[{"quality_controlled":"1","project":[{"name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z"}],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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":{"eissn":["1091-6490"],"issn":["0027-8424"]},"pmid":1,"_id":"14666","article_processing_charge":"Yes (in subscription journal)","oa":1,"volume":120,"date_updated":"2023-12-11T12:47:41Z","author":[{"first_name":"Chaitanya","full_name":"Chintaluri, Chaitanya","last_name":"Chintaluri","id":"E4EDB536-3485-11EA-98D2-20AF3DDC885E"},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","first_name":"Tim P"}],"abstract":[{"lang":"eng","text":"So-called spontaneous activity is a central hallmark of most nervous systems. Such non-causal firing is contrary to the tenet of spikes as a means of communication, and its purpose remains unclear. We propose that self-initiated firing can serve as a release valve to protect neurons from the toxic conditions arising in mitochondria from lower-than-baseline energy consumption. To demonstrate the viability of our hypothesis, we built a set of models that incorporate recent experimental results indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP), adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing. We explore the relationship of metabolic cost of spiking with its effect on the temporal patterning of spikes and reproduce experimentally observed changes in intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with ROS-modulated potassium channels. We also show that metabolic spiking homeostasis can produce indefinitely sustained avalanche dynamics in cortical circuits. Our theory can account for key features of neuronal activity observed in many studies ranging from ion channel function all the way to resting state dynamics. We finish with a set of experimental predictions that would confirm an integrated, crucial role for metabolically regulated spiking and firmly link metabolic homeostasis and neuronal function."}],"citation":{"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.","short":"C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ama":"Chintaluri C, Vogels TP. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(48). doi:10.1073/pnas.2306525120","mla":"Chintaluri, Chaitanya, and Tim P. Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48, e2306525120, National Academy of Sciences, 2023, doi:10.1073/pnas.2306525120.","chicago":"Chintaluri, Chaitanya, and Tim P Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2306525120.","ieee":"C. Chintaluri and T. P. Vogels, “Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48. National Academy of Sciences, 2023.","apa":"Chintaluri, C., & Vogels, T. P. (2023). Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2306525120"},"publication_status":"published","ddc":["570"],"related_material":{"link":[{"relation":"software","url":"https://github.com/ccluri/metabolic_spiking"}]},"article_number":"e2306525120","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"external_id":{"pmid":["37988463"]},"title":"Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species","doi":"10.1073/pnas.2306525120","year":"2023","file_date_updated":"2023-12-11T12:45:12Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"48","status":"public","intvolume":" 120","type":"journal_article","day":"21","file":[{"file_id":"14678","creator":"dernst","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2023-12-11T12:45:12Z","checksum":"bf4ec38602a70dae4338077a5a4d497f","date_created":"2023-12-11T12:45:12Z","file_size":16891602,"file_name":"2023_PNAS_Chintaluri.pdf"}],"date_created":"2023-12-10T23:01:00Z","department":[{"_id":"TiVo"}],"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/4.0/","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"National Academy of Sciences","date_published":"2023-11-21T00:00:00Z","article_type":"original","month":"11"},{"file":[{"content_type":"application/pdf","relation":"main_file","creator":"alisjak","file_id":"13204","file_name":"2023_PNAS_Wang.pdf","embargo":"2023-12-12","file_size":5244581,"date_created":"2023-07-10T08:48:40Z","checksum":"d800e06252eaefba28531fa9440f23f0","date_updated":"2023-12-13T23:30:03Z","access_level":"open_access"}],"date_created":"2023-07-09T22:01:12Z","department":[{"_id":"JiFr"}],"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"National Academy of Sciences","article_type":"original","date_published":"2023-06-12T00:00:00Z","month":"06","file_date_updated":"2023-12-13T23:30:03Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"25","status":"public","intvolume":" 120","type":"journal_article","day":"12","ddc":["570"],"article_number":"e2221313120","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","external_id":{"isi":["001030689600003"],"pmid":["37307446"]},"year":"2023","doi":"10.1073/pnas.2221313120","oa_version":"Published Version","quality_controlled":"1","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).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"_id":"13201","pmid":1,"article_processing_charge":"No","oa":1,"date_updated":"2023-12-13T23:30:04Z","volume":120,"author":[{"first_name":"Yalu","full_name":"Wang, Yalu","last_name":"Wang"},{"last_name":"Yuan","full_name":"Yuan, Zhi","first_name":"Zhi"},{"first_name":"Jinyi","last_name":"Wang","full_name":"Wang, Jinyi"},{"full_name":"Xiao, Huixin","last_name":"Xiao","first_name":"Huixin"},{"first_name":"Lu","last_name":"Wan","full_name":"Wan, Lu"},{"first_name":"Lanxin","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yan","full_name":"Guo, Yan","last_name":"Guo"},{"last_name":"Gong","full_name":"Gong, Zhizhong","first_name":"Zhizhong"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Jing","last_name":"Zhang","first_name":"Jing"}],"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"}],"citation":{"apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2221313120","ieee":"Y. Wang et al., “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25. National Academy of Sciences, 2023.","chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2221313120.","mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:10.1073/pnas.2221313120.","ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(25). doi:10.1073/pnas.2221313120","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.","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)."},"publication_status":"published"},{"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"e2122147119","title":"The \"New Synthesis\"","external_id":{"pmid":["35858408"]},"year":"2022","doi":"10.1073/pnas.2122147119","pmid":1,"_id":"11702","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"Published Version","volume":119,"date_updated":"2022-08-01T11:00:25Z","oa":1,"article_processing_charge":"No","abstract":[{"text":"When Mendel’s work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin’s theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher, Haldane, and Wright established a century ago, Mendelian inheritance is exactly what is needed for natural selection to work efficiently. Yet, the synthesis remains unfinished. We do not understand why sexual reproduction and a fair meiosis predominate in eukaryotes, or how far these are responsible for their diversity and complexity. Moreover, although quantitative geneticists have long known that adaptive variation is highly polygenic, and that this is essential for efficient selection, this is only now becoming appreciated by molecular biologists—and we still do not have a good framework for understanding polygenic variation or diffuse function.","lang":"eng"}],"author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","citation":{"chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122147119.","apa":"Barton, N. H. (2022). The “New Synthesis.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2122147119","ieee":"N. H. Barton, “The ‘New Synthesis,’” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 30. Proceedings of the National Academy of Sciences, 2022.","ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119.","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 30, e2122147119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2122147119.","ama":"Barton NH. The “New Synthesis.” Proceedings of the National Academy of Sciences of the United States of America. 