[{"oa_version":"Published Version","file":[{"file_name":"2022_PNAS_Hledik.pdf","access_level":"open_access","file_size":2165752,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12091","date_created":"2022-09-12T08:08:12Z","date_updated":"2022-09-12T08:08:12Z","checksum":"6dec51f6567da9039982a571508a8e4d","success":1}],"intvolume":" 119","status":"public","ddc":["570"],"title":"Accumulation and maintenance of information in evolution","_id":"12081","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"36","abstract":[{"text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.","lang":"eng"}],"type":"journal_article","date_published":"2022-08-29T00:00:00Z","article_type":"original","citation":{"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.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.","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","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.","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"},"publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","article_processing_charge":"No","day":"29","scopus_import":"1","volume":119,"date_updated":"2024-03-06T14:22:51Z","date_created":"2022-09-11T22:01:55Z","related_material":{"record":[{"id":"15020","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Hledik, Michal","last_name":"Hledik","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"1","full_name":"Tkačik, Gašper"}],"publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","year":"2022","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"file_date_updated":"2022-09-12T08:08:12Z","article_number":"e2123152119","language":[{"iso":"eng"}],"doi":"10.1073/pnas.2123152119","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["36037343"],"isi":["000889278400014"]},"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"08"},{"article_number":"e2107588118","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","extern":"1","file_date_updated":"2023-02-23T10:42:07Z","publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","year":"2021","pmid":1,"date_created":"2023-02-21T08:51:04Z","date_updated":"2023-02-23T10:45:44Z","volume":118,"author":[{"first_name":"Ling","last_name":"Li","full_name":"Li, Ling"},{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"full_name":"Yang, Haizhao","first_name":"Haizhao","last_name":"Yang"},{"full_name":"Phillips, Katherine R.","first_name":"Katherine R.","last_name":"Phillips"},{"last_name":"Jia","first_name":"Zian","full_name":"Jia, Zian"},{"first_name":"Hongshun","last_name":"Chen","full_name":"Chen, Hongshun"},{"full_name":"Wang, Lifeng","first_name":"Lifeng","last_name":"Wang"},{"full_name":"Zhong, Jinjin","last_name":"Zhong","first_name":"Jinjin"},{"last_name":"Liu","first_name":"Anhua","full_name":"Liu, Anhua"},{"full_name":"Lu, Jianfeng","last_name":"Lu","first_name":"Jianfeng"},{"first_name":"Jianwei","last_name":"Shuai","full_name":"Shuai, Jianwei"},{"last_name":"Brenner","first_name":"Michael P.","full_name":"Brenner, Michael P."},{"full_name":"Spaepen, Frans","first_name":"Frans","last_name":"Spaepen"},{"full_name":"Aizenberg, Joanna","first_name":"Joanna","last_name":"Aizenberg"}],"month":"08","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"quality_controlled":"1","external_id":{"pmid":["34341109"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2107588118","type":"journal_article","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."}],"issue":"32","title":"Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals","status":"public","ddc":["570"],"intvolume":" 118","_id":"12667","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2021_PNAS_Li.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3275944,"file_id":"12674","relation":"main_file","date_updated":"2023-02-23T10:42:07Z","date_created":"2023-02-23T10:42:07Z","success":1,"checksum":"702f7ec60ce6f2815104ab649dc661a4"}],"oa_version":"Published Version","scopus_import":"1","day":"10","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"PNAS","citation":{"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.","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.","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","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"},"date_published":"2021-08-10T00:00:00Z"},{"date_published":"2021-03-09T00:00:00Z","citation":{"ista":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences. 118(10), e2024083118.","ieee":"C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner, “Designing self-assembling kinetics with differentiable statistical physics models,” Proceedings of the National Academy of Sciences, vol. 118, no. 10. National Academy of Sciences, 2021.","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","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.","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.","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)."},"publication":"Proceedings of the National Academy of Sciences","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"09","scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2021-03-22T12:23:54Z","date_created":"2021-03-22T12:23:54Z","checksum":"5be8da2b1c0757feb1057f1a515cf9e0","success":1,"relation":"main_file","file_id":"9278","file_size":1047954,"content_type":"application/pdf","creator":"dernst","file_name":"2021_PNAS_Goodrich.pdf","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9257","intvolume":" 118","title":"Designing self-assembling kinetics with differentiable statistical physics models","status":"public","ddc":["530"],"issue":"10","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."