[{"_id":"14841","date_created":"2024-01-21T23:00:56Z","year":"2024","article_number":"e2307776121","citation":{"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. Proceedings of the National Academy of Sciences, 2024.","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.","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>","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>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2307776121\">https://doi.org/10.1073/pnas.2307776121</a>","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>. Proceedings of the 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).","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, Proceedings of the National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2307776121\">10.1073/pnas.2307776121</a>."},"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."}],"publication_status":"published","title":"A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction","oa_version":"None","article_processing_charge":"No","doi":"10.1073/pnas.2307776121","scopus_import":"1","article_type":"original","publication_identifier":{"eissn":["1091-6490"]},"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.","department":[{"_id":"TiVo"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","ec_funded":1,"date_updated":"2024-01-23T10:20:40Z","intvolume":"       121","related_material":{"link":[{"relation":"software","url":"https://github.com/ChrisCurrin/pv-kcnc2 "}]},"volume":121,"author":[{"last_name":"Clatot","first_name":"Jerome","full_name":"Clatot, Jerome"},{"full_name":"Currin, Christopher","orcid":"0000-0002-4809-5059","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","last_name":"Currin","first_name":"Christopher"},{"full_name":"Liang, Qiansheng","first_name":"Qiansheng","last_name":"Liang"},{"last_name":"Pipatpolkai","first_name":"Tanadet","full_name":"Pipatpolkai, Tanadet"},{"first_name":"Shavonne L.","last_name":"Massey","full_name":"Massey, Shavonne L."},{"full_name":"Helbig, Ingo","first_name":"Ingo","last_name":"Helbig"},{"last_name":"Delemotte","first_name":"Lucie","full_name":"Delemotte, Lucie"},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P"},{"full_name":"Covarrubias, Manuel","first_name":"Manuel","last_name":"Covarrubias"},{"first_name":"Ethan M.","last_name":"Goldberg","full_name":"Goldberg, Ethan M."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020","grant_number":"819603"}],"quality_controlled":"1","day":"16","month":"01","status":"public","language":[{"iso":"eng"}],"date_published":"2024-01-16T00:00:00Z","external_id":{"pmid":["38194456"]},"type":"journal_article","publisher":"Proceedings of the National Academy of Sciences","pmid":1},{"publisher":"Proceedings of the National Academy of Sciences","pmid":1,"date_published":"2024-02-13T00:00:00Z","external_id":{"pmid":["38335256"]},"type":"journal_article","language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"02","day":"13","quality_controlled":"1","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","grant_number":"802960"}],"issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-6160-9766","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","full_name":"Curk, Samo","first_name":"Samo","last_name":"Curk"},{"full_name":"Krausser, Johannes","last_name":"Krausser","first_name":"Johannes"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"full_name":"Frenkel, Daan","first_name":"Daan","last_name":"Frenkel"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"last_name":"Michaels","first_name":"Thomas C.T.","full_name":"Michaels, Thomas C.T."},{"full_name":"Knowles, Tuomas P.J.","first_name":"Tuomas P.J.","last_name":"Knowles"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"related_material":{"record":[{"id":"15027","relation":"research_data","status":"public"}]},"oa":1,"volume":121,"intvolume":"       121","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_updated":"2024-02-26T08:45:56Z","ec_funded":1,"department":[{"_id":"AnSa"}],"article_type":"original","publication_identifier":{"eissn":["1091-6490"]},"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","scopus_import":"1","file_date_updated":"2024-02-26T08:20:00Z","oa_version":"Published Version","article_processing_charge":"Yes","publication_status":"published","title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","abstract":[{"lang":"eng","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."}],"year":"2024","article_number":"e2220075121","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, Proceedings of the National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2220075121\">10.1073/pnas.2220075121</a>.","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>. Proceedings of the National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2220075121\">https://doi.org/10.1073/pnas.2220075121</a>.","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>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2220075121\">https://doi.org/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.","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. Proceedings of the National Academy of Sciences, 2024.","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>"},"_id":"15001","date_created":"2024-02-18T23:01:00Z","file":[{"date_created":"2024-02-26T08:20:00Z","file_size":7699487,"date_updated":"2024-02-26T08:20:00Z","relation":"main_file","success":1,"access_level":"open_access","file_name":"2024_PNAS_Curk.pdf","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b","content_type":"application/pdf","creator":"dernst","file_id":"15026"}]},{"day":"12","quality_controlled":"1","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","issue":"25","publisher":"National Academy of Sciences","pmid":1,"external_id":{"pmid":["37307446"],"isi":["001030689600003"]},"date_published":"2023-06-12T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"06","isi":1,"article_type":"original","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the  National  Natural  Science  Foundation  of  China  (32170265  and  32022007),  Hainan  Provincial  Natural  Science  Foundation  of  China  (323CXTD379),  Chinese  Universities  Scientific  Fund  (2023TC019),  Beijing  Municipal  Natural  Science  Foundation  (5192011),  Beijing  Outstanding  University  Discipline  Program,  and  China Postdoctoral Science Foundation (BH2020259460).","doi":"10.1073/pnas.2221313120","scopus_import":"1","file_date_updated":"2023-12-13T23:30:03Z","article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","abstract":[{"text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability.","lang":"eng"}],"article_number":"e2221313120","year":"2023","citation":{"chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <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.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>.","apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <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.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>","short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>.","ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(25). doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>","ieee":"Y. Wang <i>et al.</i>, “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25. National Academy of Sciences, 2023.","ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120."},"_id":"13201","file":[{"checksum":"d800e06252eaefba28531fa9440f23f0","file_id":"13204","creator":"alisjak","content_type":"application/pdf","date_created":"2023-07-10T08:48:40Z","file_size":5244581,"date_updated":"2023-12-13T23:30:03Z","relation":"main_file","embargo":"2023-12-12","access_level":"open_access","file_name":"2023_PNAS_Wang.pdf"}],"date_created":"2023-07-09T22:01:12Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Wang, Yalu","last_name":"Wang","first_name":"Yalu"},{"last_name":"Yuan","first_name":"Zhi","full_name":"Yuan, Zhi"},{"last_name":"Wang","first_name":"Jinyi","full_name":"Wang, Jinyi"},{"first_name":"Huixin","last_name":"Xiao","full_name":"Xiao, Huixin"},{"first_name":"Lu","last_name":"Wan","full_name":"Wan, Lu"},{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin"},{"full_name":"Guo, Yan","first_name":"Yan","last_name":"Guo"},{"full_name":"Gong, Zhizhong","last_name":"Gong","first_name":"Zhizhong"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"},{"full_name":"Zhang, Jing","last_name":"Zhang","first_name":"Jing"}],"oa":1,"volume":120,"intvolume":"       120","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_updated":"2023-12-13T23:30:04Z","department":[{"_id":"JiFr"}]},{"author":[{"last_name":"Barbier","first_name":"Jean","full_name":"Barbier, Jean"},{"full_name":"Camilli, Francesco","first_name":"Francesco","last_name":"Camilli"},{"last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"last_name":"Sáenz","first_name":"Manuel","full_name":"Sáenz, Manuel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"url":"https://github.com/fcamilli95/Structured-PCA-","relation":"software"}]},"oa":1,"volume":120,"intvolume":"       120","department":[{"_id":"MaMo"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_updated":"2024-09-10T13:03:18Z","doi":"10.1073/pnas.2302028120","scopus_import":"1","article_type":"original","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.","publication_identifier":{"eissn":["1091-6490"]},"publication_status":"published","title":"Fundamental limits in structured principal component analysis and how to reach them","file_date_updated":"2023-07-31T07:30:48Z","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","article_number":"e2302028120","year":"2023","citation":{"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>.","short":"J. Barbier, F. Camilli, M. Mondelli, M. Sáenz, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","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>.","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>","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.","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.","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>"},"abstract":[{"lang":"eng","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."