[{"publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"month":"09","pmid":1,"intvolume":"       121","article_number":"e2319341121","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"T. Hausel, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Hausel T. 2024. Commutative avatars of representations of semisimple Lie groups. Proceedings of the National Academy of Sciences of the United States of America. 121(38), e2319341121.","apa":"Hausel, T. (2024). Commutative avatars of representations of semisimple Lie groups. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2319341121\">https://doi.org/10.1073/pnas.2319341121</a>","mla":"Hausel, Tamás. “Commutative Avatars of Representations of Semisimple Lie Groups.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 38, e2319341121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2319341121\">10.1073/pnas.2319341121</a>.","chicago":"Hausel, Tamás. “Commutative Avatars of Representations of Semisimple Lie Groups.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2319341121\">https://doi.org/10.1073/pnas.2319341121</a>.","ieee":"T. Hausel, “Commutative avatars of representations of semisimple Lie groups,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 38. National Academy of Sciences, 2024.","ama":"Hausel T. Commutative avatars of representations of semisimple Lie groups. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(38). doi:<a href=\"https://doi.org/10.1073/pnas.2319341121\">10.1073/pnas.2319341121</a>"},"date_published":"2024-09-17T00:00:00Z","status":"public","has_accepted_license":"1","date_created":"2024-09-22T22:01:41Z","doi":"10.1073/pnas.2319341121","acknowledgement":"We thank Nigel Hitchin for discussions and the joint projects this paper has grown out from. We thank Vladyslav Zveryk for collaboration on Theorem 2.3 and on the corresponding Magma code which implements big algebras. We thank Hiraku Nakajima for discussions and pointing out Theorem 3.1.2, a result generalizing our original observation in the= = 0 case. Special thanks go to Leonid Rybnikov for patiently explaining his works, in particular crucial to Theorem 2.1. We thank Michel Brion, Michael Finkelberg, Oscar García-Prada, Jakub Löwit, Joel Kamnitzer, Friedrich Knop, Michael McBreen, Anton Mellit, Takuro Mochizuki, Shon Ngô, Kamil Rychlewicz, Shiyu Shen, Leslie Spencer, Balázs Szendr ˝ oi, András Szenes, and Oksana\r\nYakimova for comments and discussions. Kamil Rychlewicz and Daniel Bedats helped with the Mathematica files for the figures, and we used the SM_isospin Tikz package of Izaak Neutelings for drawing the baryon multiplets. We thank the referees for many useful comments. We acknowledge funding from FWF grant “Geometry of the tip of the global nilpotent cone” no. P 35847.","type":"journal_article","day":"17","issue":"38","title":"Commutative avatars of representations of semisimple Lie groups","OA_type":"hybrid","publication_identifier":{"eissn":["1091-6490"]},"scopus_import":"1","corr_author":"1","ddc":["510"],"external_id":{"pmid":["39259592"]},"author":[{"first_name":"Tamás","last_name":"Hausel","orcid":"0000-0002-9582-2634","full_name":"Hausel, Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Here we announce the construction and properties of a big commutative subalgebra of the Kirillov algebra attached to a finite dimensional irreducible representation of a complex semisimple Lie group. They are commutative finite flat algebras over the cohomology of the classifying space of the group. They are isomorphic with the equivariant intersection cohomology of affine Schubert varieties, endowing the latter with a new ring structure. Study of the finer aspects of the structure of the big algebras will also furnish the stalks of the intersection cohomology with ring structure, thus ringifying Lusztig’s q-weight multiplicity polynomials i.e., certain affine Kazhdan–Lusztig polynomials."}],"department":[{"_id":"TaHa"}],"_id":"18108","project":[{"name":"Geometry of the tip of the global nilpotent cone","_id":"34b2c9cb-11ca-11ed-8bc3-a50ba74ca4a3","grant_number":"P35847"}],"oa_version":"Published Version","article_type":"original","oa":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/big-algebras-a-dictionary-of-abstract-math/","relation":"press_release"}]},"file":[{"file_name":"2024_PNAS_Hausel.pdf","content_type":"application/pdf","file_id":"18127","relation":"main_file","file_size":3764695,"date_updated":"2024-09-23T11:22:56Z","access_level":"open_access","date_created":"2024-09-23T11:22:56Z","checksum":"df80c873633c6734d2e324841e69db58","creator":"dernst","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","volume":121,"APC_amount":"2742,92 EUR","publication_status":"published","date_updated":"2025-05-08T09:57:59Z","file_date_updated":"2024-09-23T11:22:56Z"},{"volume":121,"year":"2024","publication_status":"published","file":[{"date_created":"2024-11-04T10:29:43Z","checksum":"73db3c87b35753e0f4324417f164a35e","creator":"dernst","success":1,"access_level":"open_access","file_id":"18501","content_type":"application/pdf","relation":"main_file","date_updated":"2024-11-04T10:29:43Z","file_size":1299095,"file_name":"2024_PNAS_McDonough.pdf"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-11-04T10:29:43Z","date_updated":"2025-09-08T14:31:58Z","department":[{"_id":"BeVi"}],"external_id":{"pmid":["39436652"],"isi":["001359216400017"]},"author":[{"last_name":"Mcdonough","first_name":"Yasmine","full_name":"Mcdonough, Yasmine"},{"first_name":"Filip","last_name":"Ruzicka","full_name":"Ruzicka, Filip","id":"347955dd-57b0-11ee-9095-c28bdd368f4b"},{"first_name":"Tim","last_name":"Connallon","full_name":"Connallon, Tim"}],"abstract":[{"lang":"eng","text":"The dominance of beneficial mutations is a key evolutionary parameter affecting the rate and genetic basis of adaptation, yet it is notoriously difficult to estimate. A leading method to infer it is to compare the relative rates of adaptive substitution for X-linked and autosomal genes, which—according to a classic model by Charlesworth et al. (1987)—is a simple function of the dominance of new beneficial mutations. Recent evidence that rates of adaptive substitution are faster for X-linked genes implies, accordingly, that beneficial mutations are usually recessive. However, this conclusion is incompatible with leading theories of dominance, which predict that beneficial mutations tend to be dominant or overdominant with respect to fitness. To address this incompatibility, we use Fisher’s geometric model to predict the distribution of fitness effects of new mutations and the relative rates of positively selected substitution on the X and autosomes. Previous predictions of faster-X theory emerge as a special case of our model in which the phenotypic effects of mutations are small relative to the distance to the phenotypic optimum. But as mutational effects become large relative to the optimum, we observe an elevated tempo of positively selected substitutions on the X relative to the autosomes across a broader range of dominance conditions, including those predicted by theories of dominance. Our results imply that, contrary to previous models, dominant and overdominant beneficial mutations can plausibly generate patterns of faster-X adaptation. We discuss resulting implications for genomic studies of adaptation and inferences of dominance."}],"article_type":"original","oa":1,"ec_funded":1,"_id":"18479","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"oa_version":"Published Version","acknowledgement":"This work was supported by funds from the Australian Research Council and The School of Biological Sciences at Monash University. F.R. was funded by a H2020 Marie Skłodowska-Curie COFUND Action (No. 101034413). We thank three anonymous reviewers for suggestions that substantially improved the paper and breadth of the analysis.","day":"29","type":"journal_article","has_accepted_license":"1","status":"public","doi":"10.1073/pnas.2406335121","date_created":"2024-10-27T23:01:44Z","publication_identifier":{"eissn":["1091-6490"]},"scopus_import":"1","ddc":["570"],"issue":"44","title":"Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes","OA_type":"hybrid","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"pmid":1,"month":"10","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","citation":{"short":"Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Mcdonough Y, Ruzicka F, Connallon T. 2024. Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2406335121.","apa":"Mcdonough, Y., Ruzicka, F., &#38; Connallon, T. (2024). Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2406335121\">https://doi.org/10.1073/pnas.2406335121</a>","mla":"Mcdonough, Yasmine, et al. “Reconciling Theories of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2406335121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2406335121\">10.1073/pnas.2406335121</a>.","ama":"Mcdonough Y, Ruzicka F, Connallon T. Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2406335121\">10.1073/pnas.2406335121</a>","ieee":"Y. Mcdonough, F. Ruzicka, and T. Connallon, “Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","chicago":"Mcdonough, Yasmine, Filip Ruzicka, and Tim Connallon. “Reconciling Theories of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2406335121\">https://doi.org/10.1073/pnas.2406335121</a>."},"date_published":"2024-10-29T00:00:00Z","article_number":"e2406335121","intvolume":"       121","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"}},{"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_number":"e2402340121","intvolume":"       121","date_published":"2024-10-29T00:00:00Z","citation":{"mla":"Ruzickova, Natalia, et al. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2402340121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>.","chicago":"Ruzickova, Natalia, Michal Hledik, and Gašper Tkačik. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>.","ieee":"N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers interpretable genome-wide associations,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","ama":"Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable genome-wide associations. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>","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.","apa":"Ruzickova, N., Hledik, M., &#38; Tkačik, G. (2024). Quantitative omnigenic model discovers interpretable genome-wide associations. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>"},"article_processing_charge":"Yes","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","pmid":1,"month":"10","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"National Academy of Sciences","OA_type":"hybrid","issue":"44","title":"Quantitative omnigenic model discovers interpretable genome-wide associations","ddc":["570"],"corr_author":"1","scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.2402340121","date_created":"2024-11-10T23:01:59Z","status":"public","has_accepted_license":"1","type":"journal_article","day":"29","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.","oa_version":"Published Version","project":[{"_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e","name":"Collective behaviour of cells in pancreatic Islets of Langerhans"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"_id":"18525","oa":1,"article_type":"original","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"}],"author":[{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia","last_name":"Ruzickova","first_name":"Natalia"},{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","last_name":"Hledik","first_name":"Michal"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper"}],"external_id":{"pmid":["39441639"],"isi":["001349462600001"]},"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"date_updated":"2026-04-07T12:02:39Z","file_date_updated":"2024-11-11T09:31:00Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"success":1,"creator":"dernst","checksum":"d930e2ccf9ec900c7d7509a78cfb3564","date_created":"2024-11-11T09:31:00Z","access_level":"open_access","date_updated":"2024-11-11T09:31:00Z","file_size":25529709,"relation":"main_file","file_id":"18536","content_type":"application/pdf","file_name":"2024_PNAS_Ruzickova.pdf"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20357"}]},"publication_status":"published","APC_amount":"3062,93 EUR","year":"2024","volume":121},{"acknowledgement":"We would like to thank Janice Pennington for her support with electron tomography data collection, Dr. Ingrid Jordon-Thaden, director of the Botany Garden and Greenhouse of University of Wisconsin Madison, for her invaluable assistance collecting plant materials, Dr. Marie Trest for providing Chara specimens, and Dr. Nicholas Keuler for his advice on statistical analyses. We thank Charlie Hamilton for exploring the initial computational model. This work was supported by grant NSF MCB 2114603 and NIH 1S10OD026769-01 to M.S.O. F.F acknowledges support as a NOMIS Fellow from the NOMIS Foundation. A.Š. acknowledges ERC Starting Grant “NEPA” 802960.","type":"journal_article","day":"29","status":"public","has_accepted_license":"1","doi":"10.1073/pnas.2409407121","date_created":"2024-11-10T23:01:59Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1","ddc":["570"],"issue":"44","title":"Endosomal membrane budding patterns in plants","OA_type":"hybrid","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"pmid":1,"month":"10","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","citation":{"short":"E. Weiner, E. Berryman, F.F. Frey, A.G. Solís, A. Leier, T.M. Lago, A. Šarić, M.S. Otegui, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","apa":"Weiner, E., Berryman, E., Frey, F. F., Solís, A. G., Leier, A., Lago, T. M., … Otegui, M. S. (2024). Endosomal membrane budding patterns in plants. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2409407121\">https://doi.org/10.1073/pnas.2409407121</a>","ista":"Weiner E, Berryman E, Frey FF, Solís AG, Leier A, Lago TM, Šarić A, Otegui MS. 2024. Endosomal membrane budding patterns in plants. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2409407121.","mla":"Weiner, Ethan, et al. “Endosomal Membrane Budding Patterns in Plants.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2409407121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2409407121\">10.1073/pnas.2409407121</a>.","ieee":"E. Weiner <i>et al.</i>, “Endosomal membrane budding patterns in plants,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","chicago":"Weiner, Ethan, Elizabeth Berryman, Felix F Frey, Ariadna González Solís, André Leier, Tatiana Marquez Lago, Anđela Šarić, and Marisa S. Otegui. “Endosomal Membrane Budding Patterns in Plants.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2409407121\">https://doi.org/10.1073/pnas.2409407121</a>.","ama":"Weiner E, Berryman E, Frey FF, et al. Endosomal membrane budding patterns in plants. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2409407121\">10.1073/pnas.2409407121</a>"},"date_published":"2024-10-29T00:00:00Z","intvolume":"       121","article_number":"e2409407121","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2024","volume":121,"publication_status":"published","file":[{"success":1,"creator":"dernst","checksum":"21c82d2ab58ff99b2bd0489797be42e5","date_created":"2024-11-11T09:35:15Z","access_level":"open_access","file_size":5268074,"date_updated":"2024-11-11T09:35:15Z","relation":"main_file","file_id":"18538","content_type":"application/pdf","file_name":"2024_PNAS_Weiner.pdf"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"file_date_updated":"2024-11-11T09:35:15Z","date_updated":"2025-09-08T14:38:35Z","department":[{"_id":"AnSa"}],"external_id":{"pmid":["39441629"],"isi":["001349500800007"]},"author":[{"last_name":"Weiner","first_name":"Ethan","full_name":"Weiner, Ethan"},{"first_name":"Elizabeth","last_name":"Berryman","full_name":"Berryman, Elizabeth"},{"last_name":"Frey","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F","orcid":"0000-0001-8501-6017"},{"full_name":"Solís, Ariadna González","first_name":"Ariadna González","last_name":"Solís"},{"full_name":"Leier, André","last_name":"Leier","first_name":"André"},{"first_name":"Tatiana Marquez","last_name":"Lago","full_name":"Lago, Tatiana Marquez"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Otegui, Marisa S.","first_name":"Marisa S.","last_name":"Otegui"}],"abstract":[{"text":"Multivesicular endosomes (MVEs) sequester membrane proteins destined for degradation within intralumenal vesicles (ILVs), a process mediated by the membrane-remodeling action of Endosomal Sorting Complex Required for Transport (ESCRT) proteins. In Arabidopsis, endosomal membrane constriction and scission are uncoupled, resulting in the formation of extensive concatenated ILV networks and enhancing cargo sequestration efficiency. Here, we used a combination of electron tomography, computer simulations, and mathematical modeling to address the questions of when concatenated ILV networks evolved in plants and what drives their formation. Through morphometric analyses of tomographic reconstructions of endosomes across yeast, algae, and various land plants, we have found that ILV concatenation is widespread within plant species, but only prevalent in seed plants, especially in flowering plants. Multiple budding sites that require the formation of pores in the limiting membrane were only identified in hornworts and seed plants, suggesting that this mechanism has evolved independently in both plant lineages. To identify the conditions under which these multiple budding sites can arise, we used particle-based molecular dynamics simulations and found that changes in ESCRT filament properties, such as filament curvature and membrane binding energy, can generate the membrane shapes observed in multiple budding sites. To understand the relationship between membrane budding activity and ILV network topology, we performed computational simulations and identified a set of membrane remodeling parameters that can recapitulate our tomographic datasets.","lang":"eng"}],"article_type":"original","oa":1,"_id":"18526","project":[{"call_identifier":"H2020","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"ec_funded":1,"oa_version":"Published Version"},{"OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"month":"12","pmid":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","article_processing_charge":"Yes","citation":{"short":"J. Svoboda, K. Chatterjee, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","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.","apa":"Svoboda, J., &#38; Chatterjee, K. (2024). Density amplifiers of cooperation for spatial games. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2405605121\">https://doi.org/10.1073/pnas.2405605121</a>","mla":"Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation for Spatial Games.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 50, e2405605121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2405605121\">10.1073/pnas.2405605121</a>.","chicago":"Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation for Spatial Games.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2405605121\">https://doi.org/10.1073/pnas.2405605121</a>.","ieee":"J. Svoboda and K. Chatterjee, “Density amplifiers of cooperation for spatial games,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 50. National Academy of Sciences, 2024.","ama":"Svoboda J, Chatterjee K. Density amplifiers of cooperation for spatial games. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(50). doi:<a href=\"https://doi.org/10.1073/pnas.2405605121\">10.1073/pnas.2405605121</a>"},"date_published":"2024-12-10T00:00:00Z","intvolume":"       121","article_number":"e2405605121","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"acknowledgement":"J.S. and K.C. were supported by the European Research Council CoG 863818 (ForM-SMArt) and Austrian Science Fund 10.55776/COE12.","day":"10","type":"journal_article","status":"public","has_accepted_license":"1","doi":"10.1073/pnas.2405605121","date_created":"2024-12-22T23:01:47Z","scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"ddc":["000"],"corr_author":"1","issue":"50","title":"Density amplifiers of cooperation for spatial games","OA_type":"hybrid","department":[{"_id":"KrCh"}],"external_id":{"pmid":["39642209"],"isi":["001379596100014"]},"author":[{"full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","last_name":"Svoboda"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"abstract":[{"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.","lang":"eng"}],"article_type":"original","oa":1,"_id":"18703","ec_funded":1,"project":[{"call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"oa_version":"Published Version","volume":121,"year":"2024","APC_amount":"3143,76 EUR","publication_status":"published","related_material":{"record":[{"id":"20138","status":"public","relation":"dissertation_contains"}]},"file":[{"file_name":"2024_PNAS_Svoboda.pdf","file_size":2491151,"date_updated":"2025-01-02T12:14:15Z","relation":"main_file","content_type":"application/pdf","file_id":"18721","access_level":"open_access","success":1,"creator":"dernst","checksum":"0115e9090b478e0644308c6dab58605b","date_created":"2025-01-02T12:14:15Z"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2025-01-02T12:14:15Z","date_updated":"2026-04-07T11:49:11Z"},{"file_date_updated":"2025-01-29T08:43:16Z","date_updated":"2025-05-14T11:02:52Z","publication_status":"published","year":"2024","volume":121,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"18939","content_type":"application/pdf","relation":"main_file","date_updated":"2025-01-29T08:43:16Z","file_size":720902,"file_name":"2024_PNAS_Springstein.pdf","date_created":"2025-01-29T08:43:16Z","checksum":"5bd62c7cb4287e3706a1d45d6ef61fd1","creator":"dernst","success":1,"access_level":"open_access"}],"oa":1,"article_type":"original","oa_version":"Published Version","_id":"18938","department":[{"_id":"MaLo"}],"abstract":[{"text":"The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are typically nonfunctional. Despite the generally maladaptive impact of such errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends on a process known as programmed ribosomal frameshifting. The fact that these programmed events, commonly involving a shift to the –1 frame, occur at specific evolutionarily optimized “slippery” sites has facilitated mechanistic investigation. By contrast, less is known about the scope and nature of error (i.e., nonprogrammed) frameshifting. Here, we examine error frameshifting by monitoring spontaneous frameshift events that suppress the effects of single base pair deletions affecting two unrelated test proteins. To map the precise sites of frameshifting, we developed a targeted mass spectrometry–based method called “translational tiling proteomics” for interrogating the full set of possible –1 slippage events that could produce the observed frameshift suppression. Surprisingly, such events occur at many sites along the transcripts, involving up to one half of the available codons. Only a subset of these resembled canonical “slippery” sites, implicating alternative mechanisms potentially involving noncognate mispairing events. Additionally, the aggregate frequency of these events (ranging from 1 to 10% in our test cases) was higher than we might have anticipated. Our findings point to an unexpected degree of mechanistic diversity among ribosomal frameshifting events and suggest that frameshifted products may contribute more significantly to the proteome than generally assumed.","lang":"eng"}],"author":[{"orcid":"0000-0002-3461-5391","full_name":"Springstein, Benjamin L","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","first_name":"Benjamin L","last_name":"Springstein"},{"last_name":"Paulo","first_name":"Joao A.","full_name":"Paulo, Joao A."},{"last_name":"Park","first_name":"Hankum","full_name":"Park, Hankum"},{"full_name":"Henry, Kemardo","first_name":"Kemardo","last_name":"Henry"},{"full_name":"Fleming, Eleanor","last_name":"Fleming","first_name":"Eleanor"},{"first_name":"Zoë","last_name":"Feder","full_name":"Feder, Zoë"},{"first_name":"J. Wade","last_name":"Harper","full_name":"Harper, J. Wade"},{"full_name":"Hochschild, Ann","last_name":"Hochschild","first_name":"Ann"}],"external_id":{"pmid":["38289956"]},"ddc":["570"],"scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"OA_type":"hybrid","title":"Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics","issue":"6","type":"journal_article","day":"06","acknowledgement":"We thank S. L. Dove for valuable discussion and comments on the manuscript and R. Hellmiss for artwork. This work was supported by NIH grants GM136247 to A.H., AG011085 to J.W.H., and GM132129 to J.A.P.","doi":"10.1073/pnas.2317453121","date_created":"2025-01-29T08:39:27Z","status":"public","has_accepted_license":"1","date_published":"2024-02-06T00:00:00Z","citation":{"mla":"Springstein, Benjamin L., et al. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 6, e2317453121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2317453121\">10.1073/pnas.2317453121</a>.","ama":"Springstein BL, Paulo JA, Park H, et al. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(6). doi:<a href=\"https://doi.org/10.1073/pnas.2317453121\">10.1073/pnas.2317453121</a>","chicago":"Springstein, Benjamin L, Joao A. Paulo, Hankum Park, Kemardo Henry, Eleanor Fleming, Zoë Feder, J. Wade Harper, and Ann Hochschild. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2317453121\">https://doi.org/10.1073/pnas.2317453121</a>.","ieee":"B. L. Springstein <i>et al.</i>, “Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 6. National Academy of Sciences, 2024.","short":"B.L. Springstein, J.A. Paulo, H. Park, K. Henry, E. Fleming, Z. Feder, J.W. Harper, A. Hochschild, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","apa":"Springstein, B. L., Paulo, J. A., Park, H., Henry, K., Fleming, E., Feder, Z., … Hochschild, A. (2024). Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2317453121\">https://doi.org/10.1073/pnas.2317453121</a>","ista":"Springstein BL, Paulo JA, Park H, Henry K, Fleming E, Feder Z, Harper JW, Hochschild A. 2024. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. 121(6), e2317453121."},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_number":"e2317453121","intvolume":"       121","pmid":1,"month":"02","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"National Academy of Sciences","article_processing_charge":"No","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"author":[{"full_name":"Habig, Michael","last_name":"Habig","first_name":"Michael"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse"},{"full_name":"Müller, Judith","first_name":"Judith","last_name":"Müller"},{"last_name":"Stukenbrock","first_name":"Eva H.","full_name":"Stukenbrock, Eva H."},{"id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","full_name":"Leitner, Hanna","last_name":"Leitner","first_name":"Hanna"},{"first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001207630200005"],"pmid":["38442176"]},"abstract":[{"lang":"eng","text":"Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungus<jats:italic>Metarhizium robertsii</jats:italic>during experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment between<jats:italic>M. robertsii</jats:italic>and another congeneric insect pathogen,<jats:italic>M. guizhouense</jats:italic>. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.</jats:p><jats:sec><jats:title>Significance Statement</jats:title><jats:p>The enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens."}],"department":[{"_id":"SyCr"}],"project":[{"call_identifier":"H2020","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip"}],"_id":"14478","ec_funded":1,"oa_version":"Published Version","article_type":"original","oa":1,"file":[{"file_name":"2024_PNAS_Habig.pdf","file_size":5750361,"date_updated":"2024-03-19T09:02:57Z","content_type":"application/pdf","file_id":"15124","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"date_created":"2024-03-19T09:02:57Z","checksum":"f5e871db617b682edc71fcd08670dc81"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"APC_amount":"3040,36 EUR","volume":121,"year":"2024","publication_status":"published","date_updated":"2025-08-05T13:30:51Z","file_date_updated":"2024-03-19T09:02:57Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","OA_place":"publisher","month":"03","pmid":1,"article_number":"e2316284121","intvolume":"       121","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"date_published":"2024-03-12T00:00:00Z","citation":{"mla":"Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11, e2316284121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2316284121\">10.1073/pnas.2316284121</a>.","ama":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(11). doi:<a href=\"https://doi.org/10.1073/pnas.2316284121\">10.1073/pnas.2316284121</a>","chicago":"Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2316284121\">https://doi.org/10.1073/pnas.2316284121</a>.","ieee":"M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer, “Frequent horizontal chromosome transfer between asexual fungal insect pathogens,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11. National Academy of Sciences, 2024.","short":"M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","apa":"Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., &#38; Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal insect pathogens. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2316284121\">https://doi.org/10.1073/pnas.2316284121</a>","ista":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2316284121."},"status":"public","has_accepted_license":"1","doi":"10.1073/pnas.2316284121","date_created":"2023-10-31T13:30:00Z","acknowledgement":"We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V. Meyling for the fungal strains. We further thank Chengshu Wang for providing the short sequencing reads for M. guizhouense ARESF977 he used for his published genome assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the manuscript. Fig. 1A was created with BioRender.com. This study received funding by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German Research Foundation (DFG grant HA9263/1-1) to M.H.","day":"12","type":"journal_article","OA_type":"hybrid","title":"Frequent horizontal chromosome transfer between asexual fungal insect pathogens","issue":"11","corr_author":"1","ddc":["570"],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1"},{"publication_status":"published","volume":121,"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"related_material":{"link":[{"url":"https://github.com/ChrisCurrin/pv-kcnc2 ","relation":"software"}]},"file":[{"access_level":"open_access","checksum":"f498c643be81895dd3a69ee90115a782","date_created":"2025-04-23T13:51:16Z","success":1,"creator":"dernst","file_name":"2024_PNAS_Clatot.pdf","relation":"main_file","content_type":"application/pdf","file_id":"19613","file_size":3060109,"date_updated":"2025-04-23T13:51:16Z"}],"file_date_updated":"2025-04-23T13:51:16Z","date_updated":"2025-09-04T11:47:47Z","department":[{"_id":"TiVo"}],"abstract":[{"lang":"eng","text":"De novo heterozygous variants in KCNC2 encoding the voltage-gated potassium (K+) channel subunit Kv3.2 are a recently described cause of developmental and epileptic encephalopathy (DEE). A de novo variant in KCNC2 c.374G > A (p.Cys125Tyr) was identified via exome sequencing in a patient with DEE. Relative to wild-type Kv3.2, Kv3.2-p.Cys125Tyr induces K+ currents exhibiting a large hyperpolarizing shift in the voltage dependence of activation, accelerated activation, and delayed deactivation consistent with a relative stabilization of the open conformation, along with increased current density. Leveraging the cryogenic electron microscopy (cryo-EM) structure of Kv3.1, molecular dynamic simulations suggest that a strong π-π stacking interaction between the variant Tyr125 and Tyr156 in the α-6 helix of the T1 domain promotes a relative stabilization of the open conformation of the channel, which underlies the observed gain of function. A multicompartment computational model of a Kv3-expressing parvalbumin-positive cerebral cortex fast-spiking γ-aminobutyric acidergic (GABAergic) interneuron (PV-IN) demonstrates how the Kv3.2-Cys125Tyr variant impairs neuronal excitability and dysregulates inhibition in cerebral cortex circuits to explain the resulting epilepsy."