}],"type":"journal_article","doi":"10.1073/pnas.2024083118","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["33653960"],"isi":["000627429100097"]},"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"03","author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"},{"last_name":"King","first_name":"Ella M.","full_name":"King, Ella M."},{"full_name":"Schoenholz, Samuel S.","last_name":"Schoenholz","first_name":"Samuel S."},{"full_name":"Cubuk, Ekin D.","first_name":"Ekin D.","last_name":"Cubuk"},{"full_name":"Brenner, Michael P.","first_name":"Michael P.","last_name":"Brenner"}],"volume":118,"date_created":"2021-03-21T23:01:20Z","date_updated":"2023-08-07T14:19:34Z","pmid":1,"year":"2021","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.","publisher":"National Academy of Sciences","department":[{"_id":"CaGo"}],"publication_status":"published","file_date_updated":"2021-03-22T12:23:54Z","article_number":"e2024083118"},{"doi":"10.1073/pnas.2104445118","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000685037700012"],"pmid":["34272287"]},"quality_controlled":"1","isi":1,"month":"07","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"author":[{"first_name":"Jessica A.","last_name":"Rodrigues","full_name":"Rodrigues, Jessica A."},{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"full_name":"Ruan, Deling","first_name":"Deling","last_name":"Ruan"},{"first_name":"Toshiro","last_name":"Nishimura","full_name":"Nishimura, 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","last_name":"Ye","full_name":"Ye, XinYi"},{"full_name":"Nguyen, Nicholas D.","last_name":"Nguyen","first_name":"Nicholas D."},{"first_name":"Sukhranjan","last_name":"Nijjar","full_name":"Nijjar, Sukhranjan"},{"full_name":"Ronald, Pamela C.","last_name":"Ronald","first_name":"Pamela C."},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman"}],"date_updated":"2023-08-11T10:28:10Z","date_created":"2021-08-10T19:30:41Z","volume":118,"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.","year":"2021","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"file_date_updated":"2021-08-11T09:31:41Z","article_number":"e2104445118","date_published":"2021-07-16T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","citation":{"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.","short":"J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 118 (2021).","chicago":"Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.","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","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.","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.","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"},"article_type":"original","day":"16","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2021-08-11T09:31:41Z","date_created":"2021-08-11T09:31:41Z","checksum":"19e84ad8c03c60222744ee8e16cd6998","success":1,"relation":"main_file","file_id":"9879","file_size":1898360,"content_type":"application/pdf","creator":"asandaue","file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","access_level":"open_access"}],"_id":"9877","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["580","570"],"status":"public","title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","intvolume":" 118","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"}],"issue":"29","type":"journal_article"},{"oa_version":"Preprint","title":"Experimental observation of the origin and structure of elastoinertial turbulence","status":"public","intvolume":" 118","_id":"10299","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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."}],"issue":"45","type":"journal_article","date_published":"2021-11-03T00:00:00Z","article_type":"original","publication":"Proceedings of the National Academy of Sciences","citation":{"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","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.","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.","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","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.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021).","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."