full_name":"Gail, Emma H.","first_name":"Emma H."},{"last_name":"Colyer","full_name":"Colyer, Alice","first_name":"Alice"},{"first_name":"Chen","last_name":"Davidovich","full_name":"Davidovich, Chen"},{"first_name":"Don C.","last_name":"Lamb","full_name":"Lamb, Don C."},{"first_name":"Roman","full_name":"Tuma, Roman","last_name":"Tuma"},{"first_name":"Antonio N.","last_name":"Calabrese","full_name":"Calabrese, Antonio N."},{"first_name":"Alexander","last_name":"Borodavka","full_name":"Borodavka, Alexander"}],"scopus_import":"1","date_published":"2021-10-06T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","fulldoi":"https://doi.org/10.1073/pnas.2100198118","month":"10","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2100198118","open_access":"1"}],"article_processing_charge":"No","article_type":"original","quality_controlled":"1","oa_version":"Published Version"},{"oa":1,"date_created":"2021-01-03T23:01:23Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"project":[{"_id":"2599F062-B435-11E9-9278-68D0E5697425","grant_number":"RGY0083/2016","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"scopus_import":"1","author":[{"last_name":"Düllberg","full_name":"Düllberg, Christian F","first_name":"Christian F","orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","full_name":"Auer, Albert","last_name":"Auer","first_name":"Albert"},{"full_name":"Canigova, Nikola","last_name":"Canigova","first_name":"Nikola","orcid":"0000-0002-8518-5926","id":"3795523E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Katrin","last_name":"Loibl","full_name":"Loibl, Katrin","id":"3760F32C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2429-7668"},{"first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"acknowledgement":"We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. ","status":"public","fulldoi":"https://doi.org/10.1073/pnas.2010054118","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-01-05T00:00:00Z","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2010054118"}],"article_processing_charge":"No","isi":1,"oa_version":"Published Version","department":[{"_id":"MaLo"},{"_id":"MiSi"}],"quality_controlled":"1","article_type":"original","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_number":"e2010054118","abstract":[{"text":"The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching.","lang":"eng"}],"intvolume":" 118","citation":{"short":"C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ama":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. Proceedings of the National Academy of Sciences of the United States of America. 2021;118(1). doi:10.1073/pnas.2010054118","chicago":"Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2010054118.","ieee":"C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 1. National Academy of Sciences, 2021.","ista":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. Proceedings of the National Academy of Sciences of the United States of America. 118(1), e2010054118.","mla":"Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:10.1073/pnas.2010054118.","apa":"Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., & Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2010054118"},"pmid":1,"doi":"10.1073/pnas.2010054118","issue":"1","date_updated":"2026-06-18T19:37:53Z","language":[{"iso":"eng"}],"year":"2021","_id":"8988","corr_author":"1","title":"In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1","publication":"Proceedings of the National Academy of Sciences of the United States of America","volume":118,"external_id":{"isi":["000607270100018"],"pmid":["33443153"]},"publisher":"National Academy of Sciences","ddc":["570"],"type":"journal_article","day":"05","publication_status":"published"},{"oa":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2102232118"}]},"date_created":"2021-01-03T23:01:23Z","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"scopus_import":"1","author":[{"first_name":"Lindy","last_name":"Abas","full_name":"Abas, Lindy"},{"full_name":"Kolb, Martina","last_name":"Kolb","first_name":"Martina"},{"last_name":"Stadlmann","full_name":"Stadlmann, Johannes","first_name":"Johannes"},{"full_name":"Janacek, Dorina P.","last_name":"Janacek","first_name":"Dorina P."},{"id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1581-881X","first_name":"Kristina","full_name":"Lukic, Kristina","last_name":"Lukic"},{"last_name":"Schwechheimer","full_name":"Schwechheimer, Claus","first_name":"Claus"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","full_name":"Sazanov, Leonid A","last_name":"Sazanov"},{"first_name":"Lukas","full_name":"Mach, Lukas","last_name":"Mach"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"last_name":"Hammes","full_name":"Hammes, Ulrich Z.","first_name":"Ulrich Z."