[{"page":"15138-15143","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"extern":"1","quality_controlled":"1","volume":113,"publisher":"National Academy of Sciences","date_published":"2016-12-27T00:00:00Z","publication_status":"published","external_id":{"pmid":["27956642"]},"abstract":[{"lang":"eng","text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm."}],"_id":"9477","article_type":"original","doi":"10.1073/pnas.1619047114","citation":{"ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15138-15143. doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>","ieee":"K. Park <i>et al.</i>, “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.","short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143.","mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>.","chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>.","apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>"},"date_created":"2021-06-07T07:10:59Z","keyword":["Multidisciplinary"],"year":"2016","pmid":1,"type":"journal_article","status":"public","author":[{"last_name":"Park","first_name":"Kyunghyuk","full_name":"Park, Kyunghyuk"},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"last_name":"Vickers","first_name":"Martin","full_name":"Vickers, Martin"},{"first_name":"Jin-Sup","full_name":"Park, Jin-Sup","last_name":"Park"},{"last_name":"Hyun","first_name":"Youbong","full_name":"Hyun, Youbong"},{"last_name":"Okamoto","full_name":"Okamoto, Takashi","first_name":"Takashi"},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","orcid":"0000-0002-4008-1234"},{"full_name":"Choi, Yeonhee","first_name":"Yeonhee","last_name":"Choi"},{"last_name":"Scholten","full_name":"Scholten, Stefan","first_name":"Stefan"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619047114","open_access":"1"}],"day":"27","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"12","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","oa":1,"date_updated":"2023-05-08T11:00:07Z","issue":"52","article_processing_charge":"No","intvolume":"       113","scopus_import":"1"},{"author":[{"first_name":"R.","full_name":"Araya, R.","last_name":"Araya"},{"full_name":"Vogels, Tim P","first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181"},{"first_name":"R.","full_name":"Yuste, R.","last_name":"Yuste"}],"month":"07","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104910/"}],"oa_version":"Published Version","day":"15","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","pmid":1,"status":"public","type":"journal_article","oa":1,"date_updated":"2021-01-12T08:16:34Z","article_processing_charge":"No","issue":"28","title":"Activity-dependent dendritic spine neck changes are correlated with synaptic strength","intvolume":"       111","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","publication_status":"published","external_id":{"pmid":["24982196"]},"abstract":[{"text":"Most excitatory inputs in the mammalian brain are made on dendritic spines, rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical isolation can underlie input-specific synaptic plasticity, providing a raison d'etre for spines. However, recent results indicate that the spine can experience a membrane potential different from that in the parent dendrite, as though the spine neck electrically isolated the spine. Here we use two-photon calcium imaging of mouse neocortical pyramidal neurons to analyze the correlation between the morphologies of spines activated under minimal synaptic stimulation and the excitatory postsynaptic potentials they generate. We find that excitatory postsynaptic potential amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike timing-dependent plasticity protocol, in which two-photon glutamate uncaging over a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine neck and concomitant increases in the amplitude of the evoked spine potentials. Using numerical simulations, we explore the parameter regimes for the spine neck resistance and synaptic conductance changes necessary to explain our observations. Our data, directly correlating synaptic and morphological plasticity, imply that long-necked spines have small or negligible somatic voltage contributions, but that, upon synaptic stimulation paired with postsynaptic activity, they can shorten their necks and increase synaptic efficacy, thus changing the input/output gain of pyramidal neurons. ","lang":"eng"}],"publisher":"Proceedings of the National Academy of Sciences","date_published":"2014-07-15T00:00:00Z","extern":"1","page":"E2895-E2904","volume":111,"quality_controlled":"1","year":"2014","date_created":"2020-06-25T13:06:24Z","citation":{"mla":"Araya, R., et al. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated with Synaptic Strength.