[{"issue":"19","language":[{"iso":"eng"}],"keyword":["Multidisciplinary"],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"quality_controlled":"1","doi":"10.1073/pnas.1821435116","department":[{"_id":"DaZi"}],"pmid":1,"publisher":"National Academy of Sciences","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file":[{"date_created":"2021-06-04T12:50:47Z","access_level":"open_access","date_updated":"2021-06-04T12:50:47Z","file_id":"9461","checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","content_type":"application/pdf","relation":"main_file","file_size":1142540,"creator":"asandaue","success":1,"file_name":"2019_PNAS_Kim.pdf"}],"day":"07","author":[{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"first_name":"Akemi","last_name":"Ono","full_name":"Ono, Akemi"},{"last_name":"Scholten","first_name":"Stefan","full_name":"Scholten, Stefan"},{"first_name":"Tetsu","last_name":"Kinoshita","full_name":"Kinoshita, Tetsu"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman"},{"full_name":"Okamoto, Takashi","first_name":"Takashi","last_name":"Okamoto"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"}],"title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","external_id":{"pmid":["31000601"]},"status":"public","citation":{"ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. 2019;116(19):9652-9657. doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>","ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.","mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>.","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., &#38; Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>","ieee":"M. Y. Kim <i>et al.</i>, “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>.","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657."},"intvolume":"       116","extern":"1","has_accepted_license":"1","oa":1,"publication_status":"published","ddc":["580"],"date_published":"2019-05-07T00:00:00Z","year":"2019","_id":"9460","oa_version":"Published Version","type":"journal_article","month":"05","abstract":[{"text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion.","lang":"eng"}],"date_updated":"2021-12-14T07:52:30Z","page":"9652-9657","date_created":"2021-06-04T12:38:20Z","file_date_updated":"2021-06-04T12:50:47Z","volume":116},{"author":[{"first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"full_name":"Engel, Edgar A.","first_name":"Edgar A.","last_name":"Engel"},{"full_name":"Behler, Jörg","last_name":"Behler","first_name":"Jörg"},{"last_name":"Dellago","first_name":"Christoph","full_name":"Dellago, Christoph"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"day":"22","title":"Ab initio thermodynamics of liquid and solid water","arxiv":1,"publisher":"National Academy of Sciences","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","pmid":1,"publication":"Proceedings of the National Academy of Sciences","article_type":"original","scopus_import":"1","article_processing_charge":"No","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"doi":"10.1073/pnas.1815117116","quality_controlled":"1","issue":"4","language":[{"iso":"eng"}],"page":"1110-1115","oa_version":"Published Version","type":"journal_article","month":"01","date_updated":"2023-02-23T14:05:08Z","abstract":[{"lang":"eng","text":"A central goal of computational physics and chemistry is to predict material properties by using first-principles methods based on the fundamental laws of quantum mechanics. However, the high computational costs of these methods typically prevent rigorous predictions of macroscopic quantities at finite temperatures, such as heat capacity, density, and chemical potential. Here, we enable such predictions by marrying advanced free-energy methods with data-driven machine-learning interatomic potentials. We show that, for the ubiquitous and technologically essential system of water, a first-principles thermodynamic description not only leads to excellent agreement with experiments, but also reveals the crucial role of nuclear quantum fluctuations in modulating the thermodynamic stabilities of different phases of water."}],"volume":116,"date_created":"2021-07-19T10:17:09Z","year":"2019","_id":"9689","publication_status":"published","oa":1,"date_published":"2019-01-22T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1815117116","open_access":"1"}],"status":"public","external_id":{"pmid":["30610171"],"arxiv":["1811.08630"]},"extern":"1","intvolume":"       116","citation":{"ieee":"B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio thermodynamics of liquid and solid water,” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115, 2019.","chicago":"Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1815117116\">https://doi.org/10.1073/pnas.1815117116</a>.","short":"B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of the National Academy of Sciences 116 (2019) 1110–1115.","ama":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics of liquid and solid water. <i>Proceedings of the National Academy of Sciences</i>. 2019;116(4):1110-1115. doi:<a href=\"https://doi.org/10.1073/pnas.1815117116\">10.1073/pnas.1815117116</a>","mla":"Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1110–15, doi:<a href=\"https://doi.org/10.1073/pnas.1815117116\">10.1073/pnas.1815117116</a>.","ista":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4), 1110–1115.","apa":"Cheng, B., Engel, E. A., Behler, J., Dellago, C., &#38; Ceriotti, M. (2019). Ab initio thermodynamics of liquid and solid water. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1815117116\">https://doi.org/10.1073/pnas.1815117116</a>"}},{"quality_controlled":"1","date_published":"2018-01-02T00:00:00Z","doi":"10.1073/pnas.1707227114","publication_identifier":{"issn":["0027-8424","1091-6490"]},"publication_status":"published","issue":"1","language":[{"iso":"eng"}],"citation":{"ista":"Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. 2018. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 115(1), 151–156.","mla":"Sanjak, Jaleal S., et al. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 1, Proceedings of the National Academy of Sciences, 2018, pp. 151–56, doi:<a href=\"https://doi.org/10.1073/pnas.1707227114\">10.1073/pnas.1707227114</a>.","apa":"Sanjak, J. S., Sidorenko, J., Robinson, M. R., Thornton, K. R., &#38; Visscher, P. M. (2018). Evidence of directional and stabilizing selection in contemporary humans. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1707227114\">https://doi.org/10.1073/pnas.1707227114</a>","ama":"Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. Evidence of directional and stabilizing selection in contemporary humans. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(1):151-156. doi:<a href=\"https://doi.org/10.1073/pnas.1707227114\">10.1073/pnas.1707227114</a>","short":"J.S. Sanjak, J. Sidorenko, M.R. Robinson, K.R. Thornton, P.M. Visscher, Proceedings of the National Academy of Sciences 115 (2018) 151–156.","ieee":"J. S. Sanjak, J. Sidorenko, M. R. Robinson, K. R. Thornton, and P. M. Visscher, “Evidence of directional and stabilizing selection in contemporary humans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 1. Proceedings of the National Academy of Sciences, pp. 151–156, 2018.","chicago":"Sanjak, Jaleal S., Julia Sidorenko, Matthew Richard Robinson, Kevin R. Thornton, and Peter M. Visscher. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1707227114\">https://doi.org/10.1073/pnas.1707227114</a>."},"intvolume":"       115","extern":"1","related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.1806837115","relation":"erratum"}]},"status":"public","date_created":"2020-04-30T10:45:43Z","title":"Evidence of directional and stabilizing selection in contemporary humans","volume":115,"month":"01","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T08:15:07Z","abstract":[{"lang":"eng","text":"Modern molecular genetic datasets, primarily collected to study the biology of human health and disease, can be used to directly measure the action of natural selection and reveal important features of contemporary human evolution. Here we leverage the UK Biobank data to test for the presence of linear and nonlinear natural selection in a contemporary population of the United Kingdom. We obtain phenotypic and genetic evidence consistent with the action of linear/directional selection. Phenotypic evidence suggests that stabilizing selection, which acts to reduce variance in the population without necessarily modifying the population mean, is widespread and relatively weak in comparison with estimates from other species."}],"day":"02","author":[{"full_name":"Sanjak, Jaleal S.","first_name":"Jaleal S.","last_name":"Sanjak"},{"full_name":"Sidorenko, Julia","last_name":"Sidorenko","first_name":"Julia"},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson"},{"full_name":"Thornton, Kevin R.","first_name":"Kevin R.","last_name":"Thornton"},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."