}],"_id":"13315","file":[{"relation":"main_file","date_created":"2023-07-31T07:30:48Z","date_updated":"2023-07-31T07:30:48Z","file_size":995933,"success":1,"access_level":"open_access","file_name":"2023_PNAS_Barbier.pdf","checksum":"1fc06228afdb3aa80cf8e7766bcf9dc5","file_id":"13323","creator":"dernst","content_type":"application/pdf"}],"date_created":"2023-07-30T22:01:02Z","publisher":"National Academy of Sciences","pmid":1,"external_id":{"pmid":["37463204"]},"date_published":"2023-07-25T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"ddc":["000"],"month":"07","status":"public","day":"25","quality_controlled":"1","issue":"30","license":"https://creativecommons.org/licenses/by/4.0/","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1"},{"month":"07","status":"public","ddc":["530"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2023-07-31T00:00:00Z","external_id":{"pmid":["37523549"]},"pmid":1,"publisher":"National Academy of Sciences","issue":"32","project":[{"grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","quality_controlled":"1","day":"31","department":[{"_id":"MiLe"}],"ec_funded":1,"date_updated":"2023-10-17T11:45:25Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","intvolume":"       120","volume":120,"oa":1,"author":[{"first_name":"Ofek","last_name":"Vardi","full_name":"Vardi, Ofek"},{"last_name":"Maroudas-Sklare","first_name":"Naama","full_name":"Maroudas-Sklare, Naama"},{"full_name":"Kolodny, Yuval","last_name":"Kolodny","first_name":"Yuval"},{"first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"},{"last_name":"Saragovi","first_name":"Amijai","full_name":"Saragovi, Amijai"},{"first_name":"Nir","last_name":"Galili","full_name":"Galili, Nir"},{"last_name":"Ferrera","first_name":"Stav","full_name":"Ferrera, Stav"},{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg"},{"first_name":"Nir","last_name":"Yuran","full_name":"Yuran, Nir"},{"last_name":"Affek","first_name":"Hagit P.","full_name":"Affek, Hagit P."},{"full_name":"Luz, Boaz","first_name":"Boaz","last_name":"Luz"},{"full_name":"Goldsmith, Yonaton","first_name":"Yonaton","last_name":"Goldsmith"},{"first_name":"Nir","last_name":"Keren","full_name":"Keren, Nir"},{"full_name":"Yochelis, Shira","first_name":"Shira","last_name":"Yochelis"},{"last_name":"Halevy","first_name":"Itay","full_name":"Halevy, Itay"},{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"full_name":"Paltiel, Yossi","first_name":"Yossi","last_name":"Paltiel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-13T22:01:12Z","file":[{"content_type":"application/pdf","file_id":"14047","creator":"dernst","checksum":"a5ed64788a5acef9b9a300a26fa5a177","file_name":"2023_PNAS_Vardi.pdf","success":1,"access_level":"open_access","date_created":"2023-08-14T07:43:45Z","file_size":1003092,"date_updated":"2023-08-14T07:43:45Z","relation":"main_file"}],"_id":"14037","citation":{"ama":"Vardi O, Maroudas-Sklare N, Kolodny Y, et al. Nuclear spin effects in biological processes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(32). doi:<a href=\"https://doi.org/10.1073/pnas.2300828120\">10.1073/pnas.2300828120</a>","ista":"Vardi O, Maroudas-Sklare N, Kolodny Y, Volosniev A, Saragovi A, Galili N, Ferrera S, Ghazaryan A, Yuran N, Affek HP, Luz B, Goldsmith Y, Keren N, Yochelis S, Halevy I, Lemeshko M, Paltiel Y. 2023. Nuclear spin effects in biological processes. Proceedings of the National Academy of Sciences of the United States of America. 120(32), e2300828120.","ieee":"O. Vardi <i>et al.</i>, “Nuclear spin effects in biological processes,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 32. National Academy of Sciences, 2023.","mla":"Vardi, Ofek, et al. “Nuclear Spin Effects in Biological Processes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 32, e2300828120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2300828120\">10.1073/pnas.2300828120</a>.","short":"O. Vardi, N. Maroudas-Sklare, Y. Kolodny, A. Volosniev, A. Saragovi, N. Galili, S. Ferrera, A. Ghazaryan, N. Yuran, H.P. Affek, B. Luz, Y. Goldsmith, N. Keren, S. Yochelis, I. Halevy, M. Lemeshko, Y. Paltiel, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","chicago":"Vardi, Ofek, Naama Maroudas-Sklare, Yuval Kolodny, Artem Volosniev, Amijai Saragovi, Nir Galili, Stav Ferrera, et al. “Nuclear Spin Effects in Biological Processes.” <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.2300828120\">https://doi.org/10.1073/pnas.2300828120</a>.","apa":"Vardi, O., Maroudas-Sklare, N., Kolodny, Y., Volosniev, A., Saragovi, A., Galili, N., … Paltiel, Y. (2023). Nuclear spin effects in biological processes. <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.2300828120\">https://doi.org/10.1073/pnas.2300828120</a>"},"year":"2023","article_number":"e2300828120","abstract":[{"text":"Traditionally, nuclear spin is not considered to affect biological processes. Recently, this has changed as isotopic fractionation that deviates from classical mass dependence was reported both in vitro and in vivo. In these cases, the isotopic effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial dioxygen production system and biological aquaporin channels in cells. We observe that oxygen dynamics in chiral environments (in particular its transport) depend on nuclear spin, suggesting future applications for controlled isotope separation to be used, for instance, in NMR. To demonstrate the mechanism behind our findings, we formulate theoretical models based on a nuclear-spin-enhanced switch between electronic spin states. Accounting for the role of nuclear spin in biology can provide insights into the role of quantum effects in living systems and help inspire the development of future biotechnology solutions.","lang":"eng"}],"title":"Nuclear spin effects in biological processes","publication_status":"published","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2023-08-14T07:43:45Z","scopus_import":"1","doi":"10.1073/pnas.2300828120","publication_identifier":{"eissn":["1091-6490"]},"acknowledgement":"N.M.-S. acknowledges the support of the Ministry of Energy, Israel, as part of the scholarship program for graduate students in the fields of energy. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. acknowledges the support of the Ministry of Innovation, Science and Technology, Israel Grant No. 1001593872. Y.P acknowledges the support of the BSF-NSF 094 Grant No. 2022503.","article_type":"original"},{"type":"journal_article","date_published":"2023-11-21T00:00:00Z","external_id":{"pmid":["37988463"]},"pmid":1,"publisher":"National Academy of Sciences","month":"11","status":"public","ddc":["570"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"21","issue":"48","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"grant_number":"214316/Z/18/Z","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."}],"volume":120,"oa":1,"related_material":{"link":[{"url":"https://github.com/ccluri/metabolic_spiking","relation":"software"}]},"author":[{"id":"E4EDB536-3485-11EA-98D2-20AF3DDC885E","full_name":"Chintaluri, Chaitanya","first_name":"Chaitanya","last_name":"Chintaluri"},{"orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P","first_name":"Tim P","last_name":"Vogels"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"TiVo"}],"date_updated":"2023-12-11T12:47:41Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","intvolume":"       120","publication_status":"published","title":"Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species","oa_version":"None","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2023-12-11T12:45:12Z","scopus_import":"1","doi":"10.1073/pnas.2306525120","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).","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_type":"original","file":[{"creator":"dernst","file_id":"14678","content_type":"application/pdf","checksum":"bf4ec38602a70dae4338077a5a4d497f","file_name":"2023_PNAS_Chintaluri.pdf","success":1,"access_level":"open_access","date_updated":"2023-12-11T12:45:12Z","file_size":16891602,"relation":"main_file","date_created":"2023-12-11T12:45:12Z"}],"date_created":"2023-12-10T23:01:00Z","_id":"14666","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>.","short":"C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","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>","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>.","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.","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.","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>"},"year":"2023","article_number":"e2306525120","abstract":[{"lang":"eng","text":"So-called