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 28, Proceedings of the National Academy of Sciences, 2014, pp. E2895–904, doi:<a href=\"https://doi.org/10.1073/pnas.1321869111\">10.1073/pnas.1321869111</a>.","ista":"Araya R, Vogels TP, Yuste R. 2014. Activity-dependent dendritic spine neck changes are correlated with synaptic strength. Proceedings of the National Academy of Sciences. 111(28), E2895–E2904.","chicago":"Araya, R., Tim P Vogels, and R. Yuste. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated with Synaptic Strength.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1321869111\">https://doi.org/10.1073/pnas.1321869111</a>.","ieee":"R. Araya, T. P. Vogels, and R. Yuste, “Activity-dependent dendritic spine neck changes are correlated with synaptic strength,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 28. Proceedings of the National Academy of Sciences, pp. E2895–E2904, 2014.","ama":"Araya R, Vogels TP, Yuste R. Activity-dependent dendritic spine neck changes are correlated with synaptic strength. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(28):E2895-E2904. doi:<a href=\"https://doi.org/10.1073/pnas.1321869111\">10.1073/pnas.1321869111</a>","short":"R. Araya, T.P. Vogels, R. Yuste, Proceedings of the National Academy of Sciences 111 (2014) E2895–E2904.","apa":"Araya, R., Vogels, T. P., &#38; Yuste, R. (2014). Activity-dependent dendritic spine neck changes are correlated with synaptic strength. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1321869111\">https://doi.org/10.1073/pnas.1321869111</a>"},"article_type":"original","_id":"8021","doi":"10.1073/pnas.1321869111"},{"issue":"50","article_processing_charge":"No","oa":1,"date_updated":"2021-11-29T13:29:05Z","title":"Crucial role of nonspecific interactions in amyloid nucleation","intvolume":"       111","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","arxiv":1,"author":[{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela"},{"full_name":"Chebaro, Yassmine C.","first_name":"Yassmine C.","last_name":"Chebaro"},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"},{"last_name":"Frenkel","first_name":"Daan","full_name":"Frenkel, Daan"}],"month":"12","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","day":"01","main_file_link":[{"url":"https://www.pnas.org/content/111/50/17869","open_access":"1"}],"type":"journal_article","status":"public","pmid":1,"year":"2014","acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","keyword":["multidisciplinary"],"citation":{"ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874.","mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>.","chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>.","ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014.","ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(50):17869-17874. doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>","short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874.","apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., &#38; Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>"},"date_created":"2021-11-29T13:09:53Z","_id":"10382","article_type":"original","doi":"10.1073/pnas.1410159111","publication_status":"published","abstract":[{"lang":"eng","text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory."}],"external_id":{"arxiv":["1412.0897"],"pmid":["25453085"]},"date_published":"2014-12-01T00:00:00Z","publisher":"National Academy of Sciences","volume":111,"quality_controlled":"1","page":"17869-17874","extern":"1"},{"page":"16166-16171","department":[{"_id":"DaZi"}],"extern":"1","volume":111,"quality_controlled":"1","publisher":"National Academy of Sciences","date_published":"2014-11-11T00:00:00Z","external_id":{"pmid":["25344531"]},"abstract":[{"lang":"eng","text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction."}],"publication_status":"published","doi":"10.1073/pnas.1418564111","article_type":"original","_id":"9479","date_created":"2021-06-07T07:23:43Z","citation":{"ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>"},"year":"2014","pmid":1,"type":"journal_article","status":"public","day":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1418564111"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"11","author":[{"first_name":"Zsuzsanna","full_name":"Mérai, Zsuzsanna","last_name":"Mérai"},{"last_name":"Chumak","full_name":"Chumak, Nina","first_name":"Nina"},{"full_name":"García-Aguilar, Marcelina","first_name":"Marcelina","last_name":"García-Aguilar"},{"full_name":"Hsieh, Tzung-Fu","first_name":"Tzung-Fu","last_name":"Hsieh"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"last_name":"Schoft","first_name":"Vera K.","full_name":"Schoft, Vera K."