2022;119(30). doi:10.1073/pnas.2122147119"},"date_created":"2022-07-31T22:01:47Z","file":[{"file_name":"2022_PNAS_Barton.pdf","file_size":848511,"date_created":"2022-08-01T10:58:28Z","checksum":"06c866196a8957f0c37b8a121771c885","date_updated":"2022-08-01T10:58:28Z","access_level":"open_access","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"11716","creator":"dernst"}],"has_accepted_license":"1","department":[{"_id":"NiBa"}],"publisher":"Proceedings of the National Academy of Sciences","scopus_import":"1","language":[{"iso":"eng"}],"month":"07","date_published":"2022-07-18T00:00:00Z","article_type":"original","issue":"30","publication":"Proceedings of the National Academy of Sciences of the United States of America","file_date_updated":"2022-08-01T10:58:28Z","intvolume":" 119","status":"public","day":"18","type":"journal_article"},{"day":"25","type":"journal_article","intvolume":" 119","status":"public","issue":"31","publication":"Proceedings of the National Academy of Sciences","file_date_updated":"2022-08-08T07:42:09Z","month":"07","date_published":"2022-07-25T00:00:00Z","article_type":"original","publisher":"Proceedings of the National Academy of Sciences","scopus_import":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"date_created":"2022-08-04T20:06:49Z","file":[{"date_updated":"2022-08-08T07:42:09Z","access_level":"open_access","date_created":"2022-08-08T07:42:09Z","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","file_name":"2022_PNAS_Li.pdf","file_size":2506262,"creator":"dernst","file_id":"11747","content_type":"application/pdf","relation":"main_file","success":1}],"publication_status":"published","citation":{"chicago":"Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2121058119.","ieee":"L. Li et al., “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” Proceedings of the National Academy of Sciences, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., & Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2121058119","ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. 119(31), e2121058119.","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).","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. 2022;119(31). doi:10.1073/pnas.2121058119","mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences, vol. 119, no. 31, e2121058119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2121058119."},"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."}],"author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","last_name":"Li","full_name":"Li, Lanxin","first_name":"Lanxin"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","last_name":"Chen","first_name":"Huihuang"},{"full_name":"Alotaibi, Saqer S.","last_name":"Alotaibi","first_name":"Saqer S."},{"first_name":"Aleš","full_name":"Pěnčík, Aleš","last_name":"Pěnčík"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","first_name":"Maciek"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"}],"keyword":["Multidisciplinary"],"date_updated":"2024-10-29T10:12:30Z","oa":1,"volume":119,"article_processing_charge":"No","_id":"11723","pmid":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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).”","project":[{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"_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","grant_number":"25351"}],"quality_controlled":"1","oa_version":"Published Version","doi":"10.1073/pnas.2121058119","year":"2022","external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"article_number":"e2121058119","isi":1,"ddc":["580"]},{"intvolume":" 119","status":"public","day":"28","type":"journal_article","issue":"31","publication":"Proceedings of the National Academy of Sciences of the United States of America","file_date_updated":"2023-10-04T09:05:44Z","publisher":"Proceedings of the National Academy of Sciences","scopus_import":"1","language":[{"iso":"eng"}],"month":"07","date_published":"2022-07-28T00:00:00Z","article_type":"original","date_created":"2022-08-14T22:01:45Z","file":[{"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"14386","success":1,"date_updated":"2023-10-04T09:05:44Z","access_level":"open_access","file_name":"2022_PNAS_Toprakcioglu.pdf","file_size":2476021,"date_created":"2023-10-04T09:05:44Z","checksum":"0fe3878896cbeb6c44e29222ec2f336a"}],"has_accepted_license":"1","department":[{"_id":"AnSa"}],"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."}],"author":[{"first_name":"Zenon","last_name":"Toprakcioglu","full_name":"Toprakcioglu, Zenon"},{"last_name":"Kamada","full_name":"Kamada, Ayaka","first_name":"Ayaka"},{"first_name":"Thomas C.T.","full_name":"Michaels, Thomas C.T.","last_name":"Michaels"},{"full_name":"Xie, Mengqi","last_name":"Xie","first_name":"Mengqi"},{"first_name":"Johannes","full_name":"Krausser, Johannes","last_name":"Krausser"},{"first_name":"Jiapeng","last_name":"Wei","full_name":"Wei, Jiapeng"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"},{"first_name":"Michele","full_name":"Vendruscolo, Michele","last_name":"Vendruscolo"},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."}],"publication_status":"published","citation":{"apa":"Toprakcioglu, Z., Kamada, A., Michaels, T. C. T., Xie, M., Krausser, J., Wei, J., … Knowles, T. P. J. (2022). Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2109718119","ieee":"Z. Toprakcioglu et al., “Adsorption free energy predicts amyloid protein nucleation rates,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","chicago":"Toprakcioglu, Zenon, Ayaka Kamada, Thomas C.T. Michaels, Mengqi Xie, Johannes Krausser, Jiapeng Wei, Anđela Šarić, Michele Vendruscolo, and Tuomas P.J. Knowles. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2109718119.","ama":"Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(31). doi:10.1073/pnas.2109718119","mla":"Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31, e2109718119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2109718119.","short":"Z. Toprakcioglu, A. Kamada, T.C.T. Michaels, M. Xie, J. Krausser, J. Wei, A. Šarić, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","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."},"_id":"11841","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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).","quality_controlled":"1","oa_version":"Published Version","project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"}],"oa":1,"volume":119,"date_updated":"2023-10-04T09:06:52Z","article_processing_charge":"No","external_id":{"isi":["000903753500002"]},"title":"Adsorption free energy predicts amyloid protein nucleation rates","year":"2022","doi":"10.1073/pnas.2109718119","ec_funded":1,"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"article_number":"e2109718119","isi":1},{"related_material":{"record":[{"id":"15020","relation":"dissertation_contains","status":"public"}]},"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"e2123152119","isi":1,"title":"Accumulation and maintenance of information in evolution","external_id":{"isi":["000889278400014"],"pmid":["36037343"]},"year":"2022","doi":"10.1073/pnas.2123152119","ec_funded":1,"_id":"12081","pmid":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.”","quality_controlled":"1","oa_version":"Published Version","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"}],"oa":1,"date_updated":"2025-06-30T13:21:05Z","volume":119,"article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","last_name":"Hledik","first_name":"Michal"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"1","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"publication_status":"published","citation":{"ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 2022;119(36). doi:10.1073/pnas.2123152119","mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.","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.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022.","apa":"Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119."},"date_created":"2022-09-11T22:01:55Z","file":[{"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"12091","success":1,"access_level":"open_access","date_updated":"2022-09-12T08:08:12Z","file_size":2165752,"file_name":"2022_PNAS_Hledik.pdf","checksum":"6dec51f6567da9039982a571508a8e4d","date_created":"2022-09-12T08:08:12Z"}],"has_accepted_license":"1","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Proceedings of the National Academy of Sciences","scopus_import":"1","language":[{"iso":"eng"}],"month":"08","date_published":"2022-08-29T00:00:00Z","article_type":"original","issue":"36","publication":"Proceedings of the National Academy of Sciences","file_date_updated":"2022-09-12T08:08:12Z","intvolume":" 119","status":"public","day":"29","type":"journal_article"},{"citation":{"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.","short":"A. Jouberton, T.E. Shaw, E. Miles, M. McCarthy, S. Fugger, S. Ren, A. Dehecq, W. Yang, F. Pellicciotti, PNAS 119 (2022).","ama":"Jouberton A, Shaw TE, Miles E, et al. Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau. PNAS. 2022;119(37). doi:10.1073/pnas.2109796119","mla":"Jouberton, Achille, et al. “Warming-Induced Monsoon Precipitation Phase Change Intensifies Glacier Mass Loss in the Southeastern Tibetan Plateau.” PNAS, vol. 119, no. 37, e2109796119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2109796119.","chicago":"Jouberton, Achille, Thomas E. Shaw, Evan Miles, Michael McCarthy, Stefan Fugger, Shaoting Ren, Amaury Dehecq, Wei Yang, and Francesca Pellicciotti. “Warming-Induced Monsoon Precipitation Phase Change Intensifies Glacier Mass Loss in the Southeastern Tibetan Plateau.” PNAS. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2109796119.","ieee":"A. Jouberton et al., “Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau,” PNAS, vol. 119, no. 37. Proceedings of the National Academy of Sciences, 2022.","apa":"Jouberton, A., Shaw, T. E., Miles, E., McCarthy, M., Fugger, S., Ren, S., … Pellicciotti, F. (2022). Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2109796119"},"publication_status":"published","abstract":[{"text":"Glaciers are key components of the mountain water towers of Asia and are vital for downstream domestic, agricultural, and industrial uses. The glacier mass loss rate over the southeastern Tibetan Plateau is among the highest in Asia and has accelerated in recent decades. This acceleration has been attributed to increased warming, but the mechanisms behind these glaciers’ high sensitivity to warming remain unclear, while the influence of changes in precipitation over the past decades is poorly quantified. Here, we reconstruct glacier mass changes and catchment runoff since 1975 at a benchmark glacier, Parlung No. 4, to shed light on the drivers of recent mass losses for the monsoonal, spring-accumulation glaciers of the Tibetan Plateau. Our modeling demonstrates how a temperature increase (mean of 0.39∘C ⋅dec−1since 1990) has accelerated mass loss rates by altering both the ablation and accumulation regimes in a complex manner. The majority of the post-2000 mass loss occurred during the monsoon months, caused by simultaneous decreases in the solid precipitation ratio (from 0.70 to 0.56) and precipitation amount (–10%), leading to reduced monsoon accumulation (–26%). Higher solid precipitation in spring (+18%) during the last two decades was increasingly important in mitigating glacier mass loss by providing mass to the glacier and protecting it from melting in the early monsoon. With bare ice exposed to warmer temperatures for longer periods, icemelt and catchment discharge have unsustainably intensified since the start of the 21st century, raising concerns for long-term water supply and hazard occurrence in the region.","lang":"eng"}],"author":[{"first_name":"Achille","last_name":"Jouberton","full_name":"Jouberton, Achille"},{"first_name":"Thomas E.","full_name":"Shaw, Thomas E.","last_name":"Shaw"},{"last_name":"Miles","full_name":"Miles, Evan","first_name":"Evan"},{"last_name":"McCarthy","full_name":"McCarthy, Michael","first_name":"Michael"},{"first_name":"Stefan","last_name":"Fugger","full_name":"Fugger, Stefan"},{"full_name":"Ren, Shaoting","last_name":"Ren","first_name":"Shaoting"},{"first_name":"Amaury","full_name":"Dehecq, Amaury","last_name":"Dehecq"},{"full_name":"Yang, Wei","last_name":"Yang","first_name":"Wei"},{"first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"}],"keyword":["Multidisciplinary"],"article_processing_charge":"No","volume":119,"date_updated":"2023-02-28T13:50:37Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"extern":"1","_id":"12577","oa_version":"None","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1073/pnas.2109796119","year":"2022","title":"Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau","article_number":"e2109796119","day":"06","type":"journal_article","intvolume":" 119","status":"public","publication":"PNAS","issue":"37","month":"09","article_type":"original","date_published":"2022-09-06T00:00:00Z","scopus_import":"1","publisher":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"date_created":"2023-02-20T08:10:02Z"},{"publisher":"National Academy of Sciences","scopus_import":"1","language":[{"iso":"eng"}],"month":"03","date_published":"2021-03-09T00:00:00Z","article_type":"original","date_created":"2021-03-21T23:01:20Z","file":[{"date_updated":"2021-03-22T12:23:54Z","access_level":"open_access","date_created":"2021-03-22T12:23:54Z","checksum":"5be8da2b1c0757feb1057f1a515cf9e0","file_name":"2021_PNAS_Goodrich.pdf","file_size":1047954,"file_id":"9278","creator":"dernst","content_type":"application/pdf","relation":"main_file","success":1}],"has_accepted_license":"1","department":[{"_id":"CaGo"}],"intvolume":" 118","status":"public","day":"09","type":"journal_article","issue":"10","publication":"Proceedings of the National Academy of Sciences","file_date_updated":"2021-03-22T12:23:54Z","title":"Designing self-assembling kinetics with differentiable statistical physics models","external_id":{"isi":["000627429100097"],"pmid":["33653960"]},"doi":"10.1073/pnas.2024083118","year":"2021","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"article_number":"e2024083118","isi":1,"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."}],"author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074"},{"first_name":"Ella M.","last_name":"King","full_name":"King, Ella M."},{"first_name":"Samuel S.","last_name":"Schoenholz","full_name":"Schoenholz, Samuel S."},{"first_name":"Ekin D.","last_name":"Cubuk","full_name":"Cubuk, Ekin D."},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."}],"publication_status":"published","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.","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).","mla":"Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” Proceedings of the National Academy of Sciences, vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:10.1073/pnas.2024083118.","ama":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences. 2021;118(10). doi:10.1073/pnas.2024083118","chicago":"Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk, and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2024083118.","apa":"Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., & Brenner, M. P. (2021). Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2024083118","ieee":"C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner, “Designing self-assembling kinetics with differentiable statistical physics models,” Proceedings of the National Academy of Sciences, vol. 118, no. 10. National Academy of Sciences, 2021."},"_id":"9257","pmid":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"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.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","quality_controlled":"1","oa":1,"date_updated":"2023-08-07T14:19:34Z","volume":118,"article_processing_charge":"No"},{"article_number":"e2021893118","main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv.11447775","open_access":"1"}],"isi":1,"title":"In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes","external_id":{"isi":["000637398300050"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"year":"2021","doi":"10.1073/pnas.2021893118","_id":"9301","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","quality_controlled":"1","oa_version":"Preprint","volume":118,"oa":1,"date_updated":"2023-09-05T13:27:18Z","article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"author":[{"first_name":"Christian","full_name":"Prehal, Christian","last_name":"Prehal"},{"first_name":"Aleksej","last_name":"Samojlov","full_name":"Samojlov, Aleksej"},{"first_name":"Manfred","last_name":"Nachtnebel","full_name":"Nachtnebel, Manfred"},{"id":"36DB3A20-F248-11E8-B48F-1D18A9856A87","first_name":"Ludek","orcid":"0000-0001-6206-4200","full_name":"Lovicar, Ludek","last_name":"Lovicar"},{"last_name":"Kriechbaum","full_name":"Kriechbaum, Manfred","first_name":"Manfred"},{"last_name":"Amenitsch","full_name":"Amenitsch, Heinz","first_name":"Heinz"},{"last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"keyword":["small-angle X-ray scattering","oxygen reduction","disproportionation","Li-air battery"],"publication_status":"published","citation":{"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).","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.","mla":"Prehal, Christian, et al. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences, vol. 118, no. 14, e2021893118, National Academy of Sciences, 2021, doi:10.1073/pnas.2021893118.","ama":"Prehal C, Samojlov A, Nachtnebel M, et al. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 2021;118(14). doi:10.1073/pnas.2021893118","chicago":"Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Ludek Lovicar, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2021893118.","ieee":"C. Prehal et al., “In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes,” Proceedings of the National Academy of Sciences, vol. 118, no. 14. National Academy of Sciences, 2021.","apa":"Prehal, C., Samojlov, A., Nachtnebel, M., Lovicar, L., Kriechbaum, M., Amenitsch, H., & Freunberger, S. A. (2021). In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2021893118"},"date_created":"2021-03-31T07:00:01Z","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"month":"04","article_type":"original","date_published":"2021-04-06T00:00:00Z","issue":"14","publication":"Proceedings of the National Academy of Sciences","intvolume":" 118","status":"public","day":"06","type":"journal_article"},{"publication":"Proceedings of the National Academy of Sciences","issue":"45","day":"03","type":"journal_article","intvolume":" 118","status":"public","department":[{"_id":"BjHo"}],"date_created":"2021-11-17T13:24:24Z","month":"11","date_published":"2021-11-03T00:00:00Z","article_type":"original","scopus_import":"1","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"arxiv":1,"article_processing_charge":"No","volume":118,"date_updated":"2023-08-14T11:50:10Z","oa":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"_id":"10299","pmid":1,"quality_controlled":"1","project":[{"name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF","grant_number":"I04188"}],"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","citation":{"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.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021).","ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 2021;118(45). doi:10.1073/pnas.2102350118","mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118.","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.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118.","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,” Proceedings of the National Academy of Sciences, vol. 118, no. 45. National Academy of Sciences, 2021.","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2102350118"},"publication_status":"published","abstract":[{"lang":"eng","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."}],"author":[{"first_name":"George H","full_name":"Choueiri, George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"id":"40770848-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso","orcid":"0000-0002-0384-2022","first_name":"Jose M"},{"full_name":"Varshney, Atul","last_name":"Varshney","orcid":"0000-0002-3072-5999","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sarath","full_name":"Sankar, Sarath","last_name":"Sankar"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"isi":1,"article_number":"e2102350118","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"doi":"10.1073/pnas.2102350118","year":"2021","title":"Experimental observation of the origin and structure of elastoinertial turbulence","external_id":{"arxiv":["2103.00023"],"isi":["000720926900019"],"pmid":[" 34732570"]}},{"year":"2021","doi":"10.1073/pnas.2107588118","external_id":{"pmid":["34341109"]},"title":"Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"article_number":"e2107588118","ddc":["570"],"citation":{"ieee":"L. Li et al., “Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals,” PNAS, vol. 118, no. 32. Proceedings of the National Academy of Sciences, 2021.","apa":"Li, L., Goodrich, C. P., Yang, H., Phillips, K. R., Jia, Z., Chen, H., … Aizenberg, J. (2021). Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2107588118","chicago":"Li, Ling, Carl Peter Goodrich, Haizhao Yang, Katherine R. Phillips, Zian Jia, Hongshun Chen, Lifeng Wang, et al. “Microscopic Origins of the Crystallographically Preferred Growth in Evaporation-Induced Colloidal Crystals.” PNAS. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2107588118.","mla":"Li, Ling, et al. “Microscopic Origins of the Crystallographically Preferred Growth in Evaporation-Induced Colloidal Crystals.” PNAS, vol. 118, no. 32, e2107588118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2107588118.","ama":"Li L, Goodrich CP, Yang H, et al. Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. PNAS. 2021;118(32). doi:10.1073/pnas.2107588118","short":"L. Li, C.P. Goodrich, H. Yang, K.R. Phillips, Z. Jia, H. Chen, L. Wang, J. Zhong, A. Liu, J. Lu, J. Shuai, M.P. Brenner, F. Spaepen, J. Aizenberg, PNAS 118 (2021).","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."},"publication_status":"published","abstract":[{"lang":"eng","text":"Unlike crystalline atomic and ionic solids, texture development due to crystallographically preferred growth in colloidal crystals is less studied. Here we investigate the underlying mechanisms of the texture evolution in an evaporation-induced colloidal assembly process through experiments, modeling, and theoretical analysis. In this widely used approach to obtain large-area colloidal crystals, the colloidal particles are driven to the meniscus via the evaporation of a solvent or matrix precursor solution where they close-pack to form a face-centered cubic colloidal assembly. Via two-dimensional large-area crystallographic mapping, we show that the initial crystal orientation is dominated by the interaction of particles with the meniscus, resulting in the expected coalignment of the close-packed direction with the local meniscus geometry. By combining with crystal structure analysis at a single-particle level, we further reveal that, at the later stage of self-assembly, however, the colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary dislocations (GNDs) and achieves a large-area uniform crystallographic orientation with the close-packed direction perpendicular to the meniscus and parallel to the growth direction. Classical slip analysis, finite element-based mechanical simulation, computational colloidal assembly modeling, and continuum theory unequivocally show that these GNDs result from the tensile stress field along the meniscus direction due to the constrained shrinkage of the colloidal crystal during drying. The generation of GNDs with specific slip systems within individual grains leads to crystallographic rotation to accommodate the mechanical stress. The mechanistic understanding reported here can be utilized to control crystallographic features of colloidal assemblies, and may provide further insights into crystallographically preferred growth in synthetic, biological, and geological crystals."}],"author":[{"last_name":"Li","full_name":"Li, Ling","first_name":"Ling"},{"first_name":"Carl Peter","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"first_name":"Haizhao","full_name":"Yang, Haizhao","last_name":"Yang"},{"full_name":"Phillips, Katherine R.","last_name":"Phillips","first_name":"Katherine R."},{"first_name":"Zian","full_name":"Jia, Zian","last_name":"Jia"},{"full_name":"Chen, Hongshun","last_name":"Chen","first_name":"Hongshun"},{"first_name":"Lifeng","last_name":"Wang","full_name":"Wang, Lifeng"},{"full_name":"Zhong, Jinjin","last_name":"Zhong","first_name":"Jinjin"},{"full_name":"Liu, Anhua","last_name":"Liu","first_name":"Anhua"},{"full_name":"Lu, Jianfeng","last_name":"Lu","first_name":"Jianfeng"},{"first_name":"Jianwei","full_name":"Shuai, Jianwei","last_name":"Shuai"},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."},{"last_name":"Spaepen","full_name":"Spaepen, Frans","first_name":"Frans"},{"last_name":"Aizenberg","full_name":"Aizenberg, Joanna","first_name":"Joanna"}],"article_processing_charge":"No","date_updated":"2023-02-23T10:45:44Z","oa":1,"volume":118,"extern":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"_id":"12667","pmid":1,"oa_version":"Published Version","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","date_published":"2021-08-10T00:00:00Z","article_type":"original","scopus_import":"1","publisher":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"has_accepted_license":"1","file":[{"relation":"main_file","content_type":"application/pdf","file_id":"12674","creator":"dernst","success":1,"access_level":"open_access","date_updated":"2023-02-23T10:42:07Z","file_size":3275944,"file_name":"2021_PNAS_Li.pdf","checksum":"702f7ec60ce6f2815104ab649dc661a4","date_created":"2023-02-23T10:42:07Z"}],"date_created":"2023-02-21T08:51:04Z","day":"10","type":"journal_article","intvolume":" 118","status":"public","publication":"PNAS","issue":"32","file_date_updated":"2023-02-23T10:42:07Z"},{"citation":{"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. Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118","mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.","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.","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).","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. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2104445118","ieee":"J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” Proceedings of the National Academy of Sciences, vol. 118, no. 29. National Academy of Sciences, 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.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118."},"publication_status":"published","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"}],"author":[{"last_name":"Rodrigues","full_name":"Rodrigues, Jessica A.","first_name":"Jessica A."},{"last_name":"Hsieh","full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung"},{"first_name":"Deling","full_name":"Ruan, Deling","last_name":"Ruan"},{"full_name":"Nishimura, Toshiro","last_name":"Nishimura","first_name":"Toshiro"},{"first_name":"Manoj K.","last_name":"Sharma","full_name":"Sharma, Manoj K."},{"first_name":"Rita","last_name":"Sharma","full_name":"Sharma, Rita"},{"first_name":"XinYi","full_name":"Ye, XinYi","last_name":"Ye"},{"full_name":"Nguyen, Nicholas D.","last_name":"Nguyen","first_name":"Nicholas D."},{"full_name":"Nijjar, Sukhranjan","last_name":"Nijjar","first_name":"Sukhranjan"},{"last_name":"Ronald","full_name":"Ronald, Pamela C.","first_name":"Pamela C."},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"article_processing_charge":"Yes (in subscription journal)","volume":118,"oa":1,"date_updated":"2023-08-11T10:28:10Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"_id":"9877","pmid":1,"oa_version":"Published Version","quality_controlled":"1","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.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2021","doi":"10.1073/pnas.2104445118","external_id":{"isi":["000685037700012"],"pmid":["34272287"]},"title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"article_number":"e2104445118","isi":1,"ddc":["580","570"],"day":"16","type":"journal_article","intvolume":" 118","status":"public","publication":"Proceedings of the National Academy of Sciences","issue":"29","file_date_updated":"2021-08-11T09:31:41Z","month":"07","date_published":"2021-07-16T00:00:00Z","article_type":"original","scopus_import":"1","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"DaZi"}],"date_created":"2021-08-10T19:30:41Z","file":[{"access_level":"open_access","date_updated":"2021-08-11T09:31:41Z","file_size":1898360,"file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","checksum":"19e84ad8c03c60222744ee8e16cd6998","date_created":"2021-08-11T09:31:41Z","relation":"main_file","content_type":"application/pdf","creator":"asandaue","file_id":"9879","success":1}]},{"publication":"Proceedings of the National Academy of Sciences","issue":"26","file_date_updated":"2020-07-14T12:48:07Z","day":"30","type":"journal_article","intvolume":" 117","status":"public","has_accepted_license":"1","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"file":[{"file_id":"8009","creator":"dernst","relation":"main_file","content_type":"application/pdf","checksum":"908b09437680181de9990915f2113aca","date_created":"2020-06-23T11:30:53Z","file_size":2407102,"file_name":"2020_PNAS_Hoermayer.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:07Z"}],"date_created":"2020-06-22T13:33:52Z","month":"06","article_type":"original","date_published":"2020-06-30T00:00:00Z","scopus_import":"1","publisher":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"date_updated":"2024-03-25T23:30:06Z","volume":117,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"pmid":1,"_id":"8002","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"grant_number":"P29988","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development"}],"quality_controlled":"1","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences, vol. 117, no. 26, 202003346, Proceedings of the National Academy of Sciences, 2020, doi:10.1073/pnas.2003346117.","ama":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 2020;117(26). doi:10.1073/pnas.2003346117","ista":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. 2020. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 117(26), 202003346.","short":"L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J. Friml, Proceedings of the National Academy of Sciences 117 (2020).","ieee":"L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots,” Proceedings of the National Academy of Sciences, vol. 117, no. 26. Proceedings of the National Academy of Sciences, 2020.","apa":"Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S., & Friml, J. (2020). Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2003346117","chicago":"Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2003346117."},"publication_status":"published","abstract":[{"lang":"eng","text":"Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity."}],"author":[{"first_name":"Lukas","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","first_name":"Juan C"},{"full_name":"Marhavá, Petra","last_name":"Marhavá","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","full_name":"Yoshida, Saiko","last_name":"Yoshida"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"article_number":"202003346","isi":1,"related_material":{"record":[{"id":"9992","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/"}]},"ddc":["580"],"year":"2020","doi":"10.1073/pnas.2003346117","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ec_funded":1,"external_id":{"isi":["000565729700033"],"pmid":["32541049"]},"title":"Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots"},{"related_material":{"link":[{"url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","id":"8341","relation":"dissertation_contains"}]},"main_file_link":[{"url":"https://doi.org/10.1101/776567","open_access":"1"}],"isi":1,"title":"Stochastic activation and bistability in a Rab GTPase regulatory network","external_id":{"isi":["000521821800040"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"year":"2020","doi":"10.1073/pnas.1921027117","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","oa_version":"Preprint","project":[{"grant_number":"RGY0083/2016","name":"Reconstitution of cell polarity and axis determination in a cell-free system","_id":"2599F062-B435-11E9-9278-68D0E5697425"}],"_id":"7580","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_updated":"2023-09-07T13:17:06Z","oa":1,"volume":117,"article_processing_charge":"No","author":[{"first_name":"Urban","orcid":"0000-0003-1365-5631","full_name":"Bezeljak, Urban","last_name":"Bezeljak","id":"2A58201A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hrushikesh","last_name":"Loya","full_name":"Loya, Hrushikesh"},{"full_name":"Kaczmarek, Beata M","last_name":"Kaczmarek","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Saunders","full_name":"Saunders, Timothy E.","first_name":"Timothy E."},{"first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell."}],"publication_status":"published","citation":{"apa":"Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., & Loose, M. (2020). Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1921027117","ieee":"U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic activation and bistability in a Rab GTPase regulatory network,” Proceedings of the National Academy of Sciences, vol. 117, no. 12. Proceedings of the National Academy of Sciences, pp. 6504–6549, 2020.","chicago":"Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders, and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921027117.","ama":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 2020;117(12):6504-6549. doi:10.1073/pnas.1921027117","mla":"Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences, vol. 117, no. 12, Proceedings of the National Academy of Sciences, 2020, pp. 6504–49, doi:10.1073/pnas.1921027117.","short":"U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences 117 (2020) 6504–6549.","ista":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 117(12), 6504–6549."