}],"page":"151-156","article_type":"original","article_processing_charge":"No","_id":"7724","publication":"Proceedings of the National Academy of Sciences","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Proceedings of the National Academy of Sciences"},{"pmid":1,"department":[{"_id":"MaJö"}],"publisher":"National Academy of Sciences","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","scopus_import":"1","publication":"Proceedings of the National Academy of Sciences","day":"07","author":[{"full_name":"Garrido-Charad, Florencia","last_name":"Garrido-Charad","first_name":"Florencia"},{"last_name":"Vega Zuniga","first_name":"Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","full_name":"Vega Zuniga, Tomas A"},{"last_name":"Gutiérrez-Ibáñez","first_name":"Cristián","full_name":"Gutiérrez-Ibáñez, Cristián"},{"full_name":"Fernandez, Pedro","last_name":"Fernandez","first_name":"Pedro"},{"full_name":"López-Jury, Luciana","last_name":"López-Jury","first_name":"Luciana"},{"full_name":"González-Cabrera, Cristian","last_name":"González-Cabrera","first_name":"Cristian"},{"full_name":"Karten, Harvey J.","first_name":"Harvey J.","last_name":"Karten"},{"last_name":"Luksch","first_name":"Harald","full_name":"Luksch, Harald"},{"full_name":"Marín, Gonzalo J.","first_name":"Gonzalo J.","last_name":"Marín"}],"title":"“Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network","language":[{"iso":"eng"}],"issue":"32","isi":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"quality_controlled":"1","doi":"10.1073/pnas.1804517115","year":"2018","_id":"6010","date_updated":"2023-09-19T14:35:36Z","abstract":[{"text":"The optic tectum (TeO), or superior colliculus, is a multisensory midbrain center that organizes spatially orienting responses to relevant stimuli. To define the stimulus with the highest priority at each moment, a network of reciprocal connections between the TeO and the isthmi promotes competition between concurrent tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression of tectal inputs are located in separate isthmic nuclei, facilitating the analysis of the neural processes that mediate competition. A specific subset of radial neurons in the intermediate tectal layers relay retinal inputs to the isthmi, but at present it is unclear whether separate neurons innervate individual nuclei or a single neural type sends a common input to several of them. In this study, we used in vitro neural tracing and cell-filling experiments in chickens to show that single neurons innervate, via axon collaterals, the three nuclei that comprise the isthmotectal network. This demonstrates that the input signals representing the strength of the incoming stimuli are simultaneously relayed to the mechanisms promoting both enhancement and suppression of the input signals. By performing in vivo recordings in anesthetized chicks, we also show that this common input generates synchrony between both antagonistic mechanisms, demonstrating that activity enhancement and suppression are closely coordinated. From a computational point of view, these results suggest that these tectal neurons constitute integrative nodes that combine inputs from different sources to drive in parallel several concurrent neural processes, each performing complementary functions within the network through different firing patterns and connectivity.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","month":"08","page":"E7615-E7623","date_created":"2019-02-14T14:33:34Z","volume":115,"status":"public","external_id":{"isi":["000440982000020"],"pmid":["30026198"]},"citation":{"ieee":"F. Garrido-Charad <i>et al.</i>, ““Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 32. National Academy of Sciences, pp. E7615–E7623, 2018.","chicago":"Garrido-Charad, Florencia, Tomas A Vega Zuniga, Cristián Gutiérrez-Ibáñez, Pedro Fernandez, Luciana López-Jury, Cristian González-Cabrera, Harvey J. Karten, Harald Luksch, and Gonzalo J. Marín. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1804517115\">https://doi.org/10.1073/pnas.1804517115</a>.","short":"F. Garrido-Charad, T.A. Vega Zuniga, C. Gutiérrez-Ibáñez, P. Fernandez, L. López-Jury, C. González-Cabrera, H.J. Karten, H. Luksch, G.J. Marín, Proceedings of the National Academy of Sciences 115 (2018) E7615–E7623.","ama":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, et al. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(32):E7615-E7623. doi:<a href=\"https://doi.org/10.1073/pnas.1804517115\">10.1073/pnas.1804517115</a>","ista":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, Fernandez P, López-Jury L, González-Cabrera C, Karten HJ, Luksch H, Marín GJ. 2018. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 115(32), E7615–E7623.","mla":"Garrido-Charad, Florencia, et al. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 32, National Academy of Sciences, 2018, pp. E7615–23, doi:<a href=\"https://doi.org/10.1073/pnas.1804517115\">10.1073/pnas.1804517115</a>.","apa":"Garrido-Charad, F., Vega Zuniga, T. A., Gutiérrez-Ibáñez, C., Fernandez, P., López-Jury, L., González-Cabrera, C., … Marín, G. J. (2018). “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1804517115\">https://doi.org/10.1073/pnas.1804517115</a>"},"intvolume":"       115","publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30026198"}],"date_published":"2018-08-07T00:00:00Z"},{"volume":115,"date_created":"2019-03-19T12:41:33Z","file_date_updated":"2020-07-14T12:47:19Z","page":"E6890-E6899","type":"journal_article","month":"07","oa_version":"Published Version","date_updated":"2021-01-12T08:06:09Z","abstract":[{"text":"Neuropeptides are ubiquitous modulators of behavior and physiology. They are packaged in specialized secretory organelles called dense core vesicles (DCVs) that are released upon neural stimulation. Unlike synaptic vesicles, which can be recycled and refilled close to release sites, DCVs must be replenished by de novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in a Caenorhabditis elegans sensory neuron whose tonic activity we can control using a natural stimulus. We express fluorescently tagged neuropeptides in the neuron and define parameters that describe their subcellular distribution. We measure these parameters at high and low neural activity in 187 mutants defective in proteins implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic activity. Using unsupervised hierarchical clustering methods, we analyze these data and identify 62 groups of genes with similar mutant phenotypes. We explore the function of a subset of these groups. We recapitulate many previous findings, validating our paradigm. We uncover a large battery of proteins involved in recycling DCV membrane proteins, something hitherto poorly explored. We show that the unfolded protein response promotes DCV production, which may contribute to intertissue communication of stress. We also find evidence that different mechanisms of priming and exocytosis may operate at high and low neural activity. Our work provides a defined framework to study DCV biology at different neural activity levels.","lang":"eng"}],"_id":"6109","year":"2018","ddc":["570"],"date_published":"2018-07-17T00:00:00Z","publication_status":"published","oa":1,"has_accepted_license":"1","extern":"1","intvolume":"       115","citation":{"ista":"Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. 2018. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 115(29), E6890–E6899.","mla":"Laurent, Patrick, et al. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 29, National Academy of Sciences, 2018, pp. E6890–99, doi:<a href=\"https://doi.org/10.1073/pnas.1714610115\">10.1073/pnas.1714610115</a>.","apa":"Laurent, P., Ch’ng, Q., Jospin, M., Chen, C., Lorenzo, R., &#38; de Bono, M. (2018). Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1714610115\">https://doi.org/10.1073/pnas.1714610115</a>","ama":"Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(29):E6890-E6899. doi:<a href=\"https://doi.org/10.1073/pnas.1714610115\">10.1073/pnas.1714610115</a>","short":"P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, M. de Bono, Proceedings of the National Academy of Sciences 115 (2018) E6890–E6899.","ieee":"P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, and M. de Bono, “Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 29. National Academy of Sciences, pp. E6890–E6899, 2018.","chicago":"Laurent, Patrick, QueeLim Ch’ng, Maëlle Jospin, Changchun Chen, Ramiro Lorenzo, and Mario de Bono. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1714610115\">https://doi.org/10.1073/pnas.1714610115</a>."},"status":"public","external_id":{"pmid":["29959203"]},"title":"Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron","author":[{"last_name":"Laurent","first_name":"Patrick","full_name":"Laurent, Patrick"},{"full_name":"Ch’ng, QueeLim","first_name":"QueeLim","last_name":"Ch’ng"},{"full_name":"Jospin, Maëlle","first_name":"Maëlle","last_name":"Jospin"},{"last_name":"Chen","first_name":"Changchun","full_name":"Chen, Changchun"},{"last_name":"Lorenzo","first_name":"Ramiro","full_name":"Lorenzo, Ramiro"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","first_name":"Mario","last_name":"de Bono"}],"day":"17","file":[{"creator":"kschuh","file_size":1567765,"content_type":"application/pdf","relation":"main_file","file_name":"2018_PNAS_Laurent.pdf","access_level":"open_access","date_created":"2019-03-19T13:01:58Z","checksum":"5e81665377441cdd8d99ab952c534319","file_id":"6110","date_updated":"2020-07-14T12:47:19Z"}],"publication":"Proceedings of the National Academy of Sciences","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","pmid":1,"doi":"10.1073/pnas.1714610115","quality_controlled":"1","publication_identifier":{"issn":["0027-8424","1091-6490"]},"issue":"29","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"Efficient molecular switching in confined spaces is critical for the successful development of artificial molecular machines. However, molecular switching events often entail large structural changes and therefore require conformational freedom, which is typically limited under confinement conditions. Here, we investigated the behavior of azobenzene—the key building block of light-controlled molecular machines—in a confined environment that is flexible and can adapt its shape to that of the bound guest. To this end, we encapsulated several structurally diverse azobenzenes within the cavity of a flexible, water-soluble coordination cage, and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy and a combination of NMR methods, we showed that each of the encapsulated azobenzenes exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest inclusion complex could be efficiently photoisomerized in a reversible fashion. In contrast, successful switching in inclusion complexes incorporating two azobenzene guests was dependent on the availability of free cages in the system, and it involved reversible trafficking of azobenzene between the cages. In the absence of extra cages, photoswitching was either suppressed or it involved expulsion of azobenzene from the cage and consequently its precipitation from the solution. This finding was utilized to develop an information storage medium in which messages could be written and erased in a reversible fashion using light."}],"date_updated":"2023-08-07T10:58:11Z","month":"05","oa_version":"Published Version","type":"journal_article","page":"9379-9384","date_created":"2023-08-01T09:40:00Z","volume":115,"year":"2018","_id":"13376","oa":1,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1712787115"}],"date_published":"2018-05-01T00:00:00Z","external_id":{"pmid":["29717041"]},"status":"public","citation":{"short":"D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L.J.W. Shimon, R. Klajn, Proceedings of the National Academy of Sciences 115 (2018) 9379–9384.","chicago":"Samanta, Dipak, Julius Gemen, Zonglin Chu, Yael Diskin-Posner, Linda J. W. Shimon, and Rafal Klajn. “Reversible Photoswitching of Encapsulated Azobenzenes in Water.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1712787115\">https://doi.org/10.1073/pnas.1712787115</a>.","ieee":"D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L. J. W. Shimon, and R. Klajn, “Reversible photoswitching of encapsulated azobenzenes in water,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 38. Proceedings of the National Academy of Sciences, pp. 9379–9384, 2018.","apa":"Samanta, D., Gemen, J., Chu, Z., Diskin-Posner, Y., Shimon, L. J. W., &#38; Klajn, R. (2018). Reversible photoswitching of encapsulated azobenzenes in water. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1712787115\">https://doi.org/10.1073/pnas.1712787115</a>","ista":"Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. 2018. Reversible photoswitching of encapsulated azobenzenes in water. Proceedings of the National Academy of Sciences. 115(38), 9379–9384.","mla":"Samanta, Dipak, et al. “Reversible Photoswitching of Encapsulated Azobenzenes in Water.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 38, Proceedings of the National Academy of Sciences, 2018, pp. 9379–84, doi:<a href=\"https://doi.org/10.1073/pnas.1712787115\">10.1073/pnas.1712787115</a>.","ama":"Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. Reversible photoswitching of encapsulated azobenzenes in water. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(38):9379-9384. doi:<a href=\"https://doi.org/10.1073/pnas.1712787115\">10.1073/pnas.1712787115</a>"},"intvolume":"       115","extern":"1","day":"01","author":[{"full_name":"Samanta, Dipak","last_name":"Samanta","first_name":"Dipak"},{"full_name":"Gemen, Julius","first_name":"Julius","last_name":"Gemen"},{"last_name":"Chu","first_name":"Zonglin","full_name":"Chu, Zonglin"},{"full_name":"Diskin-Posner, Yael","last_name":"Diskin-Posner","first_name":"Yael"},{"full_name":"Shimon, Linda J. W.","first_name":"Linda J. W.","last_name":"Shimon"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal"}],"title":"Reversible photoswitching of encapsulated azobenzenes in water","pmid":1,"publisher":"Proceedings of the National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","scopus_import":"1","article_type":"original","publication":"Proceedings of the National Academy of Sciences","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"quality_controlled":"1","doi":"10.1073/pnas.1712787115","language":[{"iso":"eng"}],"issue":"38","keyword":["Multidisciplinary"]},{"language":[{"iso":"eng"}],"issue":"12","keyword":["Multidisciplinary"],"quality_controlled":"1","doi":"10.1073/pnas.1719967115","publication_identifier":{"issn":["0027-8424","1091-6490"]},"article_processing_charge":"No","article_type":"original","publication":"Proceedings of the National Academy of Sciences","publisher":"Proceedings of the National Academy of Sciences","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Acceleration of tropical cyclogenesis by self-aggregation feedbacks","day":"20","author":[{"first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"},{"last_name":"Romps","first_name":"David M.","full_name":"Romps, David M."}],"citation":{"ista":"Muller CJ, Romps DM. 2018. Acceleration of tropical cyclogenesis by self-aggregation feedbacks. Proceedings of the National Academy of Sciences. 115(12), 2930–2935.","mla":"Muller, Caroline J., and David M. Romps. “Acceleration of Tropical Cyclogenesis by Self-Aggregation Feedbacks.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 12, Proceedings of the National Academy of Sciences, 2018, pp. 2930–35, doi:<a href=\"https://doi.org/10.1073/pnas.1719967115\">10.1073/pnas.1719967115</a>.","apa":"Muller, C. J., &#38; Romps, D. M. (2018). Acceleration of tropical cyclogenesis by self-aggregation feedbacks. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1719967115\">https://doi.org/10.1073/pnas.1719967115</a>","ama":"Muller CJ, Romps DM. Acceleration of tropical cyclogenesis by self-aggregation feedbacks. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(12):2930-2935. doi:<a href=\"https://doi.org/10.1073/pnas.1719967115\">10.1073/pnas.1719967115</a>","short":"C.J. Muller, D.M. Romps, Proceedings of the National Academy of Sciences 115 (2018) 2930–2935.","ieee":"C. J. Muller and D. M. Romps, “Acceleration of tropical cyclogenesis by self-aggregation feedbacks,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 12. Proceedings of the National Academy of Sciences, pp. 2930–2935, 2018.","chicago":"Muller, Caroline J, and David M. Romps. “Acceleration of Tropical Cyclogenesis by Self-Aggregation Feedbacks.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1719967115\">https://doi.org/10.1073/pnas.1719967115</a>."},"extern":"1","intvolume":"       115","status":"public","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1719967115","open_access":"1"}],"date_published":"2018-03-20T00:00:00Z","oa":1,"publication_status":"published","_id":"9135","year":"2018","date_created":"2021-02-15T14:18:16Z","volume":115,"date_updated":"2022-01-24T12:39:49Z","abstract":[{"text":"Idealized simulations of tropical moist convection have revealed that clouds can spontaneously clump together in a process called self-aggregation. This results in a state where a moist cloudy region with intense deep convection is surrounded by extremely dry subsiding air devoid of deep convection. Because of the idealized settings of the simulations where it was discovered, the relevance of self-aggregation to the real world is still debated. Here, we show that self-aggregation feedbacks play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving simulations. Those feedbacks accelerate the cyclogenesis process by a factor of 2, and the feedbacks contributing to the cyclone formation show qualitative and quantitative agreement with the self-aggregation process. Once the cyclone is formed, wind-induced surface heat exchange (WISHE) effects dominate, although we find that self-aggregation feedbacks have a small but nonnegligible contribution to the maintenance of the mature cyclone. Our results suggest that self-aggregation, and the framework developed for its study, can help shed more light into the physical processes leading to cyclogenesis and cyclone intensification. In particular, our results point out the importance of the longwave radiative cooling outside the cyclone.","lang":"eng"}],"type":"journal_article","month":"03","oa_version":"Published Version","page":"2930-2935"},{"volume":115,"date_created":"2021-06-07T06:11:28Z","file_date_updated":"2021-06-07T06:16:38Z","page":"E4720-E4729","month":"05","type":"journal_article","oa_version":"Published Version","date_updated":"2021-12-14T07:53:40Z","abstract":[{"lang":"eng","text":"The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin."}],"_id":"9471","year":"2018","ddc":["580"],"date_published":"2018-05-15T00:00:00Z","oa":1,"publication_status":"published","has_accepted_license":"1","extern":"1","related_material":{"link":[{"url":"https://doi.org/10.1101/187674 ","relation":"earlier_version"}]},"intvolume":"       115","citation":{"apa":"Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>","ista":"Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729.","mla":"Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>.","ama":"Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(20):E4720-E4729. doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>","short":"J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729.","chicago":"Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>.","ieee":"J. M. Frost <i>et al.</i>, “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018."},"status":"public","external_id":{"pmid":["29712855"]},"title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","author":[{"full_name":"Frost, Jennifer M.","last_name":"Frost","first_name":"Jennifer M."},{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"full_name":"Park, Guen Tae","last_name":"Park","first_name":"Guen Tae"},{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"last_name":"Nakamura","first_name":"Miyuki","full_name":"Nakamura, Miyuki"},{"full_name":"Lin, Samuel J. H.","first_name":"Samuel J. H.","last_name":"Lin"},{"full_name":"Yoo, Hyunjin","first_name":"Hyunjin","last_name":"Yoo"},{"full_name":"Choi, Jaemyung","last_name":"Choi","first_name":"Jaemyung"},{"full_name":"Ikeda, Yoko","last_name":"Ikeda","first_name":"Yoko"},{"full_name":"Kinoshita, Tetsu","last_name":"Kinoshita","first_name":"Tetsu"},{"first_name":"Yeonhee","last_name":"Choi","full_name":"Choi, Yeonhee"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"}],"day":"15","file":[{"file_id":"9472","date_updated":"2021-06-07T06:16:38Z","checksum":"810260dc0e3cc3033e15c19ad0dc123e","date_created":"2021-06-07T06:16:38Z","access_level":"open_access","file_name":"2018_PNAS_Frost.pdf","success":1,"file_size":3045260,"content_type":"application/pdf","relation":"main_file","creator":"asandaue"}],"publication":"Proceedings of the National Academy of Sciences","article_type":"original","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_processing_charge":"No","scopus_import":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"pmid":1,"doi":"10.1073/pnas.1713333115","quality_controlled":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"keyword":["Multidisciplinary"],"issue":"20","language":[{"iso":"eng"}]},{"title":"Aspect controls the survival of ice cliffs on debris-covered glaciers","day":"09","author":[{"full_name":"Buri, Pascal","first_name":"Pascal","last_name":"Buri"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","first_name":"Francesca","last_name":"Pellicciotti"}],"article_processing_charge":"No","scopus_import":"1","article_type":"original","publication":"PNAS","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","doi":"10.1073/pnas.1713892115","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"issue":"17","date_created":"2023-02-20T08:13:41Z","volume":115,"abstract":[{"text":"Supraglacial ice cliffs exist on debris-covered glaciers worldwide, but despite their importance as melt hot spots, their life cycle is little understood. Early field observations had advanced a hypothesis of survival of north-facing and disappearance of south-facing cliffs, which is central for predicting the contribution of cliffs to total glacier mass losses. Their role as windows of energy transfer suggests they may explain the anomalously high mass losses of debris-covered glaciers in High Mountain Asia (HMA) despite the insulating debris, currently at the center of a debated controversy. We use a 3D model of cliff evolution coupled to very high-resolution topographic data to demonstrate that ice cliffs facing south (in the Northern Hemisphere) disappear within a few months due to enhanced solar radiation receipts and that aspect is the key control on cliffs evolution. We reproduce continuous flattening of south-facing cliffs, a result of their vertical gradient of incoming solar radiation and sky view factor. Our results establish that only north-facing cliffs are recurrent features and thus stable contributors to the melting of debris-covered glaciers. Satellite observations and mass balance modeling confirms that few south-facing cliffs of small size exist on the glaciers of Langtang, and their contribution to the glacier volume losses is very small (∼1%). This has major implications for the mass balance of HMA debris-covered glaciers as it provides the basis for new parameterizations of cliff evolution and distribution to constrain volume losses in a region where glaciers are highly relevant as water sources for millions of people.","lang":"eng"}],"date_updated":"2023-02-28T11:35:18Z","month":"04","oa_version":"Published Version","type":"journal_article","page":"4369-4374","_id":"12607","year":"2018","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1713892115","open_access":"1"}],"date_published":"2018-04-09T00:00:00Z","oa":1,"publication_status":"published","citation":{"ama":"Buri P, Pellicciotti F. Aspect controls the survival of ice cliffs on debris-covered glaciers. <i>PNAS</i>. 2018;115(17):4369-4374. doi:<a href=\"https://doi.org/10.1073/pnas.1713892115\">10.1073/pnas.1713892115</a>","apa":"Buri, P., &#38; Pellicciotti, F. (2018). Aspect controls the survival of ice cliffs on debris-covered glaciers. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713892115\">https://doi.org/10.1073/pnas.1713892115</a>","mla":"Buri, Pascal, and Francesca Pellicciotti. “Aspect Controls the Survival of Ice Cliffs on Debris-Covered Glaciers.” <i>PNAS</i>, vol. 115, no. 17, Proceedings of the National Academy of Sciences, 2018, pp. 4369–74, doi:<a href=\"https://doi.org/10.1073/pnas.1713892115\">10.1073/pnas.1713892115</a>.","ista":"Buri P, Pellicciotti F. 2018. Aspect controls the survival of ice cliffs on debris-covered glaciers. PNAS. 115(17), 4369–4374.","chicago":"Buri, Pascal, and Francesca Pellicciotti. “Aspect Controls the Survival of Ice Cliffs on Debris-Covered Glaciers.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1713892115\">https://doi.org/10.1073/pnas.1713892115</a>.","ieee":"P. Buri and F. Pellicciotti, “Aspect controls the survival of ice cliffs on debris-covered glaciers,” <i>PNAS</i>, vol. 115, no. 17. Proceedings of the National Academy of Sciences, pp. 4369–4374, 2018.","short":"P. Buri, F. Pellicciotti, PNAS 115 (2018) 4369–4374."},"extern":"1","intvolume":"       115","status":"public"},{"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.1701812114","quality_controlled":"1","issue":"26","language":[{"iso":"eng"}],"author":[{"full_name":"Barron, Helen C.","last_name":"Barron","first_name":"Helen C."},{"last_name":"Vogels","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"},{"full_name":"Behrens, Timothy E.","first_name":"Timothy E.","last_name":"Behrens"},{"full_name":"Ramaswami, Mani","first_name":"Mani","last_name":"Ramaswami"}],"day":"27","title":"Inhibitory engrams in perception and memory","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"Proceedings of the National Academy of Sciences","pmid":1,"publication":"Proceedings of the National Academy of Sciences","article_type":"original","article_processing_charge":"No","oa":1,"publication_status":"published","date_published":"2017-06-27T00:00:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495250/","open_access":"1"}],"status":"public","external_id":{"pmid":["28611219"]},"extern":"1","intvolume":"       114","citation":{"ieee":"H. C. Barron, T. P. Vogels, T. E. Behrens, and M. Ramaswami, “Inhibitory engrams in perception and memory,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 26. Proceedings of the National Academy of Sciences, pp. 6666–6674, 2017.","chicago":"Barron, Helen C., Tim P Vogels, Timothy E. Behrens, and Mani Ramaswami. “Inhibitory Engrams in Perception and Memory.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1701812114\">https://doi.org/10.1073/pnas.1701812114</a>.","short":"H.C. Barron, T.P. Vogels, T.E. Behrens, M. Ramaswami, Proceedings of the National Academy of Sciences 114 (2017) 6666–6674.","ama":"Barron HC, Vogels TP, Behrens TE, Ramaswami M. Inhibitory engrams in perception and memory. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(26):6666-6674. doi:<a href=\"https://doi.org/10.1073/pnas.1701812114\">10.1073/pnas.1701812114</a>","mla":"Barron, Helen C., et al. “Inhibitory Engrams in Perception and Memory.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 26, Proceedings of the National Academy of Sciences, 2017, pp. 6666–74, doi:<a href=\"https://doi.org/10.1073/pnas.1701812114\">10.1073/pnas.1701812114</a>.","ista":"Barron HC, Vogels TP, Behrens TE, Ramaswami M. 2017. Inhibitory engrams in perception and memory. Proceedings of the National Academy of Sciences. 114(26), 6666–6674.","apa":"Barron, H. C., Vogels, T. P., Behrens, T. E., &#38; Ramaswami, M. (2017). Inhibitory engrams in perception and memory. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1701812114\">https://doi.org/10.1073/pnas.1701812114</a>"},"page":"6666-6674","type":"journal_article","oa_version":"Published Version","month":"06","abstract":[{"text":"Nervous systems use excitatory cell assemblies to encode and represent sensory percepts. Similarly, synaptically connected cell assemblies or \"engrams\" are thought to represent memories of past experience. Multiple lines of recent evidence indicate that brain systems create and use inhibitory replicas of excitatory representations for important cognitive functions. Such matched \"inhibitory engrams\" can form through homeostatic potentiation of inhibition onto postsynaptic cells that show increased levels of excitation. Inhibitory engrams can reduce behavioral responses to familiar stimuli, thereby resulting in behavioral habituation. In addition, by preventing inappropriate activation of excitatory memory engrams, inhibitory engrams can make memories quiescent, stored in a latent form that is available for context-relevant activation. In neural networks with balanced excitatory and inhibitory engrams, the release of innate responses and recall of associative memories can occur through focused disinhibition. Understanding mechanisms that regulate the formation and expression of inhibitory engrams in vivo may help not only to explain key features of cognition but also to provide insight into transdiagnostic traits associated with psychiatric conditions such as autism, schizophrenia, and posttraumatic stress disorder. ","lang":"eng"}],"date_updated":"2021-01-12T08:16:33Z","volume":114,"date_created":"2020-06-25T12:56:58Z","year":"2017","_id":"8018"},{"quality_controlled":"1","doi":"10.1073/pnas.1621096114","date_published":"2017-08-08T00:00:00Z","publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]},"language":[{"iso":"eng"}],"citation":{"ieee":"L. Yengo <i>et al.</i>, “Detection and quantification of inbreeding depression for complex traits from SNP data,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 32. Proceedings of the National Academy of Sciences, pp. 8602–8607, 2017.","chicago":"Yengo, Loic, Zhihong Zhu, Naomi R. Wray, Bruce S. Weir, Jian Yang, Matthew Richard Robinson, and Peter M. Visscher. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1621096114\">https://doi.org/10.1073/pnas.1621096114</a>.","short":"L. Yengo, Z. Zhu, N.R. Wray, B.S. Weir, J. Yang, M.R. Robinson, P.M. Visscher, Proceedings of the National Academy of Sciences 114 (2017) 8602–8607.","ama":"Yengo L, Zhu Z, Wray NR, et al. Detection and quantification of inbreeding depression for complex traits from SNP data. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(32):8602-8607. doi:<a href=\"https://doi.org/10.1073/pnas.1621096114\">10.1073/pnas.1621096114</a>","mla":"Yengo, Loic, et al. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 32, Proceedings of the National Academy of Sciences, 2017, pp. 8602–07, doi:<a href=\"https://doi.org/10.1073/pnas.1621096114\">10.1073/pnas.1621096114</a>.","ista":"Yengo L, Zhu Z, Wray NR, Weir BS, Yang J, Robinson MR, Visscher PM. 2017. Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. 114(32), 8602–8607.","apa":"Yengo, L., Zhu, Z., Wray, N. R., Weir, B. S., Yang, J., Robinson, M. R., &#38; Visscher, P. M. (2017). Detection and quantification of inbreeding depression for complex traits from SNP data. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1621096114\">https://doi.org/10.1073/pnas.1621096114</a>"},"issue":"32","extern":"1","related_material":{"link":[{"relation":"other","url":"https://doi.org/10.1073/pnas.1718598115"}]},"intvolume":"       114","status":"public","date_created":"2020-04-30T10:47:19Z","volume":114,"title":"Detection and quantification of inbreeding depression for complex traits from SNP data","day":"08","abstract":[{"lang":"eng","text":"Quantifying the effects of inbreeding is critical to characterizing the genetic architecture of complex traits. This study highlights through theory and simulations the strengths and shortcomings of three SNP-based inbreeding measures commonly used to estimate inbreeding depression (ID). We demonstrate that heterogeneity in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates, and we develop an approach to correct this bias using LD and minor allele frequency stratified inference (LDMS). We quantified ID in 25 traits measured in ∼140,000 participants of the UK Biobank, using LDMS, and confirmed previously published ID for 4 traits. We find unique evidence of ID for handgrip strength, waist/hip ratio, and visual and auditory acuity (ID between −2.3 and −5.2 phenotypic SDs for complete inbreeding; P<0.001). Our results illustrate that a careful choice of the measure of inbreeding combined with LDMS stratification improves both detection and quantification of ID using SNP data."}],"date_updated":"2021-01-12T08:15:09Z","oa_version":"None","month":"08","type":"journal_article","page":"8602-8607","author":[{"full_name":"Yengo, Loic","last_name":"Yengo","first_name":"Loic"},{"last_name":"Zhu","first_name":"Zhihong","full_name":"Zhu, Zhihong"},{"full_name":"Wray, Naomi R.","last_name":"Wray","first_name":"Naomi R."},{"last_name":"Weir","first_name":"Bruce S.","full_name":"Weir, Bruce S."},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"},{"last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."}],"article_processing_charge":"No","article_type":"original","publication":"Proceedings of the National Academy of Sciences","_id":"7729","year":"2017","publisher":"Proceedings of the National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Proceedings of the National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","publication":"Proceedings of the National Academy of Sciences","_id":"7757","article_processing_charge":"No","article_type":"original","author":[{"last_name":"Rocks","first_name":"Jason W.","full_name":"Rocks, Jason W."},{"first_name":"Nidhi","last_name":"Pashine","full_name":"Pashine, Nidhi"},{"full_name":"Bischofberger, Irmgard","last_name":"Bischofberger","first_name":"Irmgard"},{"first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"first_name":"Andrea J.","last_name":"Liu","full_name":"Liu, Andrea J."},{"first_name":"Sidney R.","last_name":"Nagel","full_name":"Nagel, Sidney R."}],"page":"2520-2525","abstract":[{"lang":"eng","text":"Recent advances in designing metamaterials have demonstrated that global mechanical properties of disordered spring networks can be tuned by selectively modifying only a small subset of bonds. Here, using a computationally efficient approach, we extend this idea to tune more general properties of networks. With nearly complete success, we are able to produce a strain between any two target nodes in a network in response to an applied source strain on any other pair of nodes by removing only ∼1% of the bonds. We are also able to control multiple pairs of target nodes, each with a different individual response, from a single source, and to tune multiple independent source/target responses simultaneously into a network. We have fabricated physical networks in macroscopic 2D and 3D systems that exhibit these responses. This work is inspired by the long-range coupled conformational changes that constitute allosteric function in proteins. The fact that allostery is a common means for regulation in biological molecules suggests that it is a relatively easy property to develop through evolution. In analogy, our results show that long-range coupled mechanical responses are similarly easy to achieve in disordered networks."}],"date_updated":"2021-01-12T08:15:19Z","day":"07","oa_version":"None","type":"journal_article","month":"03","title":"Designing allostery-inspired response in mechanical networks","volume":114,"date_created":"2020-04-30T11:38:53Z","status":"public","intvolume":"       114","extern":"1","citation":{"apa":"Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2017). Designing allostery-inspired response in mechanical networks. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1612139114\">https://doi.org/10.1073/pnas.1612139114</a>","mla":"Rocks, Jason W., et al. “Designing Allostery-Inspired Response in Mechanical Networks.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 10, Proceedings of the National Academy of Sciences, 2017, pp. 2520–25, doi:<a href=\"https://doi.org/10.1073/pnas.1612139114\">10.1073/pnas.1612139114</a>.","ista":"Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. 2017. Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. 114(10), 2520–2525.","ama":"Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. Designing allostery-inspired response in mechanical networks. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(10):2520-2525. doi:<a href=\"https://doi.org/10.1073/pnas.1612139114\">10.1073/pnas.1612139114</a>","short":"J.W. Rocks, N. Pashine, I. Bischofberger, C.P. Goodrich, A.J. Liu, S.R. Nagel, Proceedings of the National Academy of Sciences 114 (2017) 2520–2525.","chicago":"Rocks, Jason W., Nidhi Pashine, Irmgard Bischofberger, Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Designing Allostery-Inspired Response in Mechanical Networks.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1612139114\">https://doi.org/10.1073/pnas.1612139114</a>.","ieee":"J. W. Rocks, N. Pashine, I. Bischofberger, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Designing allostery-inspired response in mechanical networks,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 10. Proceedings of the National Academy of Sciences, pp. 2520–2525, 2017."},"language":[{"iso":"eng"}],"issue":"10","publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]},"date_published":"2017-03-07T00:00:00Z","doi":"10.1073/pnas.1612139114","quality_controlled":"1"},{"year":"2017","publisher":"Proceedings of the National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","article_type":"original","publication":"Proceedings of the National Academy of Sciences","_id":"7758","date_updated":"2021-01-12T08:15:20Z","day":"10","abstract":[{"lang":"eng","text":"Controlling motion at the microscopic scale is a fundamental goal in the development of biologically inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the 2D motion of active colloids so that their path has a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics simulations that, when the colloids are attached to long semiflexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that nonequilibrium assembly pathways can be designed using active particles."}],"oa_version":"None","month":"01","type":"journal_article","page":"257-262","author":[{"first_name":"Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter"},{"last_name":"Brenner","first_name":"Michael P.","full_name":"Brenner, Michael P."}],"date_created":"2020-04-30T11:39:09Z","title":"Using active colloids as machines to weave and braid on the micrometer scale","volume":114,"status":"public","language":[{"iso":"eng"}],"citation":{"ama":"Goodrich CP, Brenner MP. Using active colloids as machines to weave and braid on the micrometer scale. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(2):257-262. doi:<a href=\"https://doi.org/10.1073/pnas.1608838114\">10.1073/pnas.1608838114</a>","apa":"Goodrich, C. P., &#38; Brenner, M. P. (2017). Using active colloids as machines to weave and braid on the micrometer scale. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1608838114\">https://doi.org/10.1073/pnas.1608838114</a>","mla":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 2, Proceedings of the National Academy of Sciences, 2017, pp. 257–62, doi:<a href=\"https://doi.org/10.1073/pnas.1608838114\">10.1073/pnas.1608838114</a>.","ista":"Goodrich CP, Brenner MP. 2017. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 114(2), 257–262.","chicago":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1608838114\">https://doi.org/10.1073/pnas.1608838114</a>.","ieee":"C. P. Goodrich and M. P. Brenner, “Using active colloids as machines to weave and braid on the micrometer scale,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 2. Proceedings of the National Academy of Sciences, pp. 257–262, 2017.","short":"C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences 114 (2017) 257–262."},"issue":"2","extern":"1","intvolume":"       114","publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]},"quality_controlled":"1","date_published":"2017-01-10T00:00:00Z","doi":"10.1073/pnas.1608838114"},{"date_published":"2017-06-06T00:00:00Z","ddc":["570"],"publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":"       114","extern":"1","citation":{"short":"S. Oda, Y. Toyoshima, M. de Bono, Proceedings of the National Academy of Sciences 114 (2017) E4658–E4665.","ieee":"S. Oda, Y. Toyoshima, and M. de Bono, “Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 23. National Academy of Sciences, pp. E4658–E4665, 2017.","chicago":"Oda, Shigekazu, Yu Toyoshima, and Mario de Bono. “Modulation of Sensory Information Processing by a Neuroglobin in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1614596114\">https://doi.org/10.1073/pnas.1614596114</a>.","mla":"Oda, Shigekazu, et al. “Modulation of Sensory Information Processing by a Neuroglobin in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 23, National Academy of Sciences, 2017, pp. E4658–65, doi:<a href=\"https://doi.org/10.1073/pnas.1614596114\">10.1073/pnas.1614596114</a>.","ista":"Oda S, Toyoshima Y, de Bono M. 2017. Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 114(23), E4658–E4665.","apa":"Oda, S., Toyoshima, Y., &#38; de Bono, M. (2017). Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1614596114\">https://doi.org/10.1073/pnas.1614596114</a>","ama":"Oda S, Toyoshima Y, de Bono M. Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(23):E4658-E4665. doi:<a href=\"https://doi.org/10.1073/pnas.1614596114\">10.1073/pnas.1614596114</a>"},"external_id":{"pmid":["28536200"]},"status":"public","volume":114,"file_date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-19T13:29:51Z","page":"E4658-E4665","date_updated":"2021-01-12T08:06:11Z","type":"journal_article","month":"06","oa_version":"Published Version","_id":"6113","year":"2017","doi":"10.1073/pnas.1614596114","quality_controlled":"1","publication_identifier":{"issn":["0027-8424","1091-6490"]},"language":[{"iso":"eng"}],"issue":"23","title":"Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans","author":[{"last_name":"Oda","first_name":"Shigekazu","full_name":"Oda, Shigekazu"},{"first_name":"Yu","last_name":"Toyoshima","full_name":"Toyoshima, Yu"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario"}],"file":[{"access_level":"open_access","date_created":"2019-03-19T13:42:58Z","checksum":"9e42ce47090ecdad7d76f2dbdebb924e","file_id":"6114","date_updated":"2020-07-14T12:47:19Z","creator":"kschuh","file_size":1469622,"content_type":"application/pdf","relation":"main_file","file_name":"2017_PNAS_Oda.pdf"}],"day":"06","publication":"Proceedings of the National Academy of Sciences","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","pmid":1},{"quality_controlled":"1","doi":"10.1073/pnas.1618934114","publication_identifier":{"issn":["0027-8424","1091-6490"]},"issue":"16","language":[{"iso":"eng"}],"title":"Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans","day":"18","file":[{"creator":"kschuh","file_size":1217696,"content_type":"application/pdf","relation":"main_file","file_name":"2017_PNAS_Fenk.pdf","access_level":"open_access","date_created":"2019-03-19T14:00:42Z","checksum":"1801bc8319b752fa17598004ec375279","file_id":"6116","date_updated":"2020-07-14T12:47:20Z"}],"author":[{"full_name":"Fenk, Lorenz A.","last_name":"Fenk","first_name":"Lorenz A."},{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"de Bono"}],"publication":"Proceedings of the National Academy of Sciences","pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","date_published":"2017-04-18T00:00:00Z","ddc":["570"],"has_accepted_license":"1","oa":1,"publication_status":"published","citation":{"chicago":"Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches Pheromone Valence InCaenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1618934114\">https://doi.org/10.1073/pnas.1618934114</a>.","ieee":"L. A. Fenk and M. de Bono, “Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 16. National Academy of Sciences, pp. 4195–4200, 2017.","short":"L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 114 (2017) 4195–4200.","ama":"Fenk LA, de Bono M. Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(16):4195-4200. doi:<a href=\"https://doi.org/10.1073/pnas.1618934114\">10.1073/pnas.1618934114</a>","apa":"Fenk, L. A., &#38; de Bono, M. (2017). Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1618934114\">https://doi.org/10.1073/pnas.1618934114</a>","mla":"Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches Pheromone Valence InCaenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 16, National Academy of Sciences, 2017, pp. 4195–200, doi:<a href=\"https://doi.org/10.1073/pnas.1618934114\">10.1073/pnas.1618934114</a>.","ista":"Fenk LA, de Bono M. 2017. Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences. 114(16), 4195–4200."},"extern":"1","intvolume":"       114","external_id":{"pmid":["28373553"]},"status":"public","date_created":"2019-03-19T13:46:36Z","file_date_updated":"2020-07-14T12:47:20Z","volume":114,"month":"04","type":"journal_article","oa_version":"Published Version","date_updated":"2021-01-12T08:06:11Z","abstract":[{"lang":"eng","text":"Animals adjust their behavioral priorities according to momentary needs and prior experience. We show that Caenorhabditis elegans changes how it processes sensory information according to the oxygen environment it experienced recently. C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2 levels. A sustained change in the activity of O2-sensing neurons reprograms the properties of their postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggest C. elegans stores a memory of recent O2 experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner."}],"page":"4195-4200","_id":"6115","year":"2017"},{"date_created":"2021-11-29T09:28:24Z","volume":114,"month":"04","oa_version":"Published Version","type":"journal_article","date_updated":"2021-11-29T09:59:12Z","abstract":[{"lang":"eng","text":"Electric charges are conserved. The same would be expected to hold for magnetic charges, yet magnetic monopoles have never been observed. It is therefore surprising that the laws of nonequilibrium thermodynamics, combined with Maxwell’s equations, suggest that colloidal particles heated or cooled in certain polar or paramagnetic solvents may behave as if they carry an electric/magnetic charge. Here, we present numerical simulations that show that the field distribution around a pair of such heated/cooled colloidal particles agrees quantitatively with the theoretical predictions for a pair of oppositely charged electric or magnetic monopoles. However, in other respects, the nonequilibrium colloidal particles do not behave as monopoles: They cannot be moved by a homogeneous applied field. The numerical evidence for the monopole-like fields around heated/cooled colloidal particles is crucial because the experimental and numerical determination of forces between such colloidal particles would be complicated by the presence of other effects, such as thermophoresis."}],"page":"4911-4914","_id":"10373","year":"2017","acknowledgement":"P.W. acknowledges many invaluable discussions with Martin Neumann, Chao Zhang, Michiel Sprik, Aleks Reinhardt, Carl Pölking, and Tine Curk. We acknowledge financial support from the Austrian Academy of Sciences through a doctoral (DOC) fellowship (to P.W.), the Austrian Science Fund (FWF) within the Spezialforschungsbereich Vienna Computational Materials Laboratory (Project F41) (C.D.), and the European Union Early Training Network NANOTRANS (Grant 674979 to D. Frenkel). The results presented here have been achieved in part using the Vienna Scientific Cluster.","main_file_link":[{"url":"https://www.pnas.org/content/114/19/4911","open_access":"1"}],"date_published":"2017-04-24T00:00:00Z","publication_status":"published","oa":1,"citation":{"ama":"Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. Numerical evidence for thermally induced monopoles. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(19):4911-4914. doi:<a href=\"https://doi.org/10.1073/pnas.1621494114\">10.1073/pnas.1621494114</a>","mla":"Wirnsberger, Peter, et al. “Numerical Evidence for Thermally Induced Monopoles.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 19, National Academy of Sciences, 2017, pp. 4911–14, doi:<a href=\"https://doi.org/10.1073/pnas.1621494114\">10.1073/pnas.1621494114</a>.","ista":"Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. 2017. Numerical evidence for thermally induced monopoles. Proceedings of the National Academy of Sciences. 114(19), 4911–4914.","apa":"Wirnsberger, P., Fijan, D., Lightwood, R. A., Šarić, A., Dellago, C., &#38; Frenkel, D. (2017). Numerical evidence for thermally induced monopoles. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1621494114\">https://doi.org/10.1073/pnas.1621494114</a>","ieee":"P. Wirnsberger, D. Fijan, R. A. Lightwood, A. Šarić, C. Dellago, and D. Frenkel, “Numerical evidence for thermally induced monopoles,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 19. National Academy of Sciences, pp. 4911–4914, 2017.","chicago":"Wirnsberger, Peter, Domagoj Fijan, Roger A. Lightwood, Anđela Šarić, Christoph Dellago, and Daan Frenkel. “Numerical Evidence for Thermally Induced Monopoles.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1621494114\">https://doi.org/10.1073/pnas.1621494114</a>.","short":"P. Wirnsberger, D. Fijan, R.A. Lightwood, A. Šarić, C. Dellago, D. Frenkel, Proceedings of the National Academy of Sciences 114 (2017) 4911–4914."},"extern":"1","intvolume":"       114","status":"public","external_id":{"pmid":["28439003"],"arxiv":["1610.06840"]},"arxiv":1,"title":"Numerical evidence for thermally induced monopoles","day":"24","author":[{"first_name":"Peter","last_name":"Wirnsberger","full_name":"Wirnsberger, Peter"},{"first_name":"Domagoj","last_name":"Fijan","full_name":"Fijan, Domagoj"},{"full_name":"Lightwood, Roger A.","first_name":"Roger A.","last_name":"Lightwood"},{"last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Dellago","first_name":"Christoph","full_name":"Dellago, Christoph"},{"first_name":"Daan","last_name":"Frenkel","full_name":"Frenkel, Daan"}],"article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"National Academy of Sciences","quality_controlled":"1","doi":"10.1073/pnas.1621494114","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"issue":"19","language":[{"iso":"eng"}],"keyword":["multidisciplinary"]},{"extern":"1","intvolume":"       113","issue":"41","language":[{"iso":"eng"}],"citation":{"ieee":"C. D. A. Rodrigues <i>et al.</i>, “A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 41. National Academy of Sciences, pp. 11585–11590, 2016.","chicago":"Rodrigues, Christopher D. A., Xavier Henry, Emmanuelle Neumann, Vilius Kurauskas, Laure Bellard, Yann Fichou, Paul Schanda, Guy Schoehn, David Z. Rudner, and Cecile Morlot. “A Ring-Shaped Conduit Connects the Mother Cell and Forespore during Sporulation in Bacillus Subtilis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1609604113\">https://doi.org/10.1073/pnas.1609604113</a>.","short":"C.D.A. Rodrigues, X. Henry, E. Neumann, V. Kurauskas, L. Bellard, Y. Fichou, P. Schanda, G. Schoehn, D.Z. Rudner, C. Morlot, Proceedings of the National Academy of Sciences 113 (2016) 11585–11590.","ama":"Rodrigues CDA, Henry X, Neumann E, et al. A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(41):11585-11590. doi:<a href=\"https://doi.org/10.1073/pnas.1609604113\">10.1073/pnas.1609604113</a>","ista":"Rodrigues CDA, Henry X, Neumann E, Kurauskas V, Bellard L, Fichou Y, Schanda P, Schoehn G, Rudner DZ, Morlot C. 2016. A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. Proceedings of the National Academy of Sciences. 113(41), 11585–11590.","mla":"Rodrigues, Christopher D. A., et al. “A Ring-Shaped Conduit Connects the Mother Cell and Forespore during Sporulation in Bacillus Subtilis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 41, National Academy of Sciences, 2016, pp. 11585–90, doi:<a href=\"https://doi.org/10.1073/pnas.1609604113\">10.1073/pnas.1609604113</a>.","apa":"Rodrigues, C. D. A., Henry, X., Neumann, E., Kurauskas, V., Bellard, L., Fichou, Y., … Morlot, C. (2016). A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1609604113\">https://doi.org/10.1073/pnas.1609604113</a>"},"status":"public","date_published":"2016-09-28T00:00:00Z","doi":"10.1073/pnas.1609604113","quality_controlled":"1","publication_identifier":{"issn":["0027-8424","1091-6490"]},"publication_status":"published","_id":"8452","publication":"Proceedings of the National Academy of Sciences","article_type":"original","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","year":"2016","title":"A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis","volume":113,"date_created":"2020-09-18T10:06:58Z","author":[{"first_name":"Christopher D. A.","last_name":"Rodrigues","full_name":"Rodrigues, Christopher D. A."},{"first_name":"Xavier","last_name":"Henry","full_name":"Henry, Xavier"},{"last_name":"Neumann","first_name":"Emmanuelle","full_name":"Neumann, Emmanuelle"},{"first_name":"Vilius","last_name":"Kurauskas","full_name":"Kurauskas, Vilius"},{"last_name":"Bellard","first_name":"Laure","full_name":"Bellard, Laure"},{"first_name":"Yann","last_name":"Fichou","full_name":"Fichou, Yann"},{"first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"Guy","last_name":"Schoehn","full_name":"Schoehn, Guy"},{"full_name":"Rudner, David Z.","last_name":"Rudner","first_name":"David Z."},{"full_name":"Morlot, Cecile","first_name":"Cecile","last_name":"Morlot"}],"page":"11585-11590","type":"journal_article","month":"09","oa_version":"None","date_updated":"2021-01-12T08:19:22Z","abstract":[{"text":"During spore formation in Bacillus subtilis a transenvelope complex is assembled across the double membrane that separates the mother cell and forespore. This complex (called the “A–Q complex”) is required to maintain forespore development and is composed of proteins with remote homology to components of type II, III, and IV secretion systems found in Gram-negative bacteria. Here, we show that one of these proteins, SpoIIIAG, which has remote homology to ring-forming proteins found in type III secretion systems, assembles into an oligomeric ring in the periplasmic-like space between the two membranes. Three-dimensional reconstruction of images generated by cryo-electron microscopy indicates that the SpoIIIAG ring has a cup-and-saucer architecture with a 6-nm central pore. Structural modeling of SpoIIIAG generated a 24-member ring with dimensions similar to those of the EM-derived saucer. Point mutations in the predicted oligomeric interface disrupted ring formation in vitro and impaired forespore gene expression and efficient spore formation in vivo. Taken together, our data provide strong support for the model in which the A–Q transenvelope complex contains a conduit that connects the mother cell and forespore. We propose that a set of stacked rings spans the intermembrane space, as has been found for type III secretion systems.","lang":"eng"}],"day":"28"},{"doi":"10.1073/pnas.1601858113","date_published":"2016-08-30T00:00:00Z","quality_controlled":"1","publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]},"extern":"1","intvolume":"       113","citation":{"ama":"Goodrich CP, Liu AJ, Sethna JP. Scaling ansatz for the jamming transition. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(35):9745-9750. doi:<a href=\"https://doi.org/10.1073/pnas.1601858113\">10.1073/pnas.1601858113</a>","ista":"Goodrich CP, Liu AJ, Sethna JP. 2016. Scaling ansatz for the jamming transition. Proceedings of the National Academy of Sciences. 113(35), 9745–9750.","mla":"Goodrich, Carl Peter, et al. “Scaling Ansatz for the Jamming Transition.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 35, Proceedings of the National Academy of Sciences, 2016, pp. 9745–50, doi:<a href=\"https://doi.org/10.1073/pnas.1601858113\">10.1073/pnas.1601858113</a>.","apa":"Goodrich, C. P., Liu, A. J., &#38; Sethna, J. P. (2016). Scaling ansatz for the jamming transition. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1601858113\">https://doi.org/10.1073/pnas.1601858113</a>","ieee":"C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Scaling ansatz for the jamming transition,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 35. Proceedings of the National Academy of Sciences, pp. 9745–9750, 2016.","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and James P. Sethna. “Scaling Ansatz for the Jamming Transition.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1601858113\">https://doi.org/10.1073/pnas.1601858113</a>.","short":"C.P. Goodrich, A.J. Liu, J.P. Sethna, Proceedings of the National Academy of Sciences 113 (2016) 9745–9750."},"language":[{"iso":"eng"}],"issue":"35","status":"public","title":"Scaling ansatz for the jamming transition","volume":113,"date_created":"2020-04-30T11:39:53Z","page":"9745-9750","author":[{"first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"last_name":"Sethna","first_name":"James P.","full_name":"Sethna, James P."}],"date_updated":"2021-01-12T08:15:21Z","abstract":[{"text":"We propose a Widom-like scaling ansatz for the critical jamming transition. Our ansatz for the elastic energy shows that the scaling of the energy, compressive strain, shear strain, system size, pressure, shear stress, bulk modulus, and shear modulus are all related to each other via scaling relations, with only three independent scaling exponents. We extract the values of these exponents from already known numerical or theoretical results, and we numerically verify the resulting predictions of the scaling theory for the energy and residual shear stress. We also derive a scaling relation between pressure and residual shear stress that yields insight into why the shear and bulk moduli scale differently. Our theory shows that the jamming transition exhibits an emergent scale invariance, setting the stage for the potential development of a renormalization group theory for jamming.","lang":"eng"}],"day":"30","type":"journal_article","month":"08","oa_version":"None","publication":"Proceedings of the National Academy of Sciences","_id":"7760","article_processing_charge":"No","article_type":"original","publisher":"Proceedings of the National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016"},{"_id":"14304","year":"2016","volume":113,"date_created":"2023-09-06T12:53:48Z","page":"E7456-E7463","type":"journal_article","month":"10","oa_version":"Published Version","abstract":[{"text":"Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there still exist ample opportunities for improvement in sample preparation. Macromolecular complexes may disassociate or adopt nonrandom orientations against the extended air–water interface that exists for a short time before the sample is frozen. We designed a hollow support structure using 3D DNA origami to protect complexes from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle, we concentrated on the transcription factor p53, which binds to specific DNA sequences on double-stranded DNA. The support structures spontaneously form monolayers of preoriented particles in a thin film of water, and offer advantages in particle picking and sorting. By controlling the position of the binding sequence on a single helix that spans the hollow support structure, we also sought to control the orientation of individual p53 complexes. Although the latter did not yet yield the desired results, the support structures did provide partial information about the relative orientations of individual p53 complexes. We used this information to calculate a tomographic 3D reconstruction, and refined this structure to a final resolution of ∼15 Å. This structure settles an ongoing debate about the symmetry of the p53 tetramer bound to DNA.","lang":"eng"}],"date_updated":"2023-11-07T11:53:06Z","extern":"1","intvolume":"       113","citation":{"ieee":"T. G. Martin <i>et al.</i>, “Design of a molecular support for cryo-EM structure determination,” <i>PNAS</i>, vol. 113, no. 47. Proceedings of the National Academy of Sciences, pp. E7456–E7463, 2016.","chicago":"Martin, Thomas G., Tanmay A. M. Bharat, Andreas C. Joerger, Xiao-chen Bai, Florian M Praetorius, Alan R. Fersht, Hendrik Dietz, and Sjors H. W. Scheres. “Design of a Molecular Support for Cryo-EM Structure Determination.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1612720113\">https://doi.org/10.1073/pnas.1612720113</a>.","short":"T.G. Martin, T.A.M. Bharat, A.C. Joerger, X. Bai, F.M. Praetorius, A.R. Fersht, H. Dietz, S.H.W. Scheres, PNAS 113 (2016) E7456–E7463.","ama":"Martin TG, Bharat TAM, Joerger AC, et al. Design of a molecular support for cryo-EM structure determination. <i>PNAS</i>. 2016;113(47):E7456-E7463. doi:<a href=\"https://doi.org/10.1073/pnas.1612720113\">10.1073/pnas.1612720113</a>","ista":"Martin TG, Bharat TAM, Joerger AC, Bai X, Praetorius FM, Fersht AR, Dietz H, Scheres SHW. 2016. Design of a molecular support for cryo-EM structure determination. PNAS. 113(47), E7456–E7463.","mla":"Martin, Thomas G., et al. “Design of a Molecular Support for Cryo-EM Structure Determination.” <i>PNAS</i>, vol. 113, no. 47, Proceedings of the National Academy of Sciences, 2016, pp. E7456–63, doi:<a href=\"https://doi.org/10.1073/pnas.1612720113\">10.1073/pnas.1612720113</a>.","apa":"Martin, T. G., Bharat, T. A. M., Joerger, A. C., Bai, X., Praetorius, F. M., Fersht, A. R., … Scheres, S. H. W. (2016). Design of a molecular support for cryo-EM structure determination. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1612720113\">https://doi.org/10.1073/pnas.1612720113</a>"},"status":"public","external_id":{"pmid":["27821763"]},"date_published":"2016-10-13T00:00:00Z","publication_status":"published","publication":"PNAS","article_type":"original","scopus_import":"1","article_processing_charge":"No","publisher":"Proceedings of the National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"title":"Design of a molecular support for cryo-EM structure determination","author":[{"full_name":"Martin, Thomas G.","last_name":"Martin","first_name":"Thomas G."},{"first_name":"Tanmay A. M.","last_name":"Bharat","full_name":"Bharat, Tanmay A. M."},{"last_name":"Joerger","first_name":"Andreas C.","full_name":"Joerger, Andreas C."},{"last_name":"Bai","first_name":"Xiao-chen","full_name":"Bai, Xiao-chen"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","first_name":"Florian M","last_name":"Praetorius"},{"first_name":"Alan R.","last_name":"Fersht","full_name":"Fersht, Alan R."},{"full_name":"Dietz, Hendrik","last_name":"Dietz","first_name":"Hendrik"},{"full_name":"Scheres, Sjors H. W.","last_name":"Scheres","first_name":"Sjors H. W."}],"day":"13","issue":"47","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1612720113","quality_controlled":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]}},{"oa":1,"publication_status":"published","date_published":"2016-12-27T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619074114"}],"external_id":{"pmid":["27956643"]},"status":"public","intvolume":"       113","extern":"1","citation":{"short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>.","ieee":"P.-H. Hsieh <i>et al.</i>, “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016.","apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>.","ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137.","ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15132-15137. doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>"},"page":"15132-15137","date_updated":"2023-05-08T11:00:40Z","abstract":[{"lang":"eng","text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations."}],"type":"journal_article","month":"12","oa_version":"Published Version","volume":113,"date_created":"2021-06-07T06:21:39Z","year":"2016","_id":"9473","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.1619074114","quality_controlled":"1","language":[{"iso":"eng"}],"issue":"52","author":[{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"full_name":"He, Shengbo","first_name":"Shengbo","last_name":"He"},{"full_name":"Buttress, Toby","first_name":"Toby","last_name":"Buttress"},{"full_name":"Gao, Hongbo","first_name":"Hongbo","last_name":"Gao"},{"full_name":"Couchman, Matthew","last_name":"Couchman","first_name":"Matthew"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"}],"day":"27","title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","pmid":1,"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","scopus_import":"1","article_type":"original"}]