spontaneous activity is a central hallmark of most nervous systems. Such non-causal firing is contrary to the tenet of spikes as a means of communication, and its purpose remains unclear. We propose that self-initiated firing can serve as a release valve to protect neurons from the toxic conditions arising in mitochondria from lower-than-baseline energy consumption. To demonstrate the viability of our hypothesis, we built a set of models that incorporate recent experimental results indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP), adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing. We explore the relationship of metabolic cost of spiking with its effect on the temporal patterning of spikes and reproduce experimentally observed changes in intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with ROS-modulated potassium channels. We also show that metabolic spiking homeostasis can produce indefinitely sustained avalanche dynamics in cortical circuits. Our theory can account for key features of neuronal activity observed in many studies ranging from ion channel function all the way to resting state dynamics. We finish with a set of experimental predictions that would confirm an integrated, crucial role for metabolically regulated spiking and firmly link metabolic homeostasis and neuronal function."}]},{"type":"journal_article","date_published":"2022-09-06T00:00:00Z","publisher":"Proceedings of the National Academy of Sciences","status":"public","month":"09","extern":"1","keyword":["Multidisciplinary"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"06","issue":"37","volume":119,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Jouberton, Achille","first_name":"Achille","last_name":"Jouberton"},{"first_name":"Thomas E.","last_name":"Shaw","full_name":"Shaw, Thomas E."},{"full_name":"Miles, Evan","first_name":"Evan","last_name":"Miles"},{"first_name":"Michael","last_name":"McCarthy","full_name":"McCarthy, Michael"},{"last_name":"Fugger","first_name":"Stefan","full_name":"Fugger, Stefan"},{"last_name":"Ren","first_name":"Shaoting","full_name":"Ren, Shaoting"},{"last_name":"Dehecq","first_name":"Amaury","full_name":"Dehecq, Amaury"},{"first_name":"Wei","last_name":"Yang","full_name":"Yang, Wei"},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca"}],"date_updated":"2023-02-28T13:50:37Z","publication":"PNAS","intvolume":"       119","oa_version":"None","article_processing_charge":"No","title":"Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_type":"original","scopus_import":"1","doi":"10.1073/pnas.2109796119","date_created":"2023-02-20T08:10:02Z","_id":"12577","abstract":[{"text":"Glaciers are key components of the mountain water towers of Asia and are vital for downstream domestic, agricultural, and industrial uses. The glacier mass loss rate over the southeastern Tibetan Plateau is among the highest in Asia and has accelerated in recent decades. This acceleration has been attributed to increased warming, but the mechanisms behind these glaciers’ high sensitivity to warming remain unclear, while the influence of changes in precipitation over the past decades is poorly quantified. Here, we reconstruct glacier mass changes and catchment runoff since 1975 at a benchmark glacier, Parlung No. 4, to shed light on the drivers of recent mass losses for the monsoonal, spring-accumulation glaciers of the Tibetan Plateau. Our modeling demonstrates how a temperature increase (mean of 0.39<jats:sup>∘</jats:sup>C ⋅dec<jats:sup>−1</jats:sup>since 1990) has accelerated mass loss rates by altering both the ablation and accumulation regimes in a complex manner. The majority of the post-2000 mass loss occurred during the monsoon months, caused by simultaneous decreases in the solid precipitation ratio (from 0.70 to 0.56) and precipitation amount (–10%), leading to reduced monsoon accumulation (–26%). Higher solid precipitation in spring (+18%) during the last two decades was increasingly important in mitigating glacier mass loss by providing mass to the glacier and protecting it from melting in the early monsoon. With bare ice exposed to warmer temperatures for longer periods, icemelt and catchment discharge have unsustainably intensified since the start of the 21st century, raising concerns for long-term water supply and hazard occurrence in the region.","lang":"eng"}],"citation":{"mla":"Jouberton, Achille, et al. “Warming-Induced Monsoon Precipitation Phase Change Intensifies Glacier Mass Loss in the Southeastern Tibetan Plateau.” <i>PNAS</i>, vol. 119, no. 37, e2109796119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2109796119\">10.1073/pnas.2109796119</a>.","short":"A. Jouberton, T.E. Shaw, E. Miles, M. McCarthy, S. Fugger, S. Ren, A. Dehecq, W. Yang, F. Pellicciotti, PNAS 119 (2022).","chicago":"Jouberton, Achille, Thomas E. Shaw, Evan Miles, Michael McCarthy, Stefan Fugger, Shaoting Ren, Amaury Dehecq, Wei Yang, and Francesca Pellicciotti. “Warming-Induced Monsoon Precipitation Phase Change Intensifies Glacier Mass Loss in the Southeastern Tibetan Plateau.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2109796119\">https://doi.org/10.1073/pnas.2109796119</a>.","apa":"Jouberton, A., Shaw, T. E., Miles, E., McCarthy, M., Fugger, S., Ren, S., … Pellicciotti, F. (2022). Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2109796119\">https://doi.org/10.1073/pnas.2109796119</a>","ama":"Jouberton A, Shaw TE, Miles E, et al. Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau. <i>PNAS</i>. 2022;119(37). doi:<a href=\"https://doi.org/10.1073/pnas.2109796119\">10.1073/pnas.2109796119</a>","ieee":"A. Jouberton <i>et al.</i>, “Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau,” <i>PNAS</i>, vol. 119, no. 37. Proceedings of the National Academy of Sciences, 2022.","ista":"Jouberton A, Shaw TE, Miles E, McCarthy M, Fugger S, Ren S, Dehecq A, Yang W, Pellicciotti F. 2022. Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau. PNAS. 119(37), e2109796119."},"year":"2022","article_number":"e2109796119"},{"issue":"11","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"day":"07","quality_controlled":"1","language":[{"iso":"eng"}],"ddc":["580"],"month":"03","isi":1,"status":"public","publisher":"Proceedings of the National Academy of Sciences","pmid":1,"date_published":"2022-03-07T00:00:00Z","external_id":{"pmid":["35254915"],"isi":["000771756300008"]},"type":"journal_article","year":"2022","article_number":"e2118220119","citation":{"chicago":"Lu, Qing, Yonghong Zhang, Joakim Hellner, Caterina Giannini, Xiangyu Xu, Jarne Pauwels, Qian Ma, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>.","short":"Q. Lu, Y. Zhang, J. Hellner, C. Giannini, X. Xu, J. Pauwels, Q. Ma, W. Dejonghe, H. Han, B. Van De Cotte, F. Impens, K. Gevaert, I. De Smet, J. Friml, D.M. Molina, E. Russinova, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","apa":"Lu, Q., Zhang, Y., Hellner, J., Giannini, C., Xu, X., Pauwels, J., … Russinova, E. (2022). Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>","mla":"Lu, Qing, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11, e2118220119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>.","ista":"Lu Q, Zhang Y, Hellner J, Giannini C, Xu X, Pauwels J, Ma Q, Dejonghe W, Han H, Van De Cotte B, Impens F, Gevaert K, De Smet I, Friml J, Molina DM, Russinova E. 2022. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. 119(11), e2118220119.","ieee":"Q. Lu <i>et al.</i>, “Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11. Proceedings of the National Academy of Sciences, 2022.","ama":"Lu Q, Zhang Y, Hellner J, et al. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(11). doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>"},"abstract":[{"lang":"eng","text":"Despite the growing interest in using chemical genetics in plant research, small molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or posttranslational modifications, allows the discovery of drug targets or the study of protein–metabolite and protein–protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf, thus revealing cross-talk between brassinosteroid and auxin signaling."