}],"external_id":{"pmid":["38194456"],"isi":["001167401000001"]},"author":[{"full_name":"Clatot, Jerome","last_name":"Clatot","first_name":"Jerome"},{"orcid":"0000-0002-4809-5059","full_name":"Currin, Christopher","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","first_name":"Christopher","last_name":"Currin"},{"last_name":"Liang","first_name":"Qiansheng","full_name":"Liang, Qiansheng"},{"full_name":"Pipatpolkai, Tanadet","first_name":"Tanadet","last_name":"Pipatpolkai"},{"first_name":"Shavonne L.","last_name":"Massey","full_name":"Massey, Shavonne L."},{"full_name":"Helbig, Ingo","first_name":"Ingo","last_name":"Helbig"},{"first_name":"Lucie","last_name":"Delemotte","full_name":"Delemotte, Lucie"},{"first_name":"Tim P","last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"first_name":"Manuel","last_name":"Covarrubias","full_name":"Covarrubias, Manuel"},{"first_name":"Ethan M.","last_name":"Goldberg","full_name":"Goldberg, Ethan M."}],"oa":1,"article_type":"original","oa_version":"Published Version","ec_funded":1,"_id":"14841","project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020","grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"}],"day":"16","type":"journal_article","acknowledgement":"This work was supported by an ERC Consolidator Grant (SYNAPSEEK) to T.P.V., the NOMIS Foundation through the NOMIS Fellowships program at IST Austria to C.B.C., a Jefferson Synaptic Biology Center Pilot Project Grant to M.C., NIH NINDS U54 NS108874 (PI, Alfred L. George), and NIH NINDS R01 NS122887 to E.M.G. The computations were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at the PDC Center for High-Performance Computing, KTH Royal Institute of Technology, partially funded by the Swedish Research Council through grant agreement no. 2018-05973. We thank Akshay Sridhar for the fruitful discussion of the project.","date_created":"2024-01-21T23:00:56Z","doi":"10.1073/pnas.2307776121","status":"public","has_accepted_license":"1","publication_identifier":{"eissn":["1091-6490"]},"scopus_import":"1","ddc":["570"],"issue":"3","title":"A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction","OA_type":"hybrid","pmid":1,"month":"01","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"mla":"Clatot, Jerome, et al. “A Structurally Precise Mechanism Links an Epilepsy-Associated KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 3, e2307776121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2307776121\">10.1073/pnas.2307776121</a>.","ama":"Clatot J, Currin C, Liang Q, et al. A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(3). doi:<a href=\"https://doi.org/10.1073/pnas.2307776121\">10.1073/pnas.2307776121</a>","ieee":"J. Clatot <i>et al.</i>, “A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 3. National Academy of Sciences, 2024.","chicago":"Clatot, Jerome, Christopher Currin, Qiansheng Liang, Tanadet Pipatpolkai, Shavonne L. Massey, Ingo Helbig, Lucie Delemotte, Tim P Vogels, Manuel Covarrubias, and Ethan M. Goldberg. “A Structurally Precise Mechanism Links an Epilepsy-Associated KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2307776121\">https://doi.org/10.1073/pnas.2307776121</a>.","short":"J. Clatot, C. Currin, Q. Liang, T. Pipatpolkai, S.L. Massey, I. Helbig, L. Delemotte, T.P. Vogels, M. Covarrubias, E.M. Goldberg, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","apa":"Clatot, J., Currin, C., Liang, Q., Pipatpolkai, T., Massey, S. L., Helbig, I., … Goldberg, E. M. (2024). A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2307776121\">https://doi.org/10.1073/pnas.2307776121</a>","ista":"Clatot J, Currin C, Liang Q, Pipatpolkai T, Massey SL, Helbig I, Delemotte L, Vogels TP, Covarrubias M, Goldberg EM. 2024. A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of the National Academy of Sciences of the United States of America. 121(3), e2307776121."},"date_published":"2024-01-16T00:00:00Z","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"intvolume":"       121","article_number":"e2307776121"},{"type":"journal_article","day":"13","acknowledgement":"We acknowledge support from the Erasmus programme and the University College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K., S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C. and A.Š.).","doi":"10.1073/pnas.2220075121","date_created":"2024-02-18T23:01:00Z","status":"public","has_accepted_license":"1","corr_author":"1","ddc":["570"],"scopus_import":"1","publication_identifier":{"eissn":["1091-6490"]},"OA_type":"hybrid","issue":"7","title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","month":"02","pmid":1,"language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"National Academy of Sciences","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_published":"2024-02-13T00:00:00Z","citation":{"mla":"Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 7, e2220075121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2220075121\">10.1073/pnas.2220075121</a>.","ieee":"S. Curk <i>et al.</i>, “Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 7. National Academy of Sciences, 2024.","chicago":"Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2220075121\">https://doi.org/10.1073/pnas.2220075121</a>.","ama":"Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(7). doi:<a href=\"https://doi.org/10.1073/pnas.2220075121\">10.1073/pnas.2220075121</a>","short":"S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 121(7), e2220075121.","apa":"Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C. T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2220075121\">https://doi.org/10.1073/pnas.2220075121</a>"},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_number":"e2220075121","intvolume":"       121","publication_status":"published","APC_amount":"5936,71 EUR","year":"2024","volume":121,"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"access_level":"open_access","creator":"dernst","success":1,"date_created":"2024-02-26T08:20:00Z","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b","file_name":"2024_PNAS_Curk.pdf","date_updated":"2024-02-26T08:20:00Z","file_size":7699487,"file_id":"15026","content_type":"application/pdf","relation":"main_file"}],"related_material":{"record":[{"id":"15027","status":"public","relation":"research_data"}]},"file_date_updated":"2024-02-26T08:20:00Z","date_updated":"2025-09-04T12:03:12Z","department":[{"_id":"AnSa"}],"abstract":[{"text":"Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.","lang":"eng"}],"author":[{"full_name":"Curk, Samo","orcid":"0000-0001-6160-9766","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","first_name":"Samo","last_name":"Curk"},{"last_name":"Krausser","first_name":"Johannes","full_name":"Krausser, Johannes"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"full_name":"Frenkel, Daan","last_name":"Frenkel","first_name":"Daan"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"full_name":"Michaels, Thomas C.T.","last_name":"Michaels","first_name":"Thomas C.T."},{"last_name":"Knowles","first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J."},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"}],"external_id":{"pmid":["38335256"],"isi":["001169063600007"]},"oa":1,"article_type":"original","oa_version":"Published Version","_id":"15001","ec_funded":1,"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","call_identifier":"H2020"}]},{"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_number":"e2315558121","intvolume":"       121","citation":{"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).","apa":"Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., &#38; Kleshnina, M. (2024). Efficiency and resilience of cooperation in asymmetric social dilemmas. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2315558121\">https://doi.org/10.1073/pnas.2315558121</a>","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.","mla":"Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 10, e2315558121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2315558121\">10.1073/pnas.2315558121</a>.","ieee":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency and resilience of cooperation in asymmetric social dilemmas,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, 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.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2315558121\">https://doi.org/10.1073/pnas.2315558121</a>.","ama":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience of cooperation in asymmetric social dilemmas. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(10). doi:<a href=\"https://doi.org/10.1073/pnas.2315558121\">10.1073/pnas.2315558121</a>"},"date_published":"2024-03-05T00:00:00Z","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences of the United States of America","pmid":1,"month":"03","publisher":"National Academy of Sciences","OA_place":"publisher","language":[{"iso":"eng"}],"title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","issue":"10","OA_type":"hybrid","scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"corr_author":"1","ddc":["000"],"date_created":"2024-03-05T09:18:49Z","doi":"10.1073/pnas.2315558121","has_accepted_license":"1","status":"public","type":"journal_article","day":"05","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.).","oa_version":"Published Version","_id":"15083","ec_funded":1,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"oa":1,"article_type":"original","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."