},{"full_name":"Bindics, János","first_name":"János","last_name":"Bindics"},{"last_name":"Ślusarz","first_name":"Lucyna","full_name":"Ślusarz, Lucyna"},{"full_name":"Arnoux, Stéphanie","first_name":"Stéphanie","last_name":"Arnoux"},{"first_name":"Susanne","full_name":"Opravil, Susanne","last_name":"Opravil"},{"full_name":"Mechtler, Karl","first_name":"Karl","last_name":"Mechtler"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"},{"first_name":"Hisashi","full_name":"Tamaru, Hisashi","last_name":"Tamaru"}],"publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":"       111","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","oa":1,"date_updated":"2021-12-14T08:23:26Z","article_processing_charge":"No","issue":"45"},{"doi":"10.1073/pnas.1306164110","_id":"9481","article_type":"original","year":"2013","date_created":"2021-06-07T07:31:02Z","citation":{"apa":"Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>","chicago":"Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>.","ista":"Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 110(19), 7934–7939.","mla":"Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7934–39, doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>.","ama":"Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2013;110(19):7934-7939. doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>","ieee":"J. A. Rodrigues <i>et al.</i>, “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013.","short":"J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939."},"keyword":["Multidisciplinary"],"publisher":"National Academy of Sciences","date_published":"2013-05-07T00:00:00Z","department":[{"_id":"DaZi"}],"page":"7934-7939","extern":"1","quality_controlled":"1","volume":110,"external_id":{"pmid":["23613580"]},"abstract":[{"lang":"eng","text":"Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants."}],"publication_status":"published","publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"intvolume":"       110","scopus_import":"1","date_updated":"2021-12-14T08:26:44Z","oa":1,"issue":"19","article_processing_charge":"No","title":"Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm","pmid":1,"type":"journal_article","status":"public","month":"05","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1306164110"}],"oa_version":"Published Version","day":"07","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"last_name":"Ruan","first_name":"Randy","full_name":"Ruan, Randy"},{"full_name":"Nishimura, Toshiro","first_name":"Toshiro","last_name":"Nishimura"},{"last_name":"Sharma","full_name":"Sharma, Manoj K.","first_name":"Manoj K."},{"last_name":"Sharma","first_name":"Rita","full_name":"Sharma, Rita"},{"last_name":"Ronald","first_name":"Pamela C","full_name":"Ronald, Pamela C"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel"}]},{"language":[{"iso":"eng"}],"publication":"PNAS","title":"Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction","article_processing_charge":"No","issue":"10","date_updated":"2023-11-07T11:50:29Z","oa":1,"scopus_import":"1","intvolume":"       108","type":"journal_article","status":"public","pmid":1,"author":[{"last_name":"Bachmann","full_name":"Bachmann, Annett","first_name":"Annett"},{"last_name":"Wildemann","first_name":"Dirk","full_name":"Wildemann, Dirk"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","first_name":"Florian M","full_name":"Praetorius, Florian M"},{"last_name":"Fischer","first_name":"Gunter","full_name":"Fischer, Gunter"},{"full_name":"Kiefhaber, Thomas","first_name":"Thomas","last_name":"Kiefhaber"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1012668108","open_access":"1"}],"day":"12","oa_version":"Published Version","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"01","article_type":"original","_id":"14305","doi":"10.1073/pnas.1012668108","keyword":["Multidisciplinary"],"citation":{"apa":"Bachmann, A., Wildemann, D., Praetorius, F. M., Fischer, G., &#38; Kiefhaber, T. (2011). Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1012668108\">https://doi.org/10.1073/pnas.1012668108</a>","ieee":"A. Bachmann, D. Wildemann, F. M. Praetorius, G. Fischer, and T. Kiefhaber, “Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction,” <i>PNAS</i>, vol. 108, no. 10. Proceedings of the National Academy of Sciences, pp. 3952–3957, 2011.","ama":"Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. <i>PNAS</i>. 2011;108(10):3952-3957. doi:<a href=\"https://doi.org/10.1073/pnas.1012668108\">10.1073/pnas.1012668108</a>","short":"A. Bachmann, D. Wildemann, F.M. Praetorius, G. Fischer, T. Kiefhaber, PNAS 108 (2011) 3952–3957.","ista":"Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. 2011. Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. PNAS. 108(10), 3952–3957.","chicago":"Bachmann, Annett, Dirk Wildemann, Florian M Praetorius, Gunter Fischer, and Thomas Kiefhaber. “Mapping Backbone and Side-Chain Interactions in the Transition State of a Coupled Protein Folding and Binding Reaction.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1012668108\">https://doi.org/10.1073/pnas.1012668108</a>.","mla":"Bachmann, Annett, et al. “Mapping Backbone and Side-Chain Interactions in the Transition State of a Coupled Protein Folding and Binding Reaction.” <i>PNAS</i>, vol. 108, no. 10, Proceedings of the National Academy of Sciences, 2011, pp. 3952–57, doi:<a href=\"https://doi.org/10.1073/pnas.1012668108\">10.1073/pnas.1012668108</a>."},"date_created":"2023-09-06T12:54:36Z","year":"2011","quality_controlled":"1","volume":108,"extern":"1","page":"3952-3957","date_published":"2011-01-12T00:00:00Z","publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","abstract":[{"text":"Understanding the mechanism of protein folding requires a detailed knowledge of the structural properties of the barriers separating unfolded from native conformations. The S-peptide from ribonuclease S forms its α-helical structure only upon binding to the folded S-protein. We characterized the transition state for this binding-induced folding reaction at high resolution by determining the effect of site-specific backbone thioxylation and side-chain modifications on the kinetics and thermodynamics of the reaction, which allows us to monitor formation of backbone hydrogen bonds and side-chain interactions in the transition state. The experiments reveal that α-helical structure in the S-peptide is absent in the transition state of binding. Recognition between the unfolded S-peptide and the S-protein is mediated by loosely packed hydrophobic side-chain interactions in two well defined regions on the S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing hydrophobic residues at positions outside the recognition region can drastically slow down association.","lang":"eng"}],"external_id":{"pmid":["21325613"]}},{"pmid":1,"status":"public","type":"journal_article","author":[{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"full_name":"Shin, Juhyun","first_name":"Juhyun","last_name":"Shin"},{"last_name":"Uzawa","full_name":"Uzawa, Rie","first_name":"Rie"},{"first_name":"Pedro","full_name":"Silva, Pedro","last_name":"Silva"},{"last_name":"Cohen","first_name":"Stephanie","full_name":"Cohen, Stephanie"},{"last_name":"Bauer","full_name":"Bauer, Matthew J.","first_name":"Matthew J."},{"last_name":"Hashimoto","first_name":"Meryl","full_name":"Hashimoto, Meryl"},{"full_name":"Kirkbride, Ryan C.","first_name":"Ryan C.","last_name":"Kirkbride"},{"last_name":"Harada","first_name":"John J.","full_name":"Harada, John J."},{"first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1019273108","open_access":"1"}],"day":"01","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"02","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","title":"Regulation of imprinted gene expression in Arabidopsis endosperm","date_updated":"2021-12-14T08:33:49Z","oa":1,"issue":"5","article_processing_charge":"No","scopus_import":"1","intvolume":"       108","extern":"1","department":[{"_id":"DaZi"}],"page":"1755-1762","volume":108,"quality_controlled":"1","publisher":"National Academy of Sciences","date_published":"2011-02-01T00:00:00Z","publication_status":"published","external_id":{"pmid":["21257907"]},"abstract":[{"text":"Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development.","lang":"eng"}],"_id":"9483","article_type":"original","doi":"10.1073/pnas.1019273108","citation":{"chicago":"Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen, Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1019273108\">https://doi.org/10.1073/pnas.1019273108</a>.","ista":"Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5), 1755–1762.","mla":"Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:<a href=\"https://doi.org/10.1073/pnas.1019273108\">10.1073/pnas.1019273108</a>.","ieee":"T.-F. Hsieh <i>et al.</i>, “Regulation of imprinted gene expression in Arabidopsis endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 5. National Academy of Sciences, pp. 1755–1762, 2011.","ama":"Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2011;108(5):1755-1762. doi:<a href=\"https://doi.org/10.1073/pnas.1019273108\">10.1073/pnas.1019273108</a>","short":"T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto, R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 108 (2011) 1755–1762.","apa":"Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer, R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1019273108\">https://doi.org/10.1073/pnas.1019273108</a>"},"date_created":"2021-06-07T07:40:38Z","year":"2011"},{"publication_status":"published","abstract":[{"lang":"eng","text":"Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops."}],"external_id":{"pmid":["20937895"]},"date_published":"2010-10-26T00:00:00Z","publisher":"National Academy of Sciences","quality_controlled":"1","volume":107,"department":[{"_id":"DaZi"}],"extern":"1","page":"18729-18734","year":"2010","citation":{"apa":"Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., &#38; Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>","chicago":"Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>.","mla":"Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>.","ista":"Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734.","ama":"Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2010;107(43):18729-18734. doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>","ieee":"A. Zemach <i>et al.</i>, “Local DNA hypomethylation activates genes in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.","short":"A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D. Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734."},"date_created":"2021-06-07T09:31:01Z","_id":"9485","article_type":"original","doi":"10.1073/pnas.1009695107","author":[{"first_name":"Assaf","full_name":"Zemach, Assaf","last_name":"Zemach"},{"first_name":"M. Yvonne","full_name":"Kim, M. Yvonne","last_name":"Kim"},{"first_name":"Pedro","full_name":"Silva, Pedro","last_name":"Silva"},{"last_name":"Rodrigues","full_name":"Rodrigues, Jessica A.","first_name":"Jessica A."},{"last_name":"Dotson","first_name":"Bradley","full_name":"Dotson, Bradley"},{"last_name":"Brooks","full_name":"Brooks, Matthew D.","first_name":"Matthew D."},{"first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"}],"month":"10","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1009695107","open_access":"1"}],"oa_version":"Published Version","day":"26","type":"journal_article","status":"public","pmid":1,"issue":"43","article_processing_charge":"No","date_updated":"2021-12-14T08:40:02Z","oa":1,"title":"Local DNA hypomethylation activates genes in rice endosperm","intvolume":"       107","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences"},{"date_updated":"2021-01-12T08:19:35Z","issue":"27","year":"2007","article_processing_charge":"No","date_created":"2020-09-18T10:12:54Z","citation":{"apa":"Schanda, P., Forge, V., &#38; Brutscher, B. (2007). Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0702069104\">https://doi.org/10.1073/pnas.0702069104</a>","ista":"Schanda P, Forge V, Brutscher B. 2007. Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. Proceedings of the National Academy of Sciences. 104(27), 11257–11262.","mla":"Schanda, Paul, et al. “Protein Folding and Unfolding Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 27, National Academy of Sciences, 2007, pp. 11257–62, doi:<a href=\"https://doi.org/10.1073/pnas.0702069104\">10.1073/pnas.0702069104</a>.","chicago":"Schanda, Paul, V. Forge, and B. Brutscher. “Protein Folding and Unfolding Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0702069104\">https://doi.org/10.1073/pnas.0702069104</a>.","short":"P. Schanda, V. Forge, B. Brutscher, Proceedings of the National Academy of Sciences 104 (2007) 11257–11262.","ieee":"P. Schanda, V. Forge, and B. Brutscher, “Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy,” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 27. National Academy of Sciences, pp. 11257–11262, 2007.","ama":"Schanda P, Forge V, Brutscher B. Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. <i>Proceedings of the National Academy of Sciences</i>. 2007;104(27):11257-11262. doi:<a href=\"https://doi.org/10.1073/pnas.0702069104\">10.1073/pnas.0702069104</a>"},"title":"Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy","keyword":["Multidisciplinary"],"intvolume":"       104","article_type":"original","_id":"8483","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.0702069104","author":[{"full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda"},{"last_name":"Forge","first_name":"V.","full_name":"Forge, V."},{"full_name":"Brutscher, B.","first_name":"B.","last_name":"Brutscher"}],"publication_status":"published","month":"07","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa_version":"None","day":"03","abstract":[{"lang":"eng","text":"Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of α-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of α-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","date_published":"2007-07-03T00:00:00Z","type":"journal_article","status":"public","page":"11257-11262","extern":"1","volume":104,"quality_controlled":"1"},{"external_id":{"pmid":["17563381"]},"abstract":[{"lang":"eng","text":"Nanoparticles (NPs) decorated with ligands combining photoswitchable dipoles and covalent cross-linkers can be assembled by light into organized, three-dimensional suprastructures of various types and sizes. NPs covered with only few photoactive ligands form metastable crystals that can be assembled and disassembled “on demand” by using light of different wavelengths. For higher surface concentrations, self-assembly is irreversible, and the NPs organize into permanently cross-linked structures including robust supracrystals and plastic spherical aggregates."