}],"_id":"10888","file":[{"success":1,"access_level":"open_access","file_name":"2022_PNAS_Lu.pdf","date_updated":"2022-03-21T09:19:47Z","relation":"main_file","file_size":2169534,"date_created":"2022-03-21T09:19:47Z","content_type":"application/pdf","creator":"dernst","file_id":"10910","checksum":"83e0fea7919570d0b519b41193342571"}],"date_created":"2022-03-20T23:01:39Z","doi":"10.1073/pnas.2118220119","scopus_import":"1","article_type":"original","publication_identifier":{"eissn":["1091-6490"]},"acknowledgement":"We thank Yanhai Yin for providing the anti-BES1 antibody, Johan Winne and Brenda Callebaut for synthesizing bikinin, Yuki Kondo and Hiroo Fukuda for published materials, Tomasz Nodzy\u0003nski for useful advice, and Martine De Cock for help in preparing the manuscript. This\r\nwork was supported by the China Scholarship Council for predoctoral (Q.L. and X.X.) and postdoctoral (Y.Z.) fellowships; the Agency for Innovation by Science and Technology for a predoctoral fellowship (W.D.); the Research Foundation-Flanders, Projects G009018N and G002121N (E.R.); and the VIB TechWatch Fund (E.R.).","publication_status":"published","title":"Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling","file_date_updated":"2022-03-21T09:19:47Z","oa_version":"Published Version","article_processing_charge":"No","intvolume":"       119","department":[{"_id":"JiFr"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_updated":"2023-08-03T06:06:27Z","author":[{"first_name":"Qing","last_name":"Lu","full_name":"Lu, Qing"},{"full_name":"Zhang, Yonghong","last_name":"Zhang","first_name":"Yonghong"},{"full_name":"Hellner, Joakim","last_name":"Hellner","first_name":"Joakim"},{"last_name":"Giannini","first_name":"Caterina","full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"full_name":"Xu, Xiangyu","last_name":"Xu","first_name":"Xiangyu"},{"last_name":"Pauwels","first_name":"Jarne","full_name":"Pauwels, Jarne"},{"first_name":"Qian","last_name":"Ma","full_name":"Ma, Qian"},{"full_name":"Dejonghe, Wim","last_name":"Dejonghe","first_name":"Wim"},{"last_name":"Han","first_name":"Huibin","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte","first_name":"Brigitte"},{"last_name":"Impens","first_name":"Francis","full_name":"Impens, Francis"},{"last_name":"Gevaert","first_name":"Kris","full_name":"Gevaert, Kris"},{"full_name":"De Smet, Ive","last_name":"De Smet","first_name":"Ive"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"},{"first_name":"Daniel Martinez","last_name":"Molina","full_name":"Molina, Daniel Martinez"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":119},{"month":"07","status":"public","language":[{"iso":"eng"}],"ddc":["570"],"external_id":{"pmid":["35858408"]},"date_published":"2022-07-18T00:00:00Z","type":"journal_article","publisher":"Proceedings of the National Academy of Sciences","pmid":1,"issue":"30","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","quality_controlled":"1","day":"18","department":[{"_id":"NiBa"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_updated":"2022-08-01T11:00:25Z","intvolume":"       119","oa":1,"volume":119,"author":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11702","file":[{"date_updated":"2022-08-01T10:58:28Z","date_created":"2022-08-01T10:58:28Z","relation":"main_file","file_size":848511,"file_name":"2022_PNAS_Barton.pdf","access_level":"open_access","success":1,"checksum":"06c866196a8957f0c37b8a121771c885","file_id":"11716","creator":"dernst","content_type":"application/pdf"}],"date_created":"2022-07-31T22:01:47Z","article_number":"e2122147119","year":"2022","citation":{"ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119.","ieee":"N. H. Barton, “The ‘New Synthesis,’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30. Proceedings of the National Academy of Sciences, 2022.","ama":"Barton NH. The “New Synthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(30). doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>","chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>.","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","apa":"Barton, N. H. (2022). The “New Synthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>","mla":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30, e2122147119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>."},"abstract":[{"lang":"eng","text":"When Mendel’s work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin’s theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher, Haldane, and Wright established a century ago, Mendelian inheritance is exactly what is needed for natural selection to work efficiently. Yet, the synthesis remains unfinished. We do not understand why sexual reproduction and a fair meiosis predominate in eukaryotes, or how far these are responsible for their diversity and complexity. Moreover, although quantitative geneticists have long known that adaptive variation is highly polygenic, and that this is essential for efficient selection, this is only now becoming appreciated by molecular biologists—and we still do not have a good framework for understanding polygenic variation or diffuse function."}],"title":"The \"New Synthesis\"","publication_status":"published","file_date_updated":"2022-08-01T10:58:28Z","oa_version":"Published Version","article_processing_charge":"No","doi":"10.1073/pnas.2122147119","scopus_import":"1","article_type":"original","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments."},{"issue":"31","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"day":"25","quality_controlled":"1","ddc":["580"],"language":[{"iso":"eng"}],"keyword":["Multidisciplinary"],"isi":1,"month":"07","status":"public","pmid":1,"publisher":"Proceedings of the National Academy of Sciences","type":"journal_article","date_published":"2022-07-25T00:00:00Z","external_id":{"isi":["000881496900002"],"pmid":["35878023"]},"citation":{"mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 31, e2121058119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., &#38; Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>","chicago":"Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>.","short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences 119 (2022).","ieee":"L. Li <i>et al.</i>, “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. 119(31), e2121058119.","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>"},"year":"2022","article_number":"e2121058119","abstract":[{"lang":"eng","text":"Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term."}],"date_created":"2022-08-04T20:06:49Z","file":[{"checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","file_id":"11747","creator":"dernst","content_type":"application/pdf","relation":"main_file","date_updated":"2022-08-08T07:42:09Z","date_created":"2022-08-08T07:42:09Z","file_size":2506262,"access_level":"open_access","success":1,"file_name":"2022_PNAS_Li.pdf"}],"_id":"11723","scopus_import":"1","doi":"10.1073/pnas.2121058119","acknowledgement":"We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for kindly sharing seeds; Matyáš Fendrych for initiating this project and providing constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and Arseny Savin for contributing to genotyping. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_type":"original","title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2022-08-08T07:42:09Z","intvolume":"       119","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"date_updated":"2024-10-29T10:12:30Z","publication":"Proceedings of the National Academy of Sciences","author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","first_name":"Lanxin","last_name":"Li"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","first_name":"Huihuang","last_name":"Chen"},{"full_name":"Alotaibi, Saqer S.","last_name":"Alotaibi","first_name":"Saqer S."},{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":119,"oa":1},{"acknowledgement":"This project was funded by Swiss National Science Foundation Eccellenza Grant PCEGP3-181181(toM.R.R.) and by core funding from the Institute of Science and Technology Austria. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). K.L. and R.M. were supported by the Estonian Research Council Grant PRG687. Estonian Biobank computations were performed in the High-Performance Computing Centre, University of Tartu.","publication_identifier":{"eissn":["1091-6490"]},"article_type":"original","scopus_import":"1","doi":"10.1073/pnas.2121279119","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2022-08-08T07:31:19Z","title":"Improving GWAS discovery and genomic prediction accuracy in biobank data","publication_status":"published","abstract":[{"text":"Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h2SNP. We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies.","lang":"eng"}],"citation":{"ama":"Orliac EJ, Trejo Banos D, Ojavee SE, et al. Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>","ieee":"E. J. Orliac <i>et al.</i>, “Improving GWAS discovery and genomic prediction accuracy in biobank data,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","ista":"Orliac EJ, Trejo Banos D, Ojavee SE, Läll K, Mägi R, Visscher PM, Robinson MR. 2022. Improving GWAS discovery and genomic prediction accuracy in biobank data. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121279119.","chicago":"Orliac, Etienne J., Daniel Trejo Banos, Sven E. Ojavee, Kristi Läll, Reedik Mägi, Peter M. Visscher, and Matthew Richard Robinson. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>.","short":"E.J. Orliac, D. Trejo Banos, S.E. Ojavee, K. Läll, R. Mägi, P.M. Visscher, M.R. Robinson, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","apa":"Orliac, E. J., Trejo Banos, D., Ojavee, S. E., Läll, K., Mägi, R., Visscher, P. M., &#38; Robinson, M. R. (2022). Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>","mla":"Orliac, Etienne J., et al. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2121279119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>."