}],"acknowledgement":"This work was supported by Austrian Science Fund Grant FWF P21533-B20 (to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing access to mass spectrometry instruments at the Vienna BioCenter Core Facilities. We thank PNAS reviewers for the many comments and suggestions that helped to improve this manuscript.","fulldoi":"https://doi.org/10.1073/pnas.2020857118","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-01-05T00:00:00Z","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2020857118"}],"article_processing_charge":"No","isi":1,"oa_version":"Published Version","department":[{"_id":"JiFr"},{"_id":"LeSa"}],"quality_controlled":"1","article_type":"original","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_number":"e2020857118","abstract":[{"text":"N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism.","lang":"eng"}],"intvolume":" 118","citation":{"chicago":"Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2020857118.","ieee":"L. Abas et al., “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 1. National Academy of Sciences, 2021.","ista":"Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. Proceedings of the National Academy of Sciences of the United States of America. 118(1), e2020857118.","short":"L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer, L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ama":"Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. Proceedings of the National Academy of Sciences of the United States of America. 2021;118(1). doi:10.1073/pnas.2020857118","apa":"Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer, C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2020857118","mla":"Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 1, e2020857118, National Academy of Sciences, 2021, doi:10.1073/pnas.2020857118."},"pmid":1,"doi":"10.1073/pnas.2020857118","date_updated":"2026-06-18T19:38:20Z","issue":"1","language":[{"iso":"eng"}],"year":"2021","_id":"8993","title":"Naphthylphthalamic acid associates with and inhibits PIN auxin transporters","publication":"Proceedings of the National Academy of Sciences of the United States of America","volume":118,"ec_funded":1,"external_id":{"isi":["000607270100073"],"pmid":["33443187"]},"publisher":"National Academy of Sciences","ddc":["580"],"type":"journal_article","day":"05","publication_status":"published"},{"has_accepted_license":"1","month":"03","quality_controlled":"1","department":[{"_id":"CaGo"}],"oa_version":"Published Version","article_type":"original","article_processing_charge":"No","isi":1,"file":[{"success":1,"date_updated":"2021-03-22T12:23:54Z","file_size":1047954,"creator":"dernst","content_type":"application/pdf","file_name":"2021_PNAS_Goodrich.pdf","file_id":"9278","access_level":"open_access","date_created":"2021-03-22T12:23:54Z","relation":"main_file","checksum":"5be8da2b1c0757feb1057f1a515cf9e0"}],"oa":1,"date_created":"2021-03-21T23:01:20Z","status":"public","fulldoi":"https://doi.org/10.1073/pnas.2024083118","date_published":"2021-03-09T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter"},{"first_name":"Ella M.","full_name":"King, Ella M.","last_name":"King"},{"full_name":"Schoenholz, Samuel S.","last_name":"Schoenholz","first_name":"Samuel S."},{"first_name":"Ekin D.","full_name":"Cubuk, Ekin D.","last_name":"Cubuk"},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."}],"scopus_import":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"acknowledgement":"We thank Agnese Curatolo, Megan Engel, Ofer Kimchi, Seong Ho Pahng, and Roy Frostig for helpful discussions. This material is based on work supported by NSF Graduate Research Fellowship Grant DGE1745303. This research was funded by NSF Grant DMS-1715477, Materials Research Science and Engineering Centers Grant DMR-1420570, and Office of Naval Research Grant N00014-17-1-3029. M.P.B. is an investigator of the Simons Foundation.","external_id":{"pmid":["33653960"],"isi":["000627429100097"]},"volume":118,"publisher":"National Academy of Sciences","year":"2021","_id":"9257","file_date_updated":"2021-03-22T12:23:54Z","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"Designing self-assembling kinetics with differentiable statistical physics models","day":"09","publication_status":"published","ddc":["530"],"type":"journal_article","abstract":[{"text":"The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent kinetics, but this has received considerably less attention. Using recent advances in automatic differentiation, we show how kinetic pathways can be precisely designed by directly differentiating through statistical physics models, namely free energy calculations and molecular dynamics simulations. We consider two systems that are crucial to our understanding of structural self-assembly: bulk crystallization and small nanoclusters. In each case, we are able to assemble precise dynamical features. Using gradient information, we manipulate interactions among constituent particles to tune the rate at which these systems yield specific structures of interest. Moreover, we use this approach to learn nontrivial features about the high-dimensional design space, allowing us to accurately predict when multiple kinetic features can be simultaneously and independently controlled. These results provide a concrete and generalizable foundation for studying nonstructural self-assembly, including kinetic properties as well as other complex emergent properties, in a vast array of systems.","lang":"eng"}],"article_number":"e2024083118","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.2024083118","date_updated":"2025-05-14T10:58:42Z","issue":"10","citation":{"mla":"Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:10.1073/pnas.2024083118.","apa":"Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., & Brenner, M. P. (2021). Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2024083118","ama":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences of the United States of America. 