}],"publication_status":"published","page":"10305-10309","extern":"1","volume":104,"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","date_published":"2007-06-19T00:00:00Z","date_created":"2023-08-01T10:31:19Z","citation":{"ama":"Klajn R, Bishop KJM, Grzybowski BA. Light-controlled self-assembly of reversible and irreversible nanoparticle suprastructures. <i>Proceedings of the National Academy of Sciences</i>. 2007;104(25):10305-10309. doi:<a href=\"https://doi.org/10.1073/pnas.0611371104\">10.1073/pnas.0611371104</a>","ieee":"R. Klajn, K. J. M. Bishop, and B. A. Grzybowski, “Light-controlled self-assembly of reversible and irreversible nanoparticle suprastructures,” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 25. Proceedings of the National Academy of Sciences, pp. 10305–10309, 2007.","short":"R. Klajn, K.J.M. Bishop, B.A. Grzybowski, Proceedings of the National Academy of Sciences 104 (2007) 10305–10309.","chicago":"Klajn, Rafal, Kyle J. M. Bishop, and Bartosz A. Grzybowski. “Light-Controlled Self-Assembly of Reversible and Irreversible Nanoparticle Suprastructures.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0611371104\">https://doi.org/10.1073/pnas.0611371104</a>.","mla":"Klajn, Rafal, et al. “Light-Controlled Self-Assembly of Reversible and Irreversible Nanoparticle Suprastructures.” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 25, Proceedings of the National Academy of Sciences, 2007, pp. 10305–09, doi:<a href=\"https://doi.org/10.1073/pnas.0611371104\">10.1073/pnas.0611371104</a>.","ista":"Klajn R, Bishop KJM, Grzybowski BA. 2007. Light-controlled self-assembly of reversible and irreversible nanoparticle suprastructures. Proceedings of the National Academy of Sciences. 104(25), 10305–10309.","apa":"Klajn, R., Bishop, K. J. M., &#38; Grzybowski, B. A. (2007). Light-controlled self-assembly of reversible and irreversible nanoparticle suprastructures. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0611371104\">https://doi.org/10.1073/pnas.0611371104</a>"},"keyword":["Multidisciplinary"],"year":"2007","doi":"10.1073/pnas.0611371104","_id":"13425","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.0611371104"}],"oa_version":"Published Version","day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"author":[{"full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn"},{"last_name":"Bishop","full_name":"Bishop, Kyle J. M.","first_name":"Kyle J. M."},{"first_name":"Bartosz A.","full_name":"Grzybowski, Bartosz A.","last_name":"Grzybowski"}],"pmid":1,"status":"public","type":"journal_article","intvolume":"       104","scopus_import":"1","title":"Light-controlled self-assembly of reversible and irreversible nanoparticle suprastructures","oa":1,"date_updated":"2023-08-08T11:24:51Z","issue":"25","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}]},{"publication_status":"published","external_id":{"pmid":["17409185"]},"abstract":[{"text":"Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals. In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic background. However, the extent and function of demethylation by DEMETER-LIKE (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA hypermethylation. Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist. Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the overall distribution of WT DNA methylation. Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation.","lang":"eng"}],"publisher":"National Academy of Sciences","date_published":"2007-04-17T00:00:00Z","department":[{"_id":"DaZi"}],"page":"6752-6757","extern":"1","volume":104,"quality_controlled":"1","year":"2007","citation":{"ama":"Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA demethylation in the Arabidopsis genome. <i>Proceedings of the National Academy of Sciences</i>. 2007;104(16):6752-6757. doi:<a href=\"https://doi.org/10.1073/pnas.0701861104\">10.1073/pnas.0701861104</a>","ieee":"J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L. Fischer, “DNA demethylation in the Arabidopsis genome,” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 16. National Academy of Sciences, pp. 6752–6757, 2007.","short":"J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer, Proceedings of the National Academy of Sciences 104 (2007) 6752–6757.","mla":"Penterman, Jon, et al. “DNA Demethylation in the Arabidopsis Genome.” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 16, National Academy of Sciences, 2007, pp. 6752–57, doi:<a href=\"https://doi.org/10.1073/pnas.0701861104\">10.1073/pnas.0701861104</a>.","ista":"Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007. DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. 104(16), 6752–6757.","chicago":"Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0701861104\">https://doi.org/10.1073/pnas.0701861104</a>.","apa":"Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., &#38; Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0701861104\">https://doi.org/10.1073/pnas.0701861104</a>"},"date_created":"2021-06-07T09:38:21Z","article_type":"original","_id":"9487","doi":"10.1073/pnas.0701861104","author":[{"full_name":"Penterman, Jon","first_name":"Jon","last_name":"Penterman"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"last_name":"Huh","full_name":"Huh, Jin Hoe","first_name":"Jin Hoe"},{"first_name":"Tracy","full_name":"Ballinger, Tracy","last_name":"Ballinger"},{"last_name":"Henikoff","full_name":"Henikoff, Steven","first_name":"Steven"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."}],"month":"04","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"day":"17","main_file_link":[{"url":"https://doi.org/10.1073/pnas.0701861104","open_access":"1"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","pmid":1,"type":"journal_article","status":"public","date_updated":"2021-12-14T08:55:12Z","oa":1,"issue":"16","article_processing_charge":"No","title":"DNA demethylation in the Arabidopsis genome","scopus_import":"1","intvolume":"       104","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences"},{"author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"last_name":"Lawrence","full_name":"Lawrence, Steve","first_name":"Steve"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC387294/","open_access":"1"}],"oa_version":"Published Version","day":"06","month":"04","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"status":"public","type":"journal_article","pmid":1,"title":"Extracting knowledge from the World Wide Web","issue":"suppl_1","article_processing_charge":"No","oa":1,"date_updated":"2023-02-17T12:21:43Z","scopus_import":"1","intvolume":"       101","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","publication_status":"published","abstract":[{"lang":"eng","text":"The World Wide Web provides a unprecedented opportunity to automatically analyze a large sample of interests and activity in the world. We discuss methods for extracting knowledge from the web by randomly sampling and analyzing hosts and pages, and by analyzing the link structure of the web and how links accumulate over time. A variety of interesting and valuable information can be extracted, such as the distribution of web pages over domains, the distribution of interest in different areas, communities related to different topics, the nature of competition in different categories of sites, and the degree of communication between different communities or countries."}],"external_id":{"pmid":["14745041"]},"quality_controlled":"1","volume":101,"page":"5186-5191","extern":"1","date_published":"2004-04-06T00:00:00Z","publisher":"Proceedings of the National Academy of Sciences","date_created":"2022-08-16T13:06:10Z","citation":{"mla":"Henzinger, Monika H., and Steve Lawrence. “Extracting Knowledge from the World Wide Web.” <i>Proceedings of the National Academy of Sciences</i>, vol. 101, no. suppl_1, Proceedings of the National Academy of Sciences, 2004, pp. 5186–91, doi:<a href=\"https://doi.org/10.1073/pnas.0307528100\">10.1073/pnas.0307528100</a>.","chicago":"Henzinger, Monika H, and Steve Lawrence. “Extracting Knowledge from the World Wide Web.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2004. <a href=\"https://doi.org/10.1073/pnas.0307528100\">https://doi.org/10.1073/pnas.0307528100</a>.","ista":"Henzinger MH, Lawrence S. 2004. Extracting knowledge from the World Wide Web. Proceedings of the National Academy of Sciences. 101(suppl_1), 5186–5191.","short":"M.H. Henzinger, S. Lawrence, Proceedings of the National Academy of Sciences 101 (2004) 5186–5191.","ieee":"M. H. Henzinger and S. Lawrence, “Extracting knowledge from the World Wide Web,” <i>Proceedings of the National Academy of Sciences</i>, vol. 101, no. suppl_1. Proceedings of the National Academy of Sciences, pp. 5186–5191, 2004.","ama":"Henzinger MH, Lawrence S. Extracting knowledge from the World Wide Web. <i>Proceedings of the National Academy of Sciences</i>. 