},"article_number":"e2121279119","year":"2022","file":[{"content_type":"application/pdf","file_id":"11745","creator":"dernst","checksum":"b5d2024e19fbad6f85a5e384e44d0f3b","success":1,"access_level":"open_access","file_name":"2022_PNAS_Orliac.pdf","date_updated":"2022-08-08T07:31:19Z","date_created":"2022-08-08T07:31:19Z","file_size":1001164,"relation":"main_file"}],"date_created":"2022-08-07T22:01:56Z","_id":"11733","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Orliac, Etienne J.","first_name":"Etienne J.","last_name":"Orliac"},{"first_name":"Daniel","last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel"},{"full_name":"Ojavee, Sven E.","last_name":"Ojavee","first_name":"Sven E."},{"full_name":"Läll, Kristi","last_name":"Läll","first_name":"Kristi"},{"first_name":"Reedik","last_name":"Mägi","full_name":"Mägi, Reedik"},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"}],"volume":119,"oa":1,"related_material":{"record":[{"id":"13064","relation":"research_data","status":"public"}]},"intvolume":"       119","date_updated":"2023-08-03T12:40:38Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","department":[{"_id":"MaRo"}],"day":"29","quality_controlled":"1","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","issue":"31","publisher":"Proceedings of the National Academy of Sciences","type":"journal_article","external_id":{"isi":["000881496900003"]},"date_published":"2022-07-29T00:00:00Z","ddc":["570"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"07"},{"author":[{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","first_name":"Rashed","last_name":"Abualia"},{"last_name":"Ötvös","first_name":"Krisztina","full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Bouguyon, Eleonore","last_name":"Bouguyon","first_name":"Eleonore"},{"last_name":"Domanegg","first_name":"Kevin","full_name":"Domanegg, Kevin","orcid":"0000-0002-1215-4264","id":"a24c7829-16e8-11ed-8527-c4d36ffb7539"},{"full_name":"Krapp, Anne","first_name":"Anne","last_name":"Krapp"},{"full_name":"Nacry, Philip","last_name":"Nacry","first_name":"Philip"},{"last_name":"Gojon","first_name":"Alain","full_name":"Gojon, Alain"},{"last_name":"Lacombe","first_name":"Benoit","full_name":"Lacombe, Benoit"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"volume":119,"oa":1,"intvolume":"       119","department":[{"_id":"EvBe"}],"date_updated":"2023-08-03T12:39:29Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","scopus_import":"1","doi":"10.1073/pnas.2122460119","publication_identifier":{"eissn":["1091-6490"]},"acknowledgement":"We acknowledge Hana Semeradova, Juan Carlos Montesinos, Nicola Cavallari, Marc¸al Gallem\u0003ı, Kaori Tabata, Andrej Hurn\u0003y, and Sascha Waidmann for sharing materials; and Marina Borges Osorio for critical reading of the manuscript. Work in the E. Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to K.O., R.A., and E. Benkova. We acknowledge the Bioimaging Facility and Life Science Facilities of the Institute of Science\r\nand Technology Austria. We give sincere thanks to Hana Martınkova and Petra Amakorova for their help with cytokinin analyses. This work was funded by the Czech Science Foundation (Project No. 19-00973S).","article_type":"original","title":"Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses","publication_status":"published","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2022-08-08T07:09:58Z","citation":{"mla":"Abualia, Rashed, et al. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2122460119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>.","apa":"Abualia, R., Ötvös, K., Novák, O., Bouguyon, E., Domanegg, K., Krapp, A., … Benková, E. (2022). Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>","chicago":"Abualia, Rashed, Krisztina Ötvös, Ondřej Novák, Eleonore Bouguyon, Kevin Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, and Eva Benková. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>.","short":"R. Abualia, K. Ötvös, O. Novák, E. Bouguyon, K. Domanegg, A. Krapp, P. Nacry, A. Gojon, B. Lacombe, E. Benková, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ieee":"R. Abualia <i>et al.</i>, “Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","ista":"Abualia R, Ötvös K, Novák O, Bouguyon E, Domanegg K, Krapp A, Nacry P, Gojon A, Lacombe B, Benková E. 2022. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2122460119.","ama":"Abualia R, Ötvös K, Novák O, et al. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>"},"year":"2022","article_number":"e2122460119","abstract":[{"text":"Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.","lang":"eng"}],"date_created":"2022-08-07T22:01:57Z","file":[{"content_type":"application/pdf","file_id":"11744","creator":"dernst","checksum":"6e97dedc281247fc3fe238a209f14af0","file_name":"2022_PNAS_Abualia.pdf","success":1,"access_level":"open_access","date_updated":"2022-08-08T07:09:58Z","relation":"main_file","date_created":"2022-08-08T07:09:58Z","file_size":3092330}],"_id":"11734","pmid":1,"publisher":"Proceedings of the National Academy of Sciences","type":"journal_article","external_id":{"pmid":["35878040"],"isi":["000881496900007"]},"date_published":"2022-07-25T00:00:00Z","ddc":["570"],"language":[{"iso":"eng"}],"isi":1,"month":"07","status":"public","day":"25","quality_controlled":"1","issue":"31","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"project":[{"call_identifier":"FWF","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development"}],"has_accepted_license":"1"},{"quality_controlled":"1","day":"28","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960"}],"has_accepted_license":"1","issue":"31","type":"journal_article","external_id":{"isi":["000903753500002"]},"date_published":"2022-07-28T00:00:00Z","publisher":"Proceedings of the National Academy of Sciences","status":"public","isi":1,"month":"07","ddc":["570"],"language":[{"iso":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2023-10-04T09:05:44Z","title":"Adsorption free energy predicts amyloid protein nucleation rates","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt\r\n(agreement 337969). We are grateful for financial support from the Biotechnology and Biological Sciences Research Council (BBSRC) (T.P.J.K.), the Newman\r\nFoundation (T.P.J.K.), the Wellcome Trust (T.P.J.K. and M.V.), Peterhouse College\r\nCambridge (T.C.T.M.), the ERC Starting Grant (StG) Non-Equilibrium Protein Assembly (NEPA) (A.S.), the Royal Society (A.S.), the Academy of Medical Sciences\r\n(A.S. and J.K.), and the Cambridge Centre for Misfolding Diseases (CMD).","article_type":"original","scopus_import":"1","doi":"10.1073/pnas.2109718119","date_created":"2022-08-14T22:01:45Z","file":[{"creator":"dernst","file_id":"14386","content_type":"application/pdf","checksum":"0fe3878896cbeb6c44e29222ec2f336a","file_name":"2022_PNAS_Toprakcioglu.pdf","success":1,"access_level":"open_access","relation":"main_file","date_created":"2023-10-04T09:05:44Z","file_size":2476021,"date_updated":"2023-10-04T09:05:44Z"}],"_id":"11841","abstract":[{"lang":"eng","text":"Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process."}],"citation":{"ieee":"Z. Toprakcioglu <i>et al.</i>, “Adsorption free energy predicts amyloid protein nucleation rates,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","ista":"Toprakcioglu Z, Kamada A, Michaels TCT, Xie M, Krausser J, Wei J, Šarić A, Vendruscolo M, Knowles TPJ. 2022. Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2109718119.","ama":"Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>","mla":"Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2109718119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>.","short":"Z. Toprakcioglu, A. Kamada, T.C.T. Michaels, M. Xie, J. Krausser, J. Wei, A. Šarić, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","chicago":"Toprakcioglu, Zenon, Ayaka Kamada, Thomas C.T. Michaels, Mengqi Xie, Johannes Krausser, Jiapeng Wei, Anđela Šarić, Michele Vendruscolo, and Tuomas P.J. Knowles. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>.","apa":"Toprakcioglu, Z., Kamada, A., Michaels, T. C. T., Xie, M., Krausser, J., Wei, J., … Knowles, T. P. J. (2022). Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>"},"article_number":"e2109718119","year":"2022","volume":119,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Toprakcioglu","first_name":"Zenon","full_name":"Toprakcioglu, Zenon"},{"full_name":"Kamada, Ayaka","first_name":"Ayaka","last_name":"Kamada"},{"first_name":"Thomas C.T.","last_name":"Michaels","full_name":"Michaels, Thomas C.T."},{"first_name":"Mengqi","last_name":"Xie","full_name":"Xie, Mengqi"},{"last_name":"Krausser","first_name":"Johannes","full_name":"Krausser, Johannes"},{"full_name":"Wei, Jiapeng","first_name":"Jiapeng","last_name":"Wei"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Vendruscolo, Michele","first_name":"Michele","last_name":"Vendruscolo"},{"last_name":"Knowles","first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J."}],"ec_funded":1,"date_updated":"2023-10-04T09:06:52Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","department":[{"_id":"AnSa"}],"intvolume":"       119"},{"abstract":[{"text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.","lang":"eng"}],"year":"2022","article_number":"e2123152119","citation":{"ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022.","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. <i>Proceedings of the National Academy of Sciences</i>. 