[{"abstract":[{"text":"We study theoretically the morphologies of biological tubes affected by various pathologies. When epithelial cells grow, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated: varicose, dilated, sinuous, or sausagelike. They are all found in pathologies of tracheal, renal tubes, or arteries. The final shape depends crucially on the mechanical parameters of the tissues: Young's modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation.","lang":"eng"}],"issue":"1","publist_id":"6519","extern":"1","type":"journal_article","author":[{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"first_name":"Jacques","last_name":"Prost","full_name":"Prost, Jacques"},{"full_name":"Joanny, Jean","first_name":"Jean","last_name":"Joanny"}],"date_created":"2018-12-11T11:49:13Z","date_updated":"2021-01-12T08:21:56Z","oa_version":"Preprint","volume":109,"year":"2012","_id":"922","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mechanical instabilities of biological tubes","status":"public","publication_status":"published","intvolume":" 109","publisher":"American Physical Society","month":"07","day":"03","article_processing_charge":"No","doi":"10.1103/PhysRevLett.109.018101","date_published":"2012-07-03T00:00