}],"external_id":{"pmid":["38408249"],"isi":["001207786500004"]},"author":[{"id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","orcid":"0009-0001-5009-4987","full_name":"Hübner, Valentin","last_name":"Hübner","first_name":"Valentin"},{"first_name":"Manuel","last_name":"Staab","full_name":"Staab, Manuel"},{"first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","last_name":"Kleshnina","full_name":"Kleshnina, Maria"}],"department":[{"_id":"KrCh"}],"date_updated":"2026-04-07T12:30:56Z","file_date_updated":"2024-03-12T13:12:22Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"id":"15108","status":"public","relation":"research_data"},{"id":"19903","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/","description":"News on ISTA Website","relation":"press_release"}]},"file":[{"file_name":"2024_PNAS_Huebner.pdf","content_type":"application/pdf","file_id":"15109","relation":"main_file","file_size":2203220,"date_updated":"2024-03-12T13:12:22Z","access_level":"open_access","date_created":"2024-03-12T13:12:22Z","checksum":"068520e3efd4d008bb9177e8aedb7d22","creator":"dernst","success":1}],"publication_status":"published","volume":121,"year":"2024","APC_amount":"3041,76 EUR"},{"oa_version":"Published Version","_id":"15116","oa":1,"article_type":"original","abstract":[{"text":"Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.","lang":"eng"}],"author":[{"last_name":"Giubertoni","first_name":"Giulia","full_name":"Giubertoni, Giulia"},{"last_name":"Feng","first_name":"Liru","full_name":"Feng, Liru"},{"full_name":"Klein, Kevin","last_name":"Klein","first_name":"Kevin"},{"full_name":"Giannetti, Guido","last_name":"Giannetti","first_name":"Guido"},{"full_name":"Rutten, Luco","first_name":"Luco","last_name":"Rutten"},{"first_name":"Yeji","last_name":"Choi","full_name":"Choi, Yeji"},{"full_name":"Van Der Net, Anouk","first_name":"Anouk","last_name":"Van Der Net"},{"full_name":"Castro-Linares, Gerard","last_name":"Castro-Linares","first_name":"Gerard"},{"first_name":"Federico","last_name":"Caporaletti","full_name":"Caporaletti, Federico"},{"full_name":"Micha, Dimitra","last_name":"Micha","first_name":"Dimitra"},{"last_name":"Hunger","first_name":"Johannes","full_name":"Hunger, Johannes"},{"full_name":"Deblais, Antoine","last_name":"Deblais","first_name":"Antoine"},{"first_name":"Daniel","last_name":"Bonn","full_name":"Bonn, Daniel"},{"full_name":"Sommerdijk, Nico","last_name":"Sommerdijk","first_name":"Nico"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela"},{"first_name":"Ioana M.","last_name":"Ilie","full_name":"Ilie, Ioana M."},{"first_name":"Gijsje H.","last_name":"Koenderink","full_name":"Koenderink, Gijsje H."},{"full_name":"Woutersen, Sander","last_name":"Woutersen","first_name":"Sander"}],"external_id":{"isi":["001206387400001"],"pmid":["38451946"]},"department":[{"_id":"AnSa"}],"date_updated":"2025-09-04T13:03:56Z","file_date_updated":"2024-03-19T10:22:42Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"file":[{"relation":"main_file","file_id":"15125","content_type":"application/pdf","file_size":12952586,"date_updated":"2024-03-19T10:22:42Z","file_name":"2024_PNAS_Giubertoni.pdf","checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05","date_created":"2024-03-19T10:22:42Z","success":1,"creator":"dernst","access_level":"open_access"}],"related_material":{"record":[{"id":"15126","relation":"research_data","status":"public"}]},"publication_status":"published","year":"2024","volume":121,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"       121","article_number":"e2313162121","date_published":"2024-03-12T00:00:00Z","citation":{"short":"G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2313162121.","apa":"Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., … Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2313162121\">https://doi.org/10.1073/pnas.2313162121</a>","mla":"Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11, e2313162121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2313162121\">10.1073/pnas.2313162121</a>.","ama":"Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(11). doi:<a href=\"https://doi.org/10.1073/pnas.2313162121\">10.1073/pnas.2313162121</a>","chicago":"Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten, Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2313162121\">https://doi.org/10.1073/pnas.2313162121</a>.","ieee":"G. Giubertoni <i>et al.</i>, “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11. National Academy of Sciences, 2024."},"article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","month":"03","pmid":1,"language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","issue":"11","ddc":["550"],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1","doi":"10.1073/pnas.2313162121","date_created":"2024-03-17T23:00:57Z","status":"public","has_accepted_license":"1","type":"journal_article","day":"12","acknowledgement":"We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla, and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education, Culture and Science (OCW) and The Netherlands Organization for Scientific Research and from NWO grant OCENW.GROOT.2019.022. This work has received support from the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project (with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from Royal Society and European Research Council Starting Grant. G. Giubertoni kindly thanks to the Care4Bones community and the Collagen Café community for reminding that we do not own the knowledge we create, but it is, rather, a collective resource intended for the advancement of human progress."},{"article_type":"original","oa":1,"_id":"15250","oa_version":"Published Version","department":[{"_id":"DaSi"}],"external_id":{"pmid":["38507452"],"isi":["001206419000003"]},"author":[{"first_name":"Danila","last_name":"Boytsov","full_name":"Boytsov, Danila"},{"last_name":"Madej","first_name":"Gregor M.","full_name":"Madej, Gregor M."},{"full_name":"Horn, Georg","last_name":"Horn","first_name":"Georg"},{"first_name":"Nadine","last_name":"Blaha","full_name":"Blaha, Nadine"},{"full_name":"Köcher, Thomas","last_name":"Köcher","first_name":"Thomas"},{"first_name":"Harald H.","last_name":"Sitte","full_name":"Sitte, Harald H."},{"first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ziegler, Christine","last_name":"Ziegler","first_name":"Christine"},{"last_name":"Sandtner","first_name":"Walter","full_name":"Sandtner, Walter"},{"id":"3047D808-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko","last_name":"Roblek","first_name":"Marko"}],"acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Orphan solute carrier (SLC) represents a group of membrane transporters whose exact functions and substrate specificities are not known. Elucidating the function and regulation of orphan SLC transporters is not only crucial for advancing our knowledge of cellular and molecular biology but can potentially lead to the development of new therapeutic strategies. Here, we provide evidence for the biological function of a ubiquitous orphan lysosomal SLC, the Major Facilitator Superfamily Domain-containing Protein 1 (MFSD1), which has remained phylogenetically unassigned. Targeted metabolomics revealed that dipeptides containing either lysine or arginine residues accumulate in lysosomes of cells lacking MFSD1. Whole-cell patch-clamp electrophysiological recordings of HEK293-cells expressing MFSD1 on the cell surface displayed transport affinities for positively charged dipeptides in the lower mM range, while dipeptides that carry a negative net charge were not transported. This was also true for single amino acids and tripeptides, which MFSD1 failed to transport. Our results identify MFSD1 as a highly selective lysosomal lysine/arginine/histidine-containing dipeptide exporter, which functions as a uniporter."}],"file_date_updated":"2024-04-02T08:54:28Z","date_updated":"2025-09-04T13:19:02Z","year":"2024","volume":121,"publication_status":"published","file":[{"file_name":"2024_PNAS_Boytsov.pdf","date_updated":"2024-04-02T08:54:28Z","file_size":2483787,"relation":"main_file","file_id":"15256","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"dernst","checksum":"06f9e60b1146a685d58bf33999422fa8","date_created":"2024-04-02T08:54:28Z"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"D. Boytsov, G.M. Madej, G. Horn, N. Blaha, T. Köcher, H.H. Sitte, D.E. Siekhaus, C. Ziegler, W. Sandtner, M. Roblek, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Boytsov D, Madej GM, Horn G, Blaha N, Köcher T, Sitte HH, Siekhaus DE, Ziegler C, Sandtner W, Roblek M. 2024. Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport. Proceedings of the National Academy of Sciences of the United States of America. 121(13), e2319686121.","apa":"Boytsov, D., Madej, G. M., Horn, G., Blaha, N., Köcher, T., Sitte, H. H., … Roblek, M. (2024). Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2319686121\">https://doi.org/10.1073/pnas.2319686121</a>","mla":"Boytsov, Danila, et al. “Orphan Lysosomal Solute Carrier MFSD1 Facilitates Highly Selective Dipeptide Transport.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 13, e2319686121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2319686121\">10.1073/pnas.2319686121</a>.","chicago":"Boytsov, Danila, Gregor M. Madej, Georg Horn, Nadine Blaha, Thomas Köcher, Harald H. Sitte, Daria E Siekhaus, Christine Ziegler, Walter Sandtner, and Marko Roblek. “Orphan Lysosomal Solute Carrier MFSD1 Facilitates Highly Selective Dipeptide Transport.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2319686121\">https://doi.org/10.1073/pnas.2319686121</a>.","ieee":"D. Boytsov <i>et al.</i>, “Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 13. National Academy of Sciences, 2024.","ama":"Boytsov D, Madej GM, Horn G, et al. Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(13). doi:<a href=\"https://doi.org/10.1073/pnas.2319686121\">10.1073/pnas.2319686121</a>"},"date_published":"2024-03-26T00:00:00Z","article_number":"e2319686121","intvolume":"       121","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"month":"03","pmid":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1091-6490"]},"scopus_import":"1","ddc":["570"],"corr_author":"1","issue":"13","title":"Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport","acknowledgement":"We thank the Metabolomics Facility at Vienna BioCenter Core Facilities, which is a member of the Vienna BioCenter and funded by the City of Vienna through the Vienna Business Agency (shared research facility), for the LC–MS/MS analysis; and the BioImaging Facility at IST Austria for technical support and assistance. The authors want to thank N. Kastner for help with the live  cell  imaging  and  A.  Korošec  for  help  with  flow  cytometry.  This  work  was  supported by the Austrian Science Fund (FWF), grant P 36621- B (to M.R.), grant P 36667 (to W.S.), and core funding from IST Austria (to D.S.).","day":"26","type":"journal_article","has_accepted_license":"1","status":"public","date_created":"2024-03-31T22:01:12Z","doi":"10.1073/pnas.2319686121"},{"publication_identifier":{"eissn":["1091-6490"]},"scopus_import":"1","ddc":["570"],"issue":"15","title":"Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic bridges","type":"journal_article","day":"09","acknowledgement":"We  thank  all  members  of  the  Spitzer  laboratory  for  discussions  and  critical  feedback;  K.  Marek  for  discussions  of  acknowledgment  signals; I. Gregor and R. Aricescu for discussions of receptor pharmacology and transsynaptic  bridges;  C.  Kintner  for  advice  on  Xenopus  blastomere  lineage;  A.  Ray and E. Park for guidance on miniature analysis; A. Glavis- Bloom, S.U. Choi, S. Atkins, M. Gupta, and S. Malladi for technical assistance; and D. K. Berg and L. R. Squire for comments on the manuscript. This work was supported by NSF 2051555 and the Overland Foundation. Microscopy for five- channel imaging utilized the UCSD School of Medicine Microscopy Core, supported by NIH grant NS047101.","doi":"10.1073/pnas.2318041121","date_created":"2024-04-21T22:00:53Z","status":"public","has_accepted_license":"1","citation":{"ista":"Godavarthi SK, Hiramoto M, Ignatyev Y, Levin JB, Li HQ, Pratelli M, Borchardt J, Czajkowski C, Borodinsky LN, Sweeney LB, Cline HT, Spitzer NC. 2024. Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic bridges. Proceedings of the National Academy of Sciences of the United States of America. 121(15), e2318041121.","apa":"Godavarthi, S. K., Hiramoto, M., Ignatyev, Y., Levin, J. B., Li, H. Q., Pratelli, M., … Spitzer, N. C. (2024). Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic bridges. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2318041121\">https://doi.org/10.1073/pnas.2318041121</a>","short":"S.K. Godavarthi, M. Hiramoto, Y. Ignatyev, J.B. Levin, H.Q. Li, M. Pratelli, J. Borchardt, C. Czajkowski, L.N. Borodinsky, L.B. Sweeney, H.T. Cline, N.C. Spitzer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","chicago":"Godavarthi, Swetha K., Masaki Hiramoto, Yuri Ignatyev, Jacqueline B. Levin, Hui Quan Li, Marta Pratelli, Jennifer Borchardt, et al. “Postsynaptic Receptors Regulate Presynaptic Transmitter Stability through Transsynaptic Bridges.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2318041121\">https://doi.org/10.1073/pnas.2318041121</a>.","ieee":"S. K. Godavarthi <i>et al.</i>, “Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic bridges,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 15. National Academy of Sciences, 2024.","ama":"Godavarthi SK, Hiramoto M, Ignatyev Y, et al. Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic bridges. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(15). doi:<a href=\"https://doi.org/10.1073/pnas.2318041121\">10.1073/pnas.2318041121</a>","mla":"Godavarthi, Swetha K., et al. “Postsynaptic Receptors Regulate Presynaptic Transmitter Stability through Transsynaptic Bridges.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 15, e2318041121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2318041121\">10.1073/pnas.2318041121</a>."},"date_published":"2024-04-09T00:00:00Z","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_number":"e2318041121","intvolume":"       121","pmid":1,"month":"04","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences of the United States of America","file_date_updated":"2024-04-23T06:53:14Z","date_updated":"2025-09-04T13:42:01Z","publication_status":"published","volume":121,"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"file":[{"success":1,"creator":"dernst","checksum":"f3b4ffad4ef3d1c443414edf0cd2392c","date_created":"2024-04-23T06:53:14Z","access_level":"open_access","date_updated":"2024-04-23T06:53:14Z","file_size":16187094,"relation":"main_file","content_type":"application/pdf","file_id":"15340","file_name":"2024_PNAS_Godavarthi.pdf"}],"oa":1,"article_type":"original","oa_version":"Published Version","_id":"15335","department":[{"_id":"LoSw"}],"abstract":[{"lang":"eng","text":"Stable matching of neurotransmitters with their receptors is fundamental to synapse function and reliable communication in neural circuits. Presynaptic neurotransmitters regulate the stabilization of postsynaptic transmitter receptors. Whether postsynaptic receptors regulate stabilization of presynaptic transmitters has received less attention. Here, we show that blockade of endogenous postsynaptic acetylcholine receptors (AChR) at the neuromuscular junction destabilizes the cholinergic phenotype in motor neurons and stabilizes an earlier, developmentally transient glutamatergic phenotype. Further, expression of exogenous postsynaptic gamma-aminobutyric acid type A receptors (GABAA receptors) in muscle cells stabilizes an earlier, developmentally transient GABAergic motor neuron phenotype. Both AChR and GABAA receptors are linked to presynaptic neurons through transsynaptic bridges. Knockdown of specific components of these transsynaptic bridges prevents stabilization of the cholinergic or GABAergic phenotypes. Bidirectional communication can enforce a match between transmitter and receptor and ensure the fidelity of synaptic transmission. Our findings suggest a potential role of dysfunctional transmitter receptors in neurological disorders that involve the loss of the presynaptic transmitter."}],"external_id":{"isi":["001243892800004"],"pmid":["38568976"]},"author":[{"full_name":"Godavarthi, Swetha K.","first_name":"Swetha K.","last_name":"Godavarthi"},{"first_name":"Masaki","last_name":"Hiramoto","full_name":"Hiramoto, Masaki"},{"full_name":"Ignatyev, Yuri","first_name":"Yuri","last_name":"Ignatyev"},{"full_name":"Levin, Jacqueline B.","first_name":"Jacqueline B.","last_name":"Levin"},{"full_name":"Li, Hui Quan","first_name":"Hui Quan","last_name":"Li"},{"full_name":"Pratelli, Marta","first_name":"Marta","last_name":"Pratelli"},{"full_name":"Borchardt, Jennifer","first_name":"Jennifer","last_name":"Borchardt"},{"full_name":"Czajkowski, Cynthia","last_name":"Czajkowski","first_name":"Cynthia"},{"full_name":"Borodinsky, Laura N.","last_name":"Borodinsky","first_name":"Laura N."},{"first_name":"Lora Beatrice Jaeger","last_name":"Sweeney","full_name":"Sweeney, Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"},{"last_name":"Cline","first_name":"Hollis T.","full_name":"Cline, Hollis T."},{"first_name":"Nicholas C.","last_name":"Spitzer","full_name":"Spitzer, Nicholas C."}]},{"file_date_updated":"2024-06-10T10:27:37Z","date_updated":"2025-09-08T07:51:01Z","year":"2024","volume":121,"APC_amount":"2570,79 EUR","publication_status":"published","related_material":{"link":[{"url":"https://github.com/dbrueckner/SelforgInformation","relation":"software"},{"description":"News on the ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/the-embryo-assembles-itself/"}]},"file":[{"file_name":"2024_PNAS_Brueckner.pdf","content_type":"application/pdf","file_id":"17130","relation":"main_file","date_updated":"2024-06-10T10:27:37Z","file_size":12329234,"access_level":"open_access","date_created":"2024-06-10T10:27:37Z","checksum":"59797a75db7beb3721ed7a4d14c241f9","creator":"dernst","success":1}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","oa":1,"_id":"17123","project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022"}],"oa_version":"Published Version","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"external_id":{"pmid":["38819997"],"isi":["001244835000006"]},"author":[{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","last_name":"Brückner","first_name":"David"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and even harnessing intrinsic and extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework to quantify the performance of such stochastic self-organizing systems. To that end, we introduce an information-theoretic measure for self-organized fate specification during embryonic development. We show that the proposed measure assesses the total information content of fate patterns and decomposes it into interpretable contributions corresponding to the positional and correlational information. By optimizing the proposed measure, our framework provides a normative theory for developmental circuits, which we demonstrate on lateral inhibition, cell type proportioning, and reaction–diffusion models of self-organization. This paves a way toward a classification of developmental systems based on a common information-theoretic language, thereby organizing the zoo of implicated chemical and mechanical signaling processes."}],"scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"ddc":["570"],"corr_author":"1","title":"Information content and optimization of self-organized developmental systems","issue":"23","OA_type":"hybrid","acknowledgement":"We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns, Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 343-2022). This research was performed in part at the Aspen Center for Physics, which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon and Betty Moore Foundation Grant No. 2919.02.","type":"journal_article","day":"04","status":"public","has_accepted_license":"1","doi":"10.1073/pnas.2322326121","date_created":"2024-06-09T22:01:02Z","citation":{"mla":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23, e2322326121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>.","chicago":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>.","ieee":"D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23. National Academy of Sciences, 2024.","ama":"Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(23). doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>","short":"D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","apa":"Brückner, D., &#38; Tkačik, G. (2024). Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>","ista":"Brückner D, Tkačik G. 2024. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 121(23), e2322326121."},"date_published":"2024-06-04T00:00:00Z","intvolume":"       121","article_number":"e2322326121","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"pmid":1,"month":"06","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)"},{"department":[{"_id":"RySh"},{"_id":"PeJo"}],"external_id":{"isi":["001208567300006"],"pmid":["38346189"]},"author":[{"orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Koppensteiner"},{"full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep","last_name":"Bhandari"},{"id":"4659D740-F248-11E8-B48F-1D18A9856A87","full_name":"Önal, Hüseyin C","orcid":"0000-0002-2771-2011","last_name":"Önal","first_name":"Hüseyin C"},{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","last_name":"Borges Merjane","first_name":"Carolina"},{"id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","last_name":"Le Monnier","first_name":"Elodie"},{"first_name":"Utsa","last_name":"Roy","full_name":"Roy, Utsa","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2"},{"last_name":"Nakamura","first_name":"Yukihiro","full_name":"Nakamura, Yukihiro"},{"last_name":"Sadakata","first_name":"Tetsushi","full_name":"Sadakata, Tetsushi"},{"last_name":"Sanbo","first_name":"Makoto","full_name":"Sanbo, Makoto"},{"last_name":"Hirabayashi","first_name":"Masumi","full_name":"Hirabayashi, Masumi"},{"full_name":"Rhee, JeongSeop","last_name":"Rhee","first_name":"JeongSeop"},{"last_name":"Brose","first_name":"Nils","full_name":"Brose, Nils"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M"},{"first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"abstract":[{"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            <jats:sup>2+</jats:sup>\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.","lang":"eng"}],"article_type":"original","oa":1,"_id":"15084","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"ec_funded":1,"oa_version":"Published Version","volume":121,"year":"2024","APC_amount":"5887,8 EUR","publication_status":"published","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/"}],"record":[{"id":"13173","relation":"research_data","status":"public"},{"status":"public","relation":"dissertation_contains","id":"19271"}]},"file":[{"date_updated":"2024-03-12T13:42:42Z","file_size":13648221,"relation":"main_file","content_type":"application/pdf","file_id":"15110","file_name":"2024_PNAS_Koppensteiner.pdf","success":1,"creator":"dernst","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","date_created":"2024-03-12T13:42:42Z","access_level":"open_access"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-03-12T13:42:42Z","date_updated":"2026-06-22T22:30:42Z","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"pmid":1,"month":"02","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","citation":{"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. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(8). doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>","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.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>.","ieee":"P. Koppensteiner <i>et al.</i>, “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8. National Academy of Sciences, 2024.","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>.","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. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>","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.","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)."},"date_published":"2024-02-20T00:00:00Z","intvolume":"       121","article_number":"e2301449121","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"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.","day":"20","type":"journal_article","has_accepted_license":"1","status":"public","date_created":"2024-03-05T09:23:55Z","doi":"10.1073/pnas.2301449121","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"scopus_import":"1","ddc":["570"],"corr_author":"1","issue":"8","title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","OA_type":"hybrid"},{"author":[{"last_name":"Lemaire","first_name":"Baptiste","full_name":"Lemaire, Baptiste"},{"full_name":"Yu, Yanhao","last_name":"Yu","first_name":"Yanhao"},{"full_name":"Molinari, Nicola","first_name":"Nicola","last_name":"Molinari"},{"first_name":"Haichao","last_name":"Wu","full_name":"Wu, Haichao"},{"full_name":"Goodwin, Zachary A. H.","first_name":"Zachary A. H.","last_name":"Goodwin"},{"last_name":"Stricker","first_name":"Friedrich J","id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745","full_name":"Stricker, Friedrich J"},{"first_name":"Boris","last_name":"Kozinsky","full_name":"Kozinsky, Boris"},{"last_name":"Aizenberg","first_name":"Joanna","full_name":"Aizenberg, Joanna"}],"external_id":{"pmid":["37579173"]},"abstract":[{"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.","lang":"eng"}],"extern":"1","article_type":"original","oa":1,"_id":"21810","oa_version":"Published Version","volume":120,"year":"2023","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-05-11T07:26:52Z","keyword":["water permeability","photoelectronic materials","device encapsulation","liquid-infused polymers"],"language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"National Academy of Sciences","pmid":1,"month":"08","publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","date_published":"2023-08-14T00:00:00Z","citation":{"mla":"Lemaire, Baptiste, et al. “Flexible Fluid-Based Encapsulation Platform for Water-Sensitive Materials.” <i>Proceedings of the National Academy of Sciences</i>, vol. 120, no. 34, e2308804120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2308804120\">10.1073/pnas.2308804120</a>.","ama":"Lemaire B, Yu Y, Molinari N, et al. Flexible fluid-based encapsulation platform for water-sensitive materials. <i>Proceedings of the National Academy of Sciences</i>. 2023;120(34). doi:<a href=\"https://doi.org/10.1073/pnas.2308804120\">10.1073/pnas.2308804120</a>","ieee":"B. Lemaire <i>et al.</i>, “Flexible fluid-based encapsulation platform for water-sensitive materials,” <i>Proceedings of the National Academy of Sciences</i>, vol. 120, no. 34. National Academy of Sciences, 2023.","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.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2308804120\">https://doi.org/10.1073/pnas.2308804120</a>.","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).","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. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2308804120\">https://doi.org/10.1073/pnas.2308804120</a>","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."},"intvolume":"       120","article_number":"e2308804120","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","day":"14","status":"public","has_accepted_license":"1","date_created":"2026-05-06T10:49:51Z","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2308804120","open_access":"1"}],"doi":"10.1073/pnas.2308804120","ddc":["540"],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1","OA_type":"hybrid","issue":"34","title":"Flexible fluid-based encapsulation platform for water-sensitive materials"},{"_id":"19821","oa_version":"Published Version","article_type":"original","oa":1,"author":[{"full_name":"Ye, Linda","first_name":"Linda","last_name":"Ye"},{"full_name":"Sun, Yue","last_name":"Sun","first_name":"Yue"},{"id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","orcid":"0000-0003-2724-3523","full_name":"Sunko, Veronika","last_name":"Sunko","first_name":"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."},{"full_name":"Worasaran, Thanapat","last_name":"Worasaran","first_name":"Thanapat"},{"full_name":"Sorensen, Matthew E.","last_name":"Sorensen","first_name":"Matthew E."},{"last_name":"Bachmann","first_name":"Maja D.","full_name":"Bachmann, Maja D."},{"full_name":"Orenstein, Joseph","last_name":"Orenstein","first_name":"Joseph"},{"first_name":"Ian R.","last_name":"Fisher","full_name":"Fisher, Ian R."}],"external_id":{"pmid":["37607225"]},"abstract":[{"lang":"eng","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."}],"extern":"1","date_updated":"2025-06-10T13:13:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":120,"year":"2023","publication_status":"published","article_number":"e2302800120","intvolume":"       120","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"date_published":"2023-08-29T00:00:00Z","citation":{"mla":"Ye, Linda, et al. “Elastocaloric Signatures of Symmetric and Antisymmetric Strain-Tuning of Quadrupolar and Magnetic Phases in DyB2C2.” <i>Proceedings of the National Academy of Sciences</i>, vol. 120, no. 35, e2302800120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2302800120\">10.1073/pnas.2302800120</a>.","ama":"Ye L, Sun Y, Sunko V, et al. Elastocaloric signatures of symmetric and antisymmetric strain-tuning of quadrupolar and magnetic phases in DyB2C2. <i>Proceedings of the National Academy of Sciences</i>. 2023;120(35). doi:<a href=\"https://doi.org/10.1073/pnas.2302800120\">10.1073/pnas.2302800120</a>","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.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2302800120\">https://doi.org/10.1073/pnas.2302800120</a>.","ieee":"L. Ye <i>et al.</i>, “Elastocaloric signatures of symmetric and antisymmetric strain-tuning of quadrupolar and magnetic phases in DyB2C2,” <i>Proceedings of the National Academy of Sciences</i>, vol. 120, no. 35. National Academy of Sciences, 2023.","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).","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. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2302800120\">https://doi.org/10.1073/pnas.2302800120</a>","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."