2022;119(36). doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>","apa":"Hledik, M., Barton, N. H., &#38; Tkačik, G. (2022). Accumulation and maintenance of information in evolution. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>.","mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>."},"_id":"12081","file":[{"checksum":"6dec51f6567da9039982a571508a8e4d","content_type":"application/pdf","file_id":"12091","creator":"dernst","file_size":2165752,"date_updated":"2022-09-12T08:08:12Z","date_created":"2022-09-12T08:08:12Z","relation":"main_file","file_name":"2022_PNAS_Hledik.pdf","success":1,"access_level":"open_access"}],"date_created":"2022-09-11T22:01:55Z","article_type":"original","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","doi":"10.1073/pnas.2123152119","scopus_import":"1","file_date_updated":"2022-09-12T08:08:12Z","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","title":"Accumulation and maintenance of information in evolution","intvolume":"       119","publication":"Proceedings of the National Academy of Sciences","date_updated":"2025-06-30T13:21:05Z","ec_funded":1,"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"1"}],"related_material":{"record":[{"id":"15020","relation":"dissertation_contains","status":"public"}]},"oa":1,"volume":119,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"has_accepted_license":"1","issue":"36","day":"29","quality_controlled":"1","language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"08","isi":1,"publisher":"Proceedings of the National Academy of Sciences","pmid":1,"date_published":"2022-08-29T00:00:00Z","external_id":{"isi":["000889278400014"],"pmid":["36037343"]},"type":"journal_article"},{"intvolume":"       118","date_updated":"2023-02-23T10:45:44Z","publication":"PNAS","author":[{"last_name":"Li","first_name":"Ling","full_name":"Li, Ling"},{"full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","last_name":"Goodrich","first_name":"Carl Peter"},{"last_name":"Yang","first_name":"Haizhao","full_name":"Yang, Haizhao"},{"full_name":"Phillips, Katherine R.","first_name":"Katherine R.","last_name":"Phillips"},{"full_name":"Jia, Zian","first_name":"Zian","last_name":"Jia"},{"full_name":"Chen, Hongshun","first_name":"Hongshun","last_name":"Chen"},{"first_name":"Lifeng","last_name":"Wang","full_name":"Wang, Lifeng"},{"full_name":"Zhong, Jinjin","first_name":"Jinjin","last_name":"Zhong"},{"full_name":"Liu, Anhua","first_name":"Anhua","last_name":"Liu"},{"full_name":"Lu, Jianfeng","last_name":"Lu","first_name":"Jianfeng"},{"last_name":"Shuai","first_name":"Jianwei","full_name":"Shuai, Jianwei"},{"last_name":"Brenner","first_name":"Michael P.","full_name":"Brenner, Michael P."},{"full_name":"Spaepen, Frans","first_name":"Frans","last_name":"Spaepen"},{"last_name":"Aizenberg","first_name":"Joanna","full_name":"Aizenberg, Joanna"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":118,"oa":1,"citation":{"ista":"Li L, Goodrich CP, Yang H, Phillips KR, Jia Z, Chen H, Wang L, Zhong J, Liu A, Lu J, Shuai J, Brenner MP, Spaepen F, Aizenberg J. 2021. Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. PNAS. 118(32), e2107588118.","ieee":"L. Li <i>et al.</i>, “Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals,” <i>PNAS</i>, vol. 118, no. 32. Proceedings of the National Academy of Sciences, 2021.","ama":"Li L, Goodrich CP, Yang H, et al. Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. <i>PNAS</i>. 2021;118(32). doi:<a href=\"https://doi.org/10.1073/pnas.2107588118\">10.1073/pnas.2107588118</a>","apa":"Li, L., Goodrich, C. P., Yang, H., Phillips, K. R., Jia, Z., Chen, H., … Aizenberg, J. (2021). Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2107588118\">https://doi.org/10.1073/pnas.2107588118</a>","short":"L. Li, C.P. Goodrich, H. Yang, K.R. Phillips, Z. Jia, H. Chen, L. Wang, J. Zhong, A. Liu, J. Lu, J. Shuai, M.P. Brenner, F. Spaepen, J. Aizenberg, PNAS 118 (2021).","chicago":"Li, Ling, Carl Peter Goodrich, Haizhao Yang, Katherine R. Phillips, Zian Jia, Hongshun Chen, Lifeng Wang, et al. “Microscopic Origins of the Crystallographically Preferred Growth in Evaporation-Induced Colloidal Crystals.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2107588118\">https://doi.org/10.1073/pnas.2107588118</a>.","mla":"Li, Ling, et al. “Microscopic Origins of the Crystallographically Preferred Growth in Evaporation-Induced Colloidal Crystals.” <i>PNAS</i>, vol. 118, no. 32, e2107588118, Proceedings of the National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2107588118\">10.1073/pnas.2107588118</a>."},"year":"2021","article_number":"e2107588118","abstract":[{"text":"Unlike crystalline atomic and ionic solids, texture development due to crystallographically preferred growth in colloidal crystals is less studied. Here we investigate the underlying mechanisms of the texture evolution in an evaporation-induced colloidal assembly process through experiments, modeling, and theoretical analysis. In this widely used approach to obtain large-area colloidal crystals, the colloidal particles are driven to the meniscus via the evaporation of a solvent or matrix precursor solution where they close-pack to form a face-centered cubic colloidal assembly. Via two-dimensional large-area crystallographic mapping, we show that the initial crystal orientation is dominated by the interaction of particles with the meniscus, resulting in the expected coalignment of the close-packed direction with the local meniscus geometry. By combining with crystal structure analysis at a single-particle level, we further reveal that, at the later stage of self-assembly, however, the colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary dislocations (GNDs) and achieves a large-area uniform crystallographic orientation with the close-packed direction perpendicular to the meniscus and parallel to the growth direction. Classical slip analysis, finite element-based mechanical simulation, computational colloidal assembly modeling, and continuum theory unequivocally show that these GNDs result from the tensile stress field along the meniscus direction due to the constrained shrinkage of the colloidal crystal during drying. The generation of GNDs with specific slip systems within individual grains leads to crystallographic rotation to accommodate the mechanical stress. The mechanistic understanding reported here can be utilized to control crystallographic features of colloidal assemblies, and may provide further insights into crystallographically preferred growth in synthetic, biological, and geological crystals.","lang":"eng"}],"file":[{"checksum":"702f7ec60ce6f2815104ab649dc661a4","content_type":"application/pdf","creator":"dernst","file_id":"12674","date_updated":"2023-02-23T10:42:07Z","relation":"main_file","date_created":"2023-02-23T10:42:07Z","file_size":3275944,"file_name":"2021_PNAS_Li.pdf","access_level":"open_access","success":1}],"date_created":"2023-02-21T08:51:04Z","_id":"12667","scopus_import":"1","doi":"10.1073/pnas.2107588118","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_type":"original","title":"Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals","publication_status":"published","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2023-02-23T10:42:07Z","ddc":["570"],"language":[{"iso":"eng"}],"extern":"1","month":"08","status":"public","pmid":1,"publisher":"Proceedings of the National Academy of Sciences","type":"journal_article","date_published":"2021-08-10T00:00:00Z","external_id":{"pmid":["34341109"]},"issue":"32","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","day":"10","quality_controlled":"1"},{"intvolume":"       118","publication":"Proceedings of the National Academy of Sciences","date_updated":"2023-08-07T14:19:34Z","department":[{"_id":"CaGo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Goodrich","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"full_name":"King, Ella M.","last_name":"King","first_name":"Ella M."},{"first_name":"Samuel S.","last_name":"Schoenholz","full_name":"Schoenholz, Samuel S."},{"full_name":"Cubuk, Ekin D.","last_name":"Cubuk","first_name":"Ekin D."},{"full_name":"Brenner, Michael P.","first_name":"Michael P.","last_name":"Brenner"}],"oa":1,"volume":118,"abstract":[{"lang":"eng","text":"The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent kinetics, but this has received considerably less attention. Using recent advances in automatic differentiation, we show how kinetic pathways can be precisely designed by directly differentiating through statistical physics models, namely free energy calculations and molecular dynamics simulations. We consider two systems that are crucial to our understanding of structural self-assembly: bulk crystallization and small nanoclusters. In each case, we are able to assemble precise dynamical features. Using gradient information, we manipulate interactions among constituent particles to tune the rate at which these systems yield specific structures of interest. Moreover, we use this approach to learn nontrivial features about the high-dimensional design space, allowing us to accurately predict when multiple kinetic features can be simultaneously and independently controlled. These results provide a concrete and generalizable foundation for studying nonstructural self-assembly, including kinetic properties as well as other complex emergent properties, in a vast array of systems."