2021;118(10). doi:10.1073/pnas.2024083118","short":"C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ieee":"C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner, “Designing self-assembling kinetics with differentiable statistical physics models,” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 10. National Academy of Sciences, 2021.","chicago":"Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk, and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2024083118.","ista":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences of the United States of America. 118(10), e2024083118."},"pmid":1,"intvolume":" 118"},{"status":"public","fulldoi":"https://doi.org/10.1073/pnas.2021893118","date_published":"2021-04-06T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Prehal, Christian","last_name":"Prehal","first_name":"Christian"},{"last_name":"Samojlov","full_name":"Samojlov, Aleksej","first_name":"Aleksej"},{"first_name":"Manfred","last_name":"Nachtnebel","full_name":"Nachtnebel, Manfred"},{"orcid":"0000-0001-6206-4200","id":"36DB3A20-F248-11E8-B48F-1D18A9856A87","full_name":"Lovicar, Ludek","last_name":"Lovicar","first_name":"Ludek"},{"full_name":"Kriechbaum, Manfred","last_name":"Kriechbaum","first_name":"Manfred"},{"first_name":"Heinz","last_name":"Amenitsch","full_name":"Amenitsch, Heinz"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander"}],"scopus_import":"1","acknowledgement":"S.A.F. and C.P. are indebted to the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 636069), the Austrian Federal Ministry of Science, Research and Economy, and the Austrian Research Promotion Agency (Grant No. 845364). We acknowledge A. Zankel and H. Schroettner for support with SEM measurements. C.P. thanks N. Kostoglou, C. Koczwara, M. Hartmann, and M. Burian for discussions on gas sorption analysis, C++ programming, Monte Carlo modeling, and in situ SAXS experiments, respectively. We thank S. Stadlbauer for help with Karl Fischer titration, R. Riccò for gas sorption measurements, and acknowledge Graz University of Technology for support through the Lead Project LP-03. Likewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. S.A.F. is indebted to Institute of Science and Technology Austria (IST Austria) for support. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility.","acknowledged_ssus":[{"_id":"EM-Fac"}],"oa":1,"date_created":"2021-03-31T07:00:01Z","quality_controlled":"1","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"oa_version":"Preprint","article_type":"original","keyword":["small-angle X-ray scattering","oxygen reduction","disproportionation","Li-air battery"],"article_processing_charge":"No","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv.11447775"}],"month":"04","doi":"10.1073/pnas.2021893118","issue":"14","date_updated":"2025-06-12T06:56:39Z","pmid":1,"citation":{"ama":"Prehal C, Samojlov A, Nachtnebel M, et al. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences of the United States of America. 2021;118(14). doi:10.1073/pnas.2021893118","short":"C. Prehal, A. Samojlov, M. Nachtnebel, L. Lovicar, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ieee":"C. Prehal et al., “In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 14. National Academy of Sciences, 2021.","chicago":"Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Ludek Lovicar, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2021893118.","ista":"Prehal C, Samojlov A, Nachtnebel M, Lovicar L, Kriechbaum M, Amenitsch H, Freunberger SA. 2021. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences of the United States of America. 118(14), e2021893118.","mla":"Prehal, Christian, et al. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 14, e2021893118, National Academy of Sciences, 2021, doi:10.1073/pnas.2021893118.","apa":"Prehal, C., Samojlov, A., Nachtnebel, M., Lovicar, L., Kriechbaum, M., Amenitsch, H., & Freunberger, S. A. (2021). In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2021893118"},"intvolume":" 118","abstract":[{"text":"Electrodepositing insulating lithium peroxide (Li2O2) is the key process during discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved lithium superoxide governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, better understanding governing factors for Li2O2 packing density and capacity requires structural sensitive in situ metrologies. Here, we establish in situ small- and wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2 phase evolution with atomic to submicrometer resolution during cycling a custom-built in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multiphase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets potentially forming large toroidal particles. Li2O2 solution growth is further justified by rotating ring-disk electrode measurements and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. Hence, mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism ought to be reconsidered.","lang":"eng"}],"article_number":"e2021893118","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"day":"06","publication_status":"published","type":"journal_article","external_id":{"isi":["000637398300050"],"pmid":["33785597"]},"volume":118,"publisher":"National Academy of Sciences","_id":"9301","year":"2021","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes"}]