},"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"National Academy of Sciences","month":"08","pmid":1,"OA_type":"hybrid","title":"Elastocaloric signatures of symmetric and antisymmetric strain-tuning of quadrupolar and magnetic phases in DyB2C2","issue":"35","ddc":["530"],"scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"has_accepted_license":"1","status":"public","date_created":"2025-06-10T09:20:12Z","doi":"10.1073/pnas.2302800120","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2302800120"}],"day":"29","type":"journal_article"},{"date_published":"2023-10-25T00:00:00Z","citation":{"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,” <i>Proceedings of the National Academy of Sciences</i>, 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.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2301064120\">https://doi.org/10.1073/pnas.2301064120</a>.","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. <i>Proceedings of the National Academy of Sciences</i>. 2023;120(44). doi:<a href=\"https://doi.org/10.1073/pnas.2301064120\">10.1073/pnas.2301064120</a>","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.” <i>Proceedings of the National Academy of Sciences</i>, vol. 120, no. 44, e2301064120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2301064120\">10.1073/pnas.2301064120</a>.","apa":"Rosenberg, A. A., Yehishalom, N., Marx, A., &#38; Bronstein, A. M. (2023). An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2301064120\">https://doi.org/10.1073/pnas.2301064120</a>","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.","short":"A.A. Rosenberg, N. Yehishalom, A. Marx, A.M. Bronstein, Proceedings of the National Academy of Sciences 120 (2023)."},"article_number":"e2301064120","intvolume":"       120","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","pmid":1,"month":"10","publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1","issue":"44","title":"An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units","type":"journal_article","day":"25","status":"public","date_created":"2024-10-08T12:50:36Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2301064120"}],"doi":"10.1073/pnas.2301064120","article_type":"original","oa":1,"_id":"18216","oa_version":"Published Version","author":[{"first_name":"Aviv A.","last_name":"Rosenberg","full_name":"Rosenberg, Aviv A."},{"last_name":"Yehishalom","first_name":"Nitsan","full_name":"Yehishalom, Nitsan"},{"full_name":"Marx, Ailie","first_name":"Ailie","last_name":"Marx"},{"first_name":"Alexander","last_name":"Bronstein","orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6"}],"external_id":{"pmid":["37878722"]},"extern":"1","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"}],"date_updated":"2024-10-09T11:55:12Z","year":"2023","volume":120,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"TiVo"}],"external_id":{"pmid":["37988463"],"isi":["001157389000005"]},"author":[{"first_name":"Chaitanya","last_name":"Chintaluri","full_name":"Chintaluri, Chaitanya","id":"E4EDB536-3485-11EA-98D2-20AF3DDC885E"},{"first_name":"Tim P","last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"abstract":[{"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.","lang":"eng"}],"article_type":"original","oa":1,"_id":"14666","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."}],"oa_version":"Published Version","year":"2023","volume":120,"publication_status":"published","related_material":{"link":[{"relation":"software","url":"https://github.com/ccluri/metabolic_spiking"}]},"file":[{"access_level":"open_access","creator":"dernst","success":1,"date_created":"2023-12-11T12:45:12Z","checksum":"bf4ec38602a70dae4338077a5a4d497f","file_name":"2023_PNAS_Chintaluri.pdf","date_updated":"2023-12-11T12:45:12Z","file_size":16891602,"content_type":"application/pdf","file_id":"14678","relation":"main_file"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-12-11T12:45:12Z","date_updated":"2025-09-24T11:16:56Z","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"pmid":1,"month":"11","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","citation":{"chicago":"Chintaluri, Chaitanya, and Tim P Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2306525120\">https://doi.org/10.1073/pnas.2306525120</a>.","ieee":"C. Chintaluri and T. P. Vogels, “Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 48. National Academy of Sciences, 2023.","ama":"Chintaluri C, Vogels TP. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(48). doi:<a href=\"https://doi.org/10.1073/pnas.2306525120\">10.1073/pnas.2306525120</a>","mla":"Chintaluri, Chaitanya, and Tim P. Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 48, e2306525120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2306525120\">10.1073/pnas.2306525120</a>.","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.","apa":"Chintaluri, C., &#38; Vogels, T. P. (2023). Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2306525120\">https://doi.org/10.1073/pnas.2306525120</a>","short":"C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences of the United States of America 120 (2023)."},"date_published":"2023-11-21T00:00:00Z","intvolume":"       120","article_number":"e2306525120","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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).","day":"21","type":"journal_article","status":"public","has_accepted_license":"1","date_created":"2023-12-10T23:01:00Z","doi":"10.1073/pnas.2306525120","scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"corr_author":"1","ddc":["570"],"issue":"48","title":"Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species","OA_type":"hybrid"},{"date_created":"2023-07-30T22:01:02Z","doi":"10.1073/pnas.2302028120","has_accepted_license":"1","status":"public","day":"25","type":"journal_article","acknowledgement":"J.B. was funded by the European Union (ERC, CHORAL, project number 101039794). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. M.M. was supported by the 2019 Lopez-Loreta Prize. We would like to thank the reviewers for the insightful comments and, in particular, for suggesting the BAMP-inspired denoisers leading to AMP-AP.","issue":"30","title":"Fundamental limits in structured principal component analysis and how to reach them","publication_identifier":{"eissn":["1091-6490"]},"scopus_import":"1","ddc":["000"],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences of the United States of America","month":"07","pmid":1,"publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"e2302028120","intvolume":"       120","citation":{"short":"J. Barbier, F. Camilli, M. Mondelli, M. Sáenz, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ista":"Barbier J, Camilli F, Mondelli M, Sáenz M. 2023. Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. 120(30), e2302028120.","apa":"Barbier, J., Camilli, F., Mondelli, M., &#38; Sáenz, M. (2023). Fundamental limits in structured principal component analysis and how to reach them. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2302028120\">https://doi.org/10.1073/pnas.2302028120</a>","mla":"Barbier, Jean, et al. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 30, e2302028120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2302028120\">10.1073/pnas.2302028120</a>.","ama":"Barbier J, Camilli F, Mondelli M, Sáenz M. Fundamental limits in structured principal component analysis and how to reach them. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(30). doi:<a href=\"https://doi.org/10.1073/pnas.2302028120\">10.1073/pnas.2302028120</a>","chicago":"Barbier, Jean, Francesco Camilli, Marco Mondelli, and Manuel Sáenz. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2302028120\">https://doi.org/10.1073/pnas.2302028120</a>.","ieee":"J. Barbier, F. Camilli, M. Mondelli, and M. Sáenz, “Fundamental limits in structured principal component analysis and how to reach them,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 30. National Academy of Sciences, 2023."},"date_published":"2023-07-25T00:00:00Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"link":[{"relation":"software","url":"https://github.com/fcamilli95/Structured-PCA-"}]},"file":[{"checksum":"1fc06228afdb3aa80cf8e7766bcf9dc5","date_created":"2023-07-31T07:30:48Z","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"13323","content_type":"application/pdf","date_updated":"2023-07-31T07:30:48Z","file_size":995933,"file_name":"2023_PNAS_Barbier.pdf"}],"publication_status":"published","volume":120,"year":"2023","date_updated":"2025-09-09T12:41:50Z","file_date_updated":"2023-07-31T07:30:48Z","abstract":[{"text":"How do statistical dependencies in measurement noise influence high-dimensional inference? To answer this, we study the paradigmatic spiked matrix model of principal components analysis (PCA), where a rank-one matrix is corrupted by additive noise. We go beyond the usual independence assumption on the noise entries, by drawing the noise from a low-order polynomial orthogonal matrix ensemble. The resulting noise correlations make the setting relevant for applications but analytically challenging. We provide characterization of the Bayes optimal limits of inference in this model. If the spike is rotation invariant, we show that standard spectral PCA is optimal. However, for more general priors, both PCA and the existing approximate message-passing algorithm (AMP) fall short of achieving the information-theoretic limits, which we compute using the replica method from statistical physics. We thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer equations, which is empirically observed to saturate the conjectured theoretical limit. This AMP comes with a rigorous state evolution analysis tracking its performance. Although we focus on specific noise distributions, our methodology can be generalized to a wide class of trace matrix ensembles at the cost of more involved expressions. Finally, despite the seemingly strong assumption of rotation-invariant noise, our theory empirically predicts algorithmic performance on real data, pointing at strong universality properties.","lang":"eng"}],"external_id":{"pmid":["37463204"],"isi":["001121663500001"]},"author":[{"full_name":"Barbier, Jean","last_name":"Barbier","first_name":"Jean"},{"full_name":"Camilli, Francesco","first_name":"Francesco","last_name":"Camilli"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco"},{"last_name":"Sáenz","first_name":"Manuel","full_name":"Sáenz, Manuel"}],"department":[{"_id":"MaMo"}],"oa_version":"Published Version","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"_id":"13315","oa":1,"article_type":"original"}]