}],"year":"2021","article_number":"e2024083118","citation":{"ista":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences. 118(10), e2024083118.","ieee":"C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner, “Designing self-assembling kinetics with differentiable statistical physics models,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 10. National Academy of Sciences, 2021.","ama":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling kinetics with differentiable statistical physics models. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(10). doi:<a href=\"https://doi.org/10.1073/pnas.2024083118\">10.1073/pnas.2024083118</a>","apa":"Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., &#38; Brenner, M. P. (2021). Designing self-assembling kinetics with differentiable statistical physics models. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/10.1073/pnas.2024083118</a>","short":"C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings of the National Academy of Sciences 118 (2021).","chicago":"Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk, and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/10.1073/pnas.2024083118</a>.","mla":"Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2024083118\">10.1073/pnas.2024083118</a>."},"_id":"9257","date_created":"2021-03-21T23:01:20Z","file":[{"content_type":"application/pdf","file_id":"9278","creator":"dernst","checksum":"5be8da2b1c0757feb1057f1a515cf9e0","file_name":"2021_PNAS_Goodrich.pdf","access_level":"open_access","success":1,"file_size":1047954,"date_updated":"2021-03-22T12:23:54Z","relation":"main_file","date_created":"2021-03-22T12:23:54Z"}],"article_type":"original","acknowledgement":"We thank Agnese Curatolo, Megan Engel, Ofer Kimchi, Seong Ho Pahng, and Roy Frostig for helpful discussions. This material is based on work supported by NSF Graduate Research Fellowship Grant DGE1745303. This research was funded by NSF Grant DMS-1715477, Materials Research Science and Engineering Centers Grant DMR-1420570, and Office of Naval Research Grant N00014-17-1-3029. M.P.B. is an investigator of the Simons Foundation.","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"doi":"10.1073/pnas.2024083118","scopus_import":"1","file_date_updated":"2021-03-22T12:23:54Z","article_processing_charge":"No","oa_version":"Published Version","title":"Designing self-assembling kinetics with differentiable statistical physics models","publication_status":"published","language":[{"iso":"eng"}],"ddc":["530"],"status":"public","month":"03","isi":1,"publisher":"National Academy of Sciences","pmid":1,"date_published":"2021-03-09T00:00:00Z","external_id":{"isi":["000627429100097"],"pmid":["33653960"]},"type":"journal_article","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"issue":"10","day":"09","quality_controlled":"1"},{"date_created":"2021-03-31T07:00:01Z","_id":"9301","abstract":[{"text":"Electrodepositing insulating lithium peroxide (Li2O2) is the key process during discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved lithium superoxide governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, better understanding governing factors for Li2O2 packing density and capacity requires structural sensitive in situ metrologies. Here, we establish in situ small- and wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2 phase evolution with atomic to submicrometer resolution during cycling a custom-built in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multiphase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets potentially forming large toroidal particles. Li2O2 solution growth is further justified by rotating ring-disk electrode measurements and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. Hence, mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism ought to be reconsidered.","lang":"eng"}],"citation":{"ama":"Prehal C, Samojlov A, Nachtnebel M, et al. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(14). doi:<a href=\"https://doi.org/10.1073/pnas.2021893118\">10.1073/pnas.2021893118</a>","ista":"Prehal C, Samojlov A, Nachtnebel M, Lovicar L, Kriechbaum M, Amenitsch H, Freunberger SA. 2021. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 118(14), e2021893118.","ieee":"C. Prehal <i>et al.</i>, “In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 14. National Academy of Sciences, 2021.","mla":"Prehal, Christian, et al. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 14, e2021893118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2021893118\">10.1073/pnas.2021893118</a>.","short":"C. Prehal, A. Samojlov, M. Nachtnebel, L. Lovicar, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, Proceedings of the National Academy of Sciences 118 (2021).","chicago":"Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Ludek Lovicar, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2021893118\">https://doi.org/10.1073/pnas.2021893118</a>.","apa":"Prehal, C., Samojlov, A., Nachtnebel, M., Lovicar, L., Kriechbaum, M., Amenitsch, H., &#38; Freunberger, S. A. (2021). In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2021893118\">https://doi.org/10.1073/pnas.2021893118</a>"},"year":"2021","article_number":"e2021893118","article_processing_charge":"No","oa_version":"Preprint","title":"In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"acknowledgement":"S.A.F. and C.P. are indebted to the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 636069), the Austrian Federal Ministry of Science, Research and Economy, and the Austrian Research Promotion Agency (Grant No. 845364). We acknowledge A. Zankel and H. Schroettner for support with SEM measurements. C.P. thanks N. Kostoglou, C. Koczwara, M. Hartmann, and M. Burian for discussions on gas sorption analysis, C++ programming, Monte Carlo modeling, and in situ SAXS experiments, respectively. We thank S. Stadlbauer for help with Karl Fischer titration, R. Riccò for gas sorption measurements, and acknowledge Graz University of Technology for support through the Lead Project LP-03. Likewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. S.A.F. is indebted to Institute of Science and Technology Austria (IST Austria) for support. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility.","article_type":"original","doi":"10.1073/pnas.2021893118","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv.11447775"}],"date_updated":"2023-09-05T13:27:18Z","publication":"Proceedings of the National Academy of Sciences","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"intvolume":"       118","volume":118,"oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"last_name":"Samojlov","first_name":"Aleksej","full_name":"Samojlov, Aleksej"},{"last_name":"Nachtnebel","first_name":"Manfred","full_name":"Nachtnebel, Manfred"},{"orcid":"0000-0001-6206-4200","id":"36DB3A20-F248-11E8-B48F-1D18A9856A87","full_name":"Lovicar, Ludek","first_name":"Ludek","last_name":"Lovicar"},{"full_name":"Kriechbaum, Manfred","first_name":"Manfred","last_name":"Kriechbaum"},{"full_name":"Amenitsch, Heinz","first_name":"Heinz","last_name":"Amenitsch"},{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander"}],"issue":"14","quality_controlled":"1","day":"06","status":"public","isi":1,"month":"04","keyword":["small-angle X-ray scattering","oxygen reduction","disproportionation","Li-air battery"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2021-04-06T00:00:00Z","external_id":{"isi":["000637398300050"]},"publisher":"National Academy of Sciences"},{"abstract":[{"lang":"eng","text":"In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium channels have been linked to synaptic functions and neurological disease. Here we show that α2δ subunits are essential for the formation and organization of glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown model, we demonstrate a failure in presynaptic differentiation evidenced by defective presynaptic calcium channel clustering and calcium influx, smaller presynaptic active zones, and a strongly reduced accumulation of presynaptic vesicle-associated proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms as synaptic organizers is highly redundant, as each individual α2δ isoform can rescue presynaptic calcium channel trafficking and expression of synaptic proteins. Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can fully rescue presynaptic synapsin expression but only partially calcium channel trafficking, suggesting that the regulatory role of α2δ subunits is independent from its role as a calcium channel subunit. Our findings influence the current view on excitatory synapse formation. First, our study suggests that postsynaptic differentiation is secondary to presynaptic differentiation. Second, the dependence of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation points for the organization of synapses. Finally, our results suggest that α2δ subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning the synaptic active zone with the postsynaptic density."}],"citation":{"ista":"Schöpf CL, Ablinger C, Geisler SM, Stanika RI, Campiglio M, Kaufmann W, Nimmervoll B, Schlick B, Brockhaus J, Missler M, Shigemoto R, Obermair GJ. 2021. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. 118(14).","ieee":"C. L. Schöpf <i>et al.</i>, “Presynaptic α2δ subunits are key organizers of glutamatergic synapses,” <i>PNAS</i>, vol. 118, no. 14. National Academy of Sciences, 2021.","ama":"Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. <i>PNAS</i>. 2021;118(14). doi:<a href=\"https://doi.org/10.1073/pnas.1920827118\">10.1073/pnas.1920827118</a>","mla":"Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” <i>PNAS</i>, vol. 118, no. 14, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.1920827118\">10.1073/pnas.1920827118</a>.","short":"C.L. Schöpf, C. Ablinger, S.M. Geisler, R.I. Stanika, M. Campiglio, W. Kaufmann, B. Nimmervoll, B. Schlick, J. Brockhaus, M. Missler, R. Shigemoto, G.J. Obermair, PNAS 118 (2021).","apa":"Schöpf, C. L., Ablinger, C., Geisler, S. M., Stanika, R. I., Campiglio, M., Kaufmann, W., … Obermair, G. J. (2021). Presynaptic α2δ subunits are key organizers of glutamatergic synapses. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1920827118\">https://doi.org/10.1073/pnas.1920827118</a>","chicago":"Schöpf, Clemens L., Cornelia Ablinger, Stefanie M. Geisler, Ruslan I. Stanika, Marta Campiglio, Walter Kaufmann, Benedikt Nimmervoll, et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” <i>PNAS</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.1920827118\">https://doi.org/10.1073/pnas.1920827118</a>."},"year":"2021","date_created":"2021-04-18T22:01:40Z","file":[{"file_id":"9340","creator":"dernst","content_type":"application/pdf","checksum":"dd014f68ae9d7d8d8fc4139a24e04506","access_level":"open_access","success":1,"file_name":"2021_PNAS_Schoepf.pdf","date_created":"2021-04-19T10:10:56Z","file_size":2603911,"date_updated":"2021-04-19T10:10:56Z","relation":"main_file"}],"_id":"9330","acknowledgement":"We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the team of the Electron Microscopy Facility at the Institute of Science and Technology Austria for technical support related to ultrastructural analysis; Hermann Dietrich and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical discussions and reading the manuscript. This study was supported by Austrian Science Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.), European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S., S.M.G., and C.A.","publication_identifier":{"eissn":["1091-6490"]},"article_type":"original","scopus_import":"1","doi":"10.1073/pnas.1920827118","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-04-19T10:10:56Z","publication_status":"published","title":"Presynaptic α2δ subunits are key organizers of glutamatergic synapses","intvolume":"       118","date_updated":"2023-08-08T13:08:47Z","ec_funded":1,"publication":"PNAS","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Schöpf","first_name":"Clemens L.","full_name":"Schöpf, Clemens L."},{"full_name":"Ablinger, Cornelia","first_name":"Cornelia","last_name":"Ablinger"},{"last_name":"Geisler","first_name":"Stefanie M.","full_name":"Geisler, Stefanie M."},{"last_name":"Stanika","first_name":"Ruslan I.","full_name":"Stanika, Ruslan I."},{"full_name":"Campiglio, Marta","last_name":"Campiglio","first_name":"Marta"},{"last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nimmervoll","first_name":"Benedikt","full_name":"Nimmervoll, Benedikt"},{"full_name":"Schlick, Bettina","last_name":"Schlick","first_name":"Bettina"},{"last_name":"Brockhaus","first_name":"Johannes","full_name":"Brockhaus, Johannes"},{"first_name":"Markus","last_name":"Missler","full_name":"Missler, Markus"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Obermair, Gerald J.","first_name":"Gerald J.","last_name":"Obermair"}],"volume":118,"oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"call_identifier":"H2020","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"has_accepted_license":"1","issue":"14","day":"06","quality_controlled":"1","ddc":["570"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"04","publisher":"National Academy of Sciences","type":"journal_article","date_published":"2021-04-06T00:00:00Z","external_id":{"isi":["000637398300002"]}},{"pmid":1,"publisher":"National Academy of Sciences","type":"journal_article","external_id":{"pmid":[" 34732570"],"arxiv":["2103.00023"],"isi":["000720926900019"]},"date_published":"2021-11-03T00:00:00Z","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"11","day":"03","quality_controlled":"1","project":[{"_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","call_identifier":"FWF","grant_number":"I04188"}],"issue":"45","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H"},{"last_name":"Lopez Alonso","first_name":"Jose M","full_name":"Lopez Alonso, Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022"},{"first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul"},{"full_name":"Sankar, Sarath","first_name":"Sarath","last_name":"Sankar"},{"last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"volume":118,"oa":1,"intvolume":"       118","arxiv":1,"date_updated":"2023-08-14T11:50:10Z","publication":"Proceedings of the National Academy of Sciences","department":[{"_id":"BjHo"}],"acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_type":"original","scopus_import":"1","doi":"10.1073/pnas.2102350118","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"oa_version":"Preprint","article_processing_charge":"No","publication_status":"published","title":"Experimental observation of the origin and structure of elastoinertial turbulence","abstract":[{"text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.","lang":"eng"}],"citation":{"ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(45). doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>","ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 118(45), e2102350118.","ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 45. National Academy of Sciences, 2021.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021).","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., &#38; Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>.","mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>."},"year":"2021","article_number":"e2102350118","date_created":"2021-11-17T13:24:24Z","_id":"10299"},{"date_published":"2021-07-16T00:00:00Z","external_id":{"pmid":["34272287"],"isi":["000685037700012"]},"type":"journal_article","publisher":"National Academy of Sciences","pmid":1,"month":"07","isi":1,"status":"public","language":[{"iso":"eng"}],"ddc":["580","570"],"quality_controlled":"1","day":"16","issue":"29","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","oa":1,"volume":118,"author":[{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung","last_name":"Hsieh"},{"full_name":"Ruan, Deling","last_name":"Ruan","first_name":"Deling"},{"full_name":"Nishimura, Toshiro","last_name":"Nishimura","first_name":"Toshiro"},{"full_name":"Sharma, Manoj K.","first_name":"Manoj K.","last_name":"Sharma"},{"last_name":"Sharma","first_name":"Rita","full_name":"Sharma, Rita"},{"full_name":"Ye, XinYi","first_name":"XinYi","last_name":"Ye"},{"full_name":"Nguyen, Nicholas D.","first_name":"Nicholas D.","last_name":"Nguyen"},{"full_name":"Nijjar, Sukhranjan","first_name":"Sukhranjan","last_name":"Nijjar"},{"first_name":"Pamela C.","last_name":"Ronald","full_name":"Ronald, Pamela C."},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"DaZi"}],"publication":"Proceedings of the National Academy of Sciences","date_updated":"2023-08-11T10:28:10Z","intvolume":"       118","publication_status":"published","title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","file_date_updated":"2021-08-11T09:31:41Z","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","doi":"10.1073/pnas.2104445118","scopus_import":"1","article_type":"original","acknowledgement":"We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing team for generating the IR64 genome sequence and initial analysis; L. Bartley and E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University of California (UC), Berkeley Sanger sequencing team for technical advice and service. This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"_id":"9877","date_created":"2021-08-10T19:30:41Z","file":[{"file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","access_level":"open_access","success":1,"file_size":1898360,"date_created":"2021-08-11T09:31:41Z","date_updated":"2021-08-11T09:31:41Z","relation":"main_file","creator":"asandaue","file_id":"9879","content_type":"application/pdf","checksum":"19e84ad8c03c60222744ee8e16cd6998"}],"year":"2021","article_number":"e2104445118","citation":{"apa":"Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>","short":"J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 118 (2021).","chicago":"Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>.","mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>.","ama":"Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(29). doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>","ieee":"J. A. Rodrigues <i>et al.</i>, “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 29. National Academy of Sciences, 2021.","ista":"Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29), e2104445118."},"abstract":[{"text":"Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.","lang":"eng"}]}]