},"date_created":"2020-03-12T05:32:26Z","department":[{"_id":"MaLo"},{"_id":"CaBe"}],"language":[{"iso":"eng"}],"publisher":"Proceedings of the National Academy of Sciences","scopus_import":"1","article_type":"original","date_published":"2020-03-24T00:00:00Z","month":"03","page":"6504-6549","issue":"12","publication":"Proceedings of the National Academy of Sciences","status":"public","intvolume":" 117","type":"journal_article","day":"24"},{"type":"journal_article","day":"08","status":"public","intvolume":" 117","page":"22101-22112","publication":"Proceedings of the National Academy of Sciences","issue":"36","article_type":"original","date_published":"2020-09-08T00:00:00Z","month":"09","language":[{"iso":"eng"}],"publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"CaBe"}],"date_created":"2024-03-04T10:03:52Z","citation":{"short":"N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan, C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia, E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings of the National Academy of Sciences 117 (2020) 22101–22112.","ista":"Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A, Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 117(36), 22101–22112.","mla":"Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences, vol. 117, no. 36, Proceedings of the National Academy of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117.","ama":"Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 2020;117(36):22101-22112. doi:10.1073/pnas.1917269117","chicago":"Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117.","ieee":"N. Pinotsis et al., “Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National Academy of Sciences, vol. 117, no. 36. Proceedings of the National Academy of Sciences, pp. 22101–22112, 2020.","apa":"Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M. B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1917269117"},"publication_status":"published","author":[{"last_name":"Pinotsis","full_name":"Pinotsis, Nikos","first_name":"Nikos"},{"last_name":"Zielinska","full_name":"Zielinska, Karolina","first_name":"Karolina"},{"first_name":"Mrigya","full_name":"Babuta, Mrigya","last_name":"Babuta"},{"first_name":"Joan L.","last_name":"Arolas","full_name":"Arolas, Joan L."},{"last_name":"Kostan","full_name":"Kostan, Julius","first_name":"Julius"},{"full_name":"Khan, Muhammad Bashir","last_name":"Khan","first_name":"Muhammad Bashir"},{"last_name":"Schreiner","full_name":"Schreiner, Claudia","first_name":"Claudia"},{"full_name":"Testa Salmazo, Anita P","last_name":"Testa Salmazo","first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luciano","last_name":"Ciccarelli","full_name":"Ciccarelli, Luciano"},{"last_name":"Puchinger","full_name":"Puchinger, Martin","first_name":"Martin"},{"first_name":"Eirini A.","last_name":"Gkougkoulia","full_name":"Gkougkoulia, Eirini A."},{"first_name":"Euripedes de Almeida","full_name":"Ribeiro, Euripedes de Almeida","last_name":"Ribeiro"},{"full_name":"Marlovits, Thomas C.","last_name":"Marlovits","first_name":"Thomas C."},{"first_name":"Alok","full_name":"Bhattacharya, Alok","last_name":"Bhattacharya"},{"full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo","first_name":"Kristina"}],"abstract":[{"text":"The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery.","lang":"eng"}],"article_processing_charge":"No","volume":117,"date_updated":"2024-03-04T10:14:44Z","oa":1,"quality_controlled":"1","oa_version":"Published Version","acknowledgement":"We thank the staff of the macromolecular crystallography (MX) and SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss Light Source for excellent support, and the Life Sciences Facility of the Institute of Science and Technology Austria for usage of the rheometer. We thank Life Sciences editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423), Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF) Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R. ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I 2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological Macromolecules. M.B. acknowledges the University Grant Commission, India, for a senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science Engineering Research Council. ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"pmid":1,"_id":"15061","doi":"10.1073/pnas.1917269117","year":"2020","acknowledged_ssus":[{"_id":"LifeSc"}],"title":"Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin","external_id":{"pmid":["32848067"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.191726911"}]},{"publication":"Proceedings of the National Academy of Sciences","issue":"52","page":"33090-33098","intvolume":" 117","status":"public","day":"16","type":"journal_article","date_created":"2021-11-25T15:07:09Z","scopus_import":"1","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"month":"12","date_published":"2020-12-16T00:00:00Z","article_type":"original","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"extern":"1","pmid":1,"_id":"10336","oa_version":"Published Version","quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"We thank T. C. T. Michaels for reading the manuscript. This work was supported by the Academy of Medical Science (J.K. and A.Š.), the Cambridge Center for Misfolding Diseases (T.P.J.K.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council Grant PhysProt Agreement 337969, the Wellcome Trust (A.Š. and T.P.J.K.), the Royal Society (A.Š.), the Medical Research Council (J.K. and A.Š.), and the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by Engineering and Physical Sciences Research Council Grant EP/P020194/1.","article_processing_charge":"No","volume":117,"date_updated":"2021-11-25T15:35:58Z","oa":1,"abstract":[{"text":"Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein–membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways—protein-rich and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity control the relative importance of those molecular pathways. We find that the membrane’s susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson’s disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context.","lang":"eng"}],"author":[{"full_name":"Krausser, Johannes","last_name":"Krausser","first_name":"Johannes"},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"citation":{"apa":"Krausser, J., Knowles, T. P. J., & Šarić, A. (2020). Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2007694117","ieee":"J. Krausser, T. P. J. Knowles, and A. Šarić, “Physical mechanisms of amyloid nucleation on fluid membranes,” Proceedings of the National Academy of Sciences, vol. 117, no. 52. National Academy of Sciences, pp. 33090–33098, 2020.","chicago":"Krausser, Johannes, Tuomas P. J. Knowles, and Anđela Šarić. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2007694117.","ama":"Krausser J, Knowles TPJ, Šarić A. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 2020;117(52):33090-33098. doi:10.1073/pnas.2007694117","mla":"Krausser, Johannes, et al. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences, vol. 117, no. 52, National Academy of Sciences, 2020, pp. 33090–98, doi:10.1073/pnas.2007694117.","short":"J. Krausser, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences 117 (2020) 33090–33098.","ista":"Krausser J, Knowles TPJ, Šarić A. 2020. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 117(52), 33090–33098."},"publication_status":"published","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2","open_access":"1"}],"title":"Physical mechanisms of amyloid nucleation on fluid membranes","external_id":{"pmid":["33328273"]},"year":"2020","doi":"10.1073/pnas.2007694117"},{"external_id":{"pmid":["32929030"]},"title":"Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors","year":"2020","doi":"10.1073/pnas.2006684117","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.02.22.960716"}],"abstract":[{"text":"Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates, and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of amyloid-aggregation inhibition that reveals the fundamental thermodynamic and kinetic signatures characterizing effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimization of inhibitors of amyloid-fibril formation, revealing in particular the important role of on-rates in the binding of the inhibitors.","lang":"eng"}],"keyword":["multidisciplinary"],"author":[{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139"},{"first_name":"Georg","full_name":"Meisl, Georg","last_name":"Meisl"},{"last_name":"Heller","full_name":"Heller, Gabriella T.","first_name":"Gabriella T."