2004;101(suppl_1):5186-5191. doi:<a href=\"https://doi.org/10.1073/pnas.0307528100\">10.1073/pnas.0307528100</a>","apa":"Henzinger, M. H., &#38; Lawrence, S. (2004). Extracting knowledge from the World Wide Web. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0307528100\">https://doi.org/10.1073/pnas.0307528100</a>"},"year":"2004","article_type":"original","_id":"11877","doi":"10.1073/pnas.0307528100"},{"doi":"10.1073/pnas.86.18.7238","article_type":"original","_id":"3466","acknowledgement":"We thank Drs. C. Baumann, D. Siemen, and W. Stuhmer for reading the manuscript and Dr. F. Dreyer for the generous gift of DTX. The study was supported by the Deutsche Forschungsgemeinschaft.","year":"1989","citation":{"apa":"Jonas, P. M., Bräu, M., Hermsteiner, M., &#38; Vogel, W. (1989). Single-channel recording in myelinated nerve fibers reveals one type of Na channel but different K channels. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.86.18.7238\">https://doi.org/10.1073/pnas.86.18.7238</a>","chicago":"Jonas, Peter M, Michael Bräu, Markus Hermsteiner, and Werner Vogel. “Single-Channel Recording in Myelinated Nerve Fibers Reveals One Type of Na Channel but Different K Channels.” <i>PNAS</i>. National Academy of Sciences, 1989. <a href=\"https://doi.org/10.1073/pnas.86.18.7238\">https://doi.org/10.1073/pnas.86.18.7238</a>.","ista":"Jonas PM, Bräu M, Hermsteiner M, Vogel W. 1989. Single-channel recording in myelinated nerve fibers reveals one type of Na channel but different K channels. PNAS. 86(18), 7238–7242.","mla":"Jonas, Peter M., et al. “Single-Channel Recording in Myelinated Nerve Fibers Reveals One Type of Na Channel but Different K Channels.” <i>PNAS</i>, vol. 86, no. 18, National Academy of Sciences, 1989, pp. 7238–42, doi:<a href=\"https://doi.org/10.1073/pnas.86.18.7238\">10.1073/pnas.86.18.7238</a>.","ama":"Jonas PM, Bräu M, Hermsteiner M, Vogel W. Single-channel recording in myelinated nerve fibers reveals one type of Na channel but different K channels. <i>PNAS</i>. 1989;86(18):7238-7242. doi:<a href=\"https://doi.org/10.1073/pnas.86.18.7238\">10.1073/pnas.86.18.7238</a>","ieee":"P. M. Jonas, M. Bräu, M. Hermsteiner, and W. Vogel, “Single-channel recording in myelinated nerve fibers reveals one type of Na channel but different K channels,” <i>PNAS</i>, vol. 86, no. 18. National Academy of Sciences, pp. 7238–7242, 1989.","short":"P.M. Jonas, M. Bräu, M. Hermsteiner, W. Vogel, PNAS 86 (1989) 7238–7242."},"publist_id":"2921","date_created":"2018-12-11T12:03:28Z","publisher":"National Academy of Sciences","date_published":"1989-09-01T00:00:00Z","extern":"1","page":"7238 - 7242","quality_controlled":"1","volume":86,"external_id":{"pmid":["2550937 "]},"abstract":[{"text":"Amphibian myelinated nerve fibers were treated with collagenase and protease. Axons with retraction of the myelin sheath were patch-clamped in the nodal and paranodal region. One type of Na channel was found. It has a single-channel conductance of 11 pS (15 degrees C) and is blocked by tetrodotoxin. Averaged events show the typical activation and inactivation kinetics of macroscopic Na current. Three potential-dependent K channels were identified (I, F, and S channel). The I channel, being the most frequent type, has a single-channel conductance of 23 pS (inward current, 105 mM K on both sides of the membrane), activates between -60 and -30 mV, deactivates with intermediate kinetics, and is sensitive to dendrotoxin. The F channel has a conductance of 30 pS, activates between -40 and 60 mV, and deactivates with fast kinetics. The former inactivates within tens of seconds; the latter inactivates within seconds. The third type, the S channel, has a conductance of 7 pS and deactivates slowly. All three channels can be blocked by external tetraethylammonium chloride. We suggest that these distinct K channel types form the basis for the different components of macroscopic K current described previously.","lang":"eng"}],"publication_status":"published","publication":"PNAS","language":[{"iso":"eng"}],"intvolume":"        86","date_updated":"2022-02-14T16:12:33Z","oa":1,"issue":"18","article_processing_charge":"No","title":"Single-channel recording in myelinated nerve fibers reveals one type of Na channel but different K channels","pmid":1,"type":"journal_article","status":"public","month":"09","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"day":"01","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC298032/?tool=pubmed"}],"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","author":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M"},{"first_name":"Michael","full_name":"Bräu, Michael","last_name":"Bräu"},{"last_name":"Hermsteiner","full_name":"Hermsteiner, Markus","first_name":"Markus"},{"last_name":"Vogel","first_name":"Werner","full_name":"Vogel, Werner"}]}]