},"day":"03","article_processing_charge":"No","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"scopus_import":"1","date_updated":"2023-08-14T11:50:10Z","date_created":"2021-11-17T13:24:24Z","volume":118,"author":[{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H","last_name":"Choueiri","full_name":"Choueiri, George H"},{"first_name":"Jose M","last_name":"Lopez Alonso","id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M"},{"first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul"},{"full_name":"Sankar, Sarath","last_name":"Sankar","first_name":"Sarath"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"National Academy of Sciences","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.","year":"2021","pmid":1,"article_number":"e2102350118","language":[{"iso":"eng"}],"doi":"10.1073/pnas.2102350118","isi":1,"quality_controlled":"1","project":[{"_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188","call_identifier":"FWF","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"external_id":{"arxiv":["2103.00023"],"isi":["000720926900019"],"pmid":[" 34732570"]},"oa":1,"month":"11","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]}},{"date_published":"2021-04-06T00:00:00Z","article_type":"original","publication":"Proceedings of the National Academy of Sciences","citation":{"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.","short":"C. Prehal, A. Samojlov, M. Nachtnebel, L. Lovicar, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, Proceedings of the National Academy of Sciences 118 (2021).","chicago":"Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Ludek Lovicar, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/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","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.","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","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."},"day":"06","article_processing_charge":"No","keyword":["small-angle X-ray scattering","oxygen reduction","disproportionation","Li-air battery"],"oa_version":"Preprint","status":"public","title":"In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes","intvolume":" 118","_id":"9301","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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."}],"issue":"14","type":"journal_article","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2021893118","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000637398300050"]},"main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv.11447775","open_access":"1"}],"month":"04","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"date_created":"2021-03-31T07:00:01Z","date_updated":"2023-09-05T13:27:18Z","volume":118,"author":[{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"full_name":"Samojlov, Aleksej","last_name":"Samojlov","first_name":"Aleksej"},{"last_name":"Nachtnebel","first_name":"Manfred","full_name":"Nachtnebel, Manfred"},{"last_name":"Lovicar","first_name":"Ludek","orcid":"0000-0001-6206-4200","id":"36DB3A20-F248-11E8-B48F-1D18A9856A87","full_name":"Lovicar, Ludek"},{"last_name":"Kriechbaum","first_name":"Manfred","full_name":"Kriechbaum, Manfred"},{"full_name":"Amenitsch, Heinz","first_name":"Heinz","last_name":"Amenitsch"},{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger"}],"publication_status":"published","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"publisher":"National Academy of Sciences","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.","year":"2021","article_number":"e2021893118"},{"type":"journal_article","issue":"52","abstract":[{"lang":"eng","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."}],"intvolume":" 117","status":"public","title":"Physical mechanisms of amyloid nucleation on fluid membranes","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10336","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"16","page":"33090-33098","article_type":"original","citation":{"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.","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.","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","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.","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."},"publication":"Proceedings of the National Academy of Sciences","date_published":"2020-12-16T00:00:00Z","extern":"1","publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2020","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.","volume":117,"date_updated":"2021-11-25T15:35:58Z","date_created":"2021-11-25T15:07:09Z","author":[{"full_name":"Krausser, Johannes","last_name":"Krausser","first_name":"Johannes"},{"full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J.","last_name":"Knowles"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"12","quality_controlled":"1","oa":1,"external_id":{"pmid":["33328273"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2007694117"},{"date_published":"2020-09-14T00:00:00Z","page":"24251-24257","article_type":"original","citation":{"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.","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","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.","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","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.","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.","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":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","day":"14","keyword":["multidisciplinary"],"scopus_import":"1","oa_version":"Published Version","intvolume":" 117","status":"public","title":"Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10347","issue":"39","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"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1073/pnas.2006684117","quality_controlled":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.22.960716","open_access":"1"}],"external_id":{"pmid":["32929030"]},"oa":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"09","volume":117,"date_updated":"2021-11-26T08:59:06Z","date_created":"2021-11-26T07:48:27Z","author":[{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela"},{"first_name":"Georg","last_name":"Meisl","full_name":"Meisl, Georg"},{"first_name":"Gabriella T.","last_name":"Heller","full_name":"Heller, Gabriella T."},{"full_name":"Curk, Samo","first_name":"Samo","last_name":"Curk"},{"full_name":"Arosio, Paolo","last_name":"Arosio","first_name":"Paolo"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"first_name":"Christopher M.","last_name":"Dobson","full_name":"Dobson, 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."}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"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).","year":"2020","extern":"1"},{"issue":"28","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"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"12526","relation":"main_file","date_created":"2023-02-07T11:29:55Z","date_updated":"2023-02-07T11:29:55Z","success":1,"checksum":"cedee184cb12f454f2fba4158ff47db9","file_name":"2020_PNAS_Bloomer.pdf","access_level":"open_access","creator":"alisjak","content_type":"application/pdf","file_size":1105414}],"intvolume":" 117","ddc":["580"],"title":"The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12188","has_accepted_license":"1","article_processing_charge":"No","day":"22","keyword":["Multidisciplinary"],"scopus_import":"1","date_published":"2020-05-22T00:00:00Z","page":"16660-16666","article_type":"original","citation":{"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.","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.","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.","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","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.","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"},"publication":"Proceedings of the National Academy of Sciences","extern":"1","file_date_updated":"2023-02-07T11:29:55Z","volume":117,"date_updated":"2023-05-08T10:53:55Z","date_created":"2023-01-16T09:15:44Z","author":[{"first_name":"Rebecca H.","last_name":"Bloomer","full_name":"Bloomer, Rebecca H."},{"last_name":"Hutchison","first_name":"Claire E.","full_name":"Hutchison, Claire E."},{"last_name":"Bäurle","first_name":"Isabel","full_name":"Bäurle, Isabel"},{"full_name":"Walker, James","first_name":"James","last_name":"Walker"},{"full_name":"Fang, Xiaofeng","first_name":"Xiaofeng","last_name":"Fang"},{"first_name":"Pumi","last_name":"Perera","full_name":"Perera, Pumi"},{"full_name":"Velanis, Christos N.","first_name":"Christos N.","last_name":"Velanis"},{"last_name":"Gümüs","first_name":"Serin","full_name":"Gümüs, Serin"},{"last_name":"Spanos","first_name":"Christos","full_name":"Spanos, Christos"},{"first_name":"Juri","last_name":"Rappsilber","full_name":"Rappsilber, Juri"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi"},{"full_name":"Goodrich, Justin","first_name":"Justin","last_name":"Goodrich"},{"last_name":"Dean","first_name":"Caroline","full_name":"Dean, Caroline"}],"department":[{"_id":"XiFe"}],"publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","pmid":1,"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).","year":"2020","publication_identifier":{"issn":["0027-8424","1091-6490"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1920621117","quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32601198"]},"oa":1},{"scopus_import":"1","day":"24","article_processing_charge":"No","article_type":"original","page":"6504-6549","publication":"Proceedings of the National Academy of Sciences","citation":{"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","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.","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.","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.","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."},"date_published":"2020-03-24T00:00:00Z","type":"journal_article","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."}],"issue":"12","status":"public","title":"Stochastic activation and bistability in a Rab GTPase regulatory network","intvolume":" 117","_id":"7580","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","month":"03","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/776567","open_access":"1"}],"external_id":{"isi":["000521821800040"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1921027117","publication_status":"published","department":[{"_id":"MaLo"},{"_id":"CaBe"}],"publisher":"Proceedings of the National Academy of Sciences","year":"2020","date_created":"2020-03-12T05:32:26Z","date_updated":"2023-09-07T13:17:06Z","volume":117,"author":[{"full_name":"Bezeljak, Urban","last_name":"Bezeljak","first_name":"Urban","orcid":"0000-0003-1365-5631","id":"2A58201A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Loya, Hrushikesh","last_name":"Loya","first_name":"Hrushikesh"},{"last_name":"Kaczmarek","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","full_name":"Kaczmarek, Beata M"},{"last_name":"Saunders","first_name":"Timothy E.","full_name":"Saunders, Timothy E."},{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8341"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/"}]}}]