},{"first_name":"Samo","full_name":"Curk, Samo","last_name":"Curk"},{"first_name":"Paolo","full_name":"Arosio, Paolo","last_name":"Arosio"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"last_name":"Dobson","full_name":"Dobson, Christopher M.","first_name":"Christopher M."},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."}],"citation":{"chicago":"Michaels, Thomas C. T., Anđela Šarić, Georg Meisl, Gabriella T. Heller, Samo Curk, Paolo Arosio, Sara Linse, Christopher M. Dobson, Michele Vendruscolo, and Tuomas P. J. Knowles. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006684117.","apa":"Michaels, T. C. T., Šarić, A., Meisl, G., Heller, G. T., Curk, S., Arosio, P., … Knowles, T. P. J. (2020). Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2006684117","ieee":"T. C. T. Michaels et al., “Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors,” Proceedings of the National Academy of Sciences, vol. 117, no. 39. National Academy of Sciences, pp. 24251–24257, 2020.","ista":"Michaels TCT, Šarić A, Meisl G, Heller GT, Curk S, Arosio P, Linse S, Dobson CM, Vendruscolo M, Knowles TPJ. 2020. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 117(39), 24251–24257.","short":"T.C.T. Michaels, A. Šarić, G. Meisl, G.T. Heller, S. Curk, P. Arosio, S. Linse, C.M. Dobson, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences 117 (2020) 24251–24257.","ama":"Michaels TCT, Šarić A, Meisl G, et al. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 2020;117(39):24251-24257. doi:10.1073/pnas.2006684117","mla":"Michaels, Thomas C. T., et al. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” Proceedings of the National Academy of Sciences, vol. 117, no. 39, National Academy of Sciences, 2020, pp. 24251–57, doi:10.1073/pnas.2006684117."},"publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"extern":"1","pmid":1,"_id":"10347","quality_controlled":"1","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"We acknowledge support from Peterhouse, Cambridge (T.C.T.M.); the Swiss National Science Foundation (T.C.T.M.); the Royal Society (A.S. and S.C.); the Academy of Medical Sciences (A.S.); Sidney Sussex College, Cambridge (G.M.); Newnham College, Cambridge (G.T.H.); the Wellcome Trust (T.P.J.K.); the Cambridge Center for Misfolding Diseases (T.P.J.K. and M.V.); the Biotechnology and Biological Sciences Research Council (T.P.J.K.); the Frances and Augustus Newman Foundation (T.P.J.K.); and the Synapsis Foundation for Alzheimer’s disease (P.A.). The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7/2007-2013) through the ERC Grant PhysProt (Agreement 337969).","article_processing_charge":"No","date_updated":"2021-11-26T08:59:06Z","volume":117,"oa":1,"scopus_import":"1","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"month":"09","date_published":"2020-09-14T00:00:00Z","article_type":"original","date_created":"2021-11-26T07:48:27Z","intvolume":" 117","status":"public","day":"14","type":"journal_article","publication":"Proceedings of the National Academy of Sciences","issue":"39","page":"24251-24257"},{"publication_status":"published","citation":{"chicago":"Bloomer, Rebecca H., Claire E. Hutchison, Isabel Bäurle, James Walker, Xiaofeng Fang, Pumi Perera, Christos N. Velanis, et al. “The Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1920621117.","ieee":"R. H. Bloomer et al., “The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2,” Proceedings of the National Academy of Sciences, vol. 117, no. 28. Proceedings of the National Academy of Sciences, pp. 16660–16666, 2020.","apa":"Bloomer, R. H., Hutchison, C. E., Bäurle, I., Walker, J., Fang, X., Perera, P., … Dean, C. (2020). The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1920621117","ista":"Bloomer RH, Hutchison CE, Bäurle I, Walker J, Fang X, Perera P, Velanis CN, Gümüs S, Spanos C, Rappsilber J, Feng X, Goodrich J, Dean C. 2020. The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 117(28), 16660–16666.","short":"R.H. Bloomer, C.E. Hutchison, I. Bäurle, J. Walker, X. Fang, P. Perera, C.N. Velanis, S. Gümüs, C. Spanos, J. Rappsilber, X. Feng, J. Goodrich, C. Dean, Proceedings of the National Academy of Sciences 117 (2020) 16660–16666.","mla":"Bloomer, Rebecca H., et al. “The Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the National Academy of Sciences, vol. 117, no. 28, Proceedings of the National Academy of Sciences, 2020, pp. 16660–66, doi:10.1073/pnas.1920621117.","ama":"Bloomer RH, Hutchison CE, Bäurle I, et al. The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 2020;117(28):16660-16666. doi:10.1073/pnas.1920621117"},"author":[{"full_name":"Bloomer, Rebecca H.","last_name":"Bloomer","first_name":"Rebecca H."},{"first_name":"Claire E.","full_name":"Hutchison, Claire E.","last_name":"Hutchison"},{"full_name":"Bäurle, Isabel","last_name":"Bäurle","first_name":"Isabel"},{"first_name":"James","full_name":"Walker, James","last_name":"Walker"},{"full_name":"Fang, Xiaofeng","last_name":"Fang","first_name":"Xiaofeng"},{"full_name":"Perera, Pumi","last_name":"Perera","first_name":"Pumi"},{"first_name":"Christos N.","last_name":"Velanis","full_name":"Velanis, Christos N."},{"full_name":"Gümüs, Serin","last_name":"Gümüs","first_name":"Serin"},{"last_name":"Spanos","full_name":"Spanos, Christos","first_name":"Christos"},{"first_name":"Juri","last_name":"Rappsilber","full_name":"Rappsilber, Juri"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi"},{"first_name":"Justin","full_name":"Goodrich, Justin","last_name":"Goodrich"},{"full_name":"Dean, Caroline","last_name":"Dean","first_name":"Caroline"}],"keyword":["Multidisciplinary"],"abstract":[{"text":"Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states.","lang":"eng"}],"date_updated":"2023-05-08T10:53:55Z","oa":1,"volume":117,"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We would like to thank Scott Berry for help with ICU-GFP nuclear localization microscopy, Hao Yu and Lisha Shen for assistance with 6mA DNA methylation analysis, Donna Gibson for graphic design assistance, and members of the C.D. and Howard laboratories for helpful discussions. This work was funded by the European Research Council grants to “MEXTIM” (to C.D.) and “SexMeth” (to X. Feng), by the Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programmes GRO (BB/J004588/1), GEN (BB/P013511/1), BBSRC grant (to X. Feng) (BB/S009620/1), and the Marie Sklodowska–Curie Postdoctoral Fellowships “UNRAVEL” (to R.H.B.) and \"WISDOM\" (to X. Fang). Additional funding via the Wellcome Trust through a Senior Research Fellowship (to J.R.) (103139) and a multiuser equipment grant (108504). The Wellcome Centre for Cell Biology is supported by core funding from the Wellcome Trust (203149).","oa_version":"Published Version","quality_controlled":"1","_id":"12188","pmid":1,"extern":"1","publication_identifier":{"issn":["0027-8424","1091-6490"]},"year":"2020","doi":"10.1073/pnas.1920621117","title":"The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2","external_id":{"pmid":["32601198"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"type":"journal_article","day":"22","status":"public","intvolume":" 117","page":"16660-16666","file_date_updated":"2023-02-07T11:29:55Z","issue":"28","publication":"Proceedings of the National Academy of Sciences","article_type":"original","date_published":"2020-05-22T00:00:00Z","month":"05","language":[{"iso":"eng"}],"publisher":"Proceedings of the National Academy of Sciences","scopus_import":"1","department":[{"_id":"XiFe"}],"has_accepted_license":"1","date_created":"2023-01-16T09:15:44Z","file":[{"relation":"main_file","content_type":"application/pdf","creator":"alisjak","file_id":"12526","success":1,"access_level":"open_access","date_updated":"2023-02-07T11:29:55Z","file_size":1105414,"file_name":"2020_PNAS_Bloomer.pdf","checksum":"cedee184cb12f454f2fba4158ff47db9","date_created":"2023-02-07T11:29:55Z"}]},{"external_id":{"pmid":["31575745"],"isi":["000490183000068"]},"title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","doi":"10.1073/pnas.1911892116","year":"2019","related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.2004738117","relation":"erratum"}]},"ddc":["580"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"isi":1,"abstract":[{"lang":"eng","text":"Plasmodesmata (PD) are plant-specific membrane-lined channels that create cytoplasmic and membrane continuities between adjacent cells, thereby facilitating cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms to regulate PD plasticity in response to numerous environmental stimuli. In particular, during defense against plant pathogens, the defense hormone, salicylic acid (SA), plays a crucial role in the regulation of PD permeability in a callose-dependent manner. Here, we uncover a mechanism by which plants restrict the spreading of virus and PD cargoes using SA signaling by increasing lipid order and closure of PD. We showed that exogenous SA application triggered the compartmentalization of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein, Remorin (REM). Genetic studies, superresolution imaging, and transmission electron microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3 are crucial for plasma membrane nanodomain assembly to control PD aperture and functionality. In addition, we also found that a 14-3-3 epsilon protein modulates REM clustering and membrane nanodomain compartmentalization through its direct interaction with REM proteins. This study unveils a molecular mechanism by which the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization, thereby regulating PD closure to impede virus spreading."}],"author":[{"full_name":"Huang, D","last_name":"Huang","first_name":"D"},{"full_name":"Sun, Y","last_name":"Sun","first_name":"Y"},{"last_name":"Ma","full_name":"Ma, Z","first_name":"Z"},{"first_name":"M","full_name":"Ke, M","last_name":"Ke"},{"last_name":"Cui","full_name":"Cui, Y","first_name":"Y"},{"last_name":"Chen","full_name":"Chen, Z","first_name":"Z"},{"last_name":"Chen","full_name":"Chen, C","first_name":"C"},{"last_name":"Ji","full_name":"Ji, C","first_name":"C"},{"first_name":"TM","full_name":"Tran, TM","last_name":"Tran"},{"last_name":"Yang","full_name":"Yang, L","first_name":"L"},{"first_name":"SM","last_name":"Lam","full_name":"Lam, SM"},{"last_name":"Han","full_name":"Han, Y","first_name":"Y"},{"first_name":"G","full_name":"Shu, G","last_name":"Shu"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Y","last_name":"Miao","full_name":"Miao, Y"},{"last_name":"Jiang","full_name":"Jiang, L","first_name":"L"},{"full_name":"Chen, X","last_name":"Chen","first_name":"X"}],"publication_status":"published","citation":{"apa":"Huang, D., Sun, Y., Ma, Z., Ke, M., Cui, Y., Chen, Z., … Chen, X. (2019). Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1911892116","ieee":"D. Huang et al., “Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42. Proceedings of the National Academy of Sciences, pp. 21274–21284, 2019.","chicago":"Huang, D, Y Sun, Z Ma, M Ke, Y Cui, Z Chen, C Chen, et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1911892116.","ama":"Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(42):21274-21284. doi:10.1073/pnas.1911892116","mla":"Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42, Proceedings of the National Academy of Sciences, 2019, pp. 21274–84, doi:10.1073/pnas.1911892116.","short":"D. Huang, Y. Sun, Z. Ma, M. Ke, Y. Cui, Z. Chen, C. Chen, C. Ji, T. Tran, L. Yang, S. Lam, Y. Han, G. Shu, J. Friml, Y. Miao, L. Jiang, X. Chen, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 21274–21284.","ista":"Huang D, Sun Y, Ma Z, Ke M, Cui Y, Chen Z, Chen C, Ji C, Tran T, Yang L, Lam S, Han Y, Shu G, Friml J, Miao Y, Jiang L, Chen X. 2019. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 116(42), 21274–21284."},"pmid":1,"_id":"6999","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","volume":116,"date_updated":"2023-10-17T12:32:37Z","oa":1,"article_processing_charge":"No","publisher":"Proceedings of the National Academy of Sciences","scopus_import":"1","language":[{"iso":"eng"}],"month":"10","date_published":"2019-10-15T00:00:00Z","article_type":"original","date_created":"2019-11-12T11:42:05Z","file":[{"checksum":"258c666bc6253eab81961f61169eefae","date_created":"2019-11-13T08:22:28Z","file_size":3287466,"file_name":"2019_PNAS_Huang.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:46Z","creator":"dernst","file_id":"7012","relation":"main_file","content_type":"application/pdf"}],"has_accepted_license":"1","department":[{"_id":"JiFr"}],"intvolume":" 116","status":"public","day":"15","type":"journal_article","issue":"42","publication":"Proceedings of the National Academy of Sciences of the United States of America","file_date_updated":"2020-07-14T12:47:46Z","page":"21274-21284"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1907189116"}],"external_id":{"arxiv":["1906.10818"],"pmid":["31723044"]},"title":"Real-time probing of chirality during a chemical reaction","year":"2019","doi":"10.1073/pnas.1907189116","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"extern":"1","_id":"14001","pmid":1,"quality_controlled":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"article_processing_charge":"No","volume":116,"oa":1,"date_updated":"2023-08-22T07:40:05Z","abstract":[{"lang":"eng","text":"Chiral molecules interact and react differently with other chiral objects, depending on their handedness. Therefore, it is essential to understand and ultimately control the evolution of molecular chirality during chemical reactions. Although highly sophisticated techniques for the controlled synthesis of chiral molecules have been developed, the observation of chirality on the natural femtosecond time scale of a chemical reaction has so far remained out of reach in the gas phase. Here, we demonstrate a general experimental technique, based on high-harmonic generation in tailored laser fields, and apply it to probe the time evolution of molecular chirality during the photodissociation of 2-iodobutane. These measurements show a change in sign and a pronounced increase in the magnitude of the chiral response over the first 100 fs, followed by its decay within less than 500 fs, revealing the photodissociation to achiral products. The observed time evolution is explained in terms of the variation of the electric and magnetic transition-dipole moments between the lowest electronic states of the cation as a function of the reaction coordinate. These results open the path to investigations of the chirality of molecular-reaction pathways, light-induced chirality in chemical processes, and the control of molecular chirality through tailored laser pulses."}],"keyword":["Multidisciplinary"],"author":[{"first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Zindel, Daniel","last_name":"Zindel","first_name":"Daniel"},{"first_name":"Vít","last_name":"Svoboda","full_name":"Svoboda, Vít"},{"first_name":"Elias","full_name":"Bommeli, Elias","last_name":"Bommeli"},{"last_name":"Ochsner","full_name":"Ochsner, Manuel","first_name":"Manuel"},{"full_name":"Tehlar, Andres","last_name":"Tehlar","first_name":"Andres"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"citation":{"ama":"Baykusheva DR, Zindel D, Svoboda V, et al. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 2019;116(48):23923-23929. doi:10.1073/pnas.1907189116","mla":"Baykusheva, Denitsa Rangelova, et al. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences, vol. 116, no. 48, Proceedings of the National Academy of Sciences, 2019, pp. 23923–29, doi:10.1073/pnas.1907189116.","short":"D.R. Baykusheva, D. Zindel, V. Svoboda, E. Bommeli, M. Ochsner, A. Tehlar, H.J. Wörner, Proceedings of the National Academy of Sciences 116 (2019) 23923–23929.","ista":"Baykusheva DR, Zindel D, Svoboda V, Bommeli E, Ochsner M, Tehlar A, Wörner HJ. 2019. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 116(48), 23923–23929.","apa":"Baykusheva, D. R., Zindel, D., Svoboda, V., Bommeli, E., Ochsner, M., Tehlar, A., & Wörner, H. J. (2019). Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1907189116","ieee":"D. R. Baykusheva et al., “Real-time probing of chirality during a chemical reaction,” Proceedings of the National Academy of Sciences, vol. 116, no. 48. Proceedings of the National Academy of Sciences, pp. 23923–23929, 2019.","chicago":"Baykusheva, Denitsa Rangelova, Daniel Zindel, Vít Svoboda, Elias Bommeli, Manuel Ochsner, Andres Tehlar, and Hans Jakob Wörner. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1907189116."},"publication_status":"published","date_created":"2023-08-09T13:10:36Z","scopus_import":"1","publisher":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"month":"11","article_type":"original","date_published":"2019-11-13T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","issue":"48","page":"23923-23929","intvolume":" 116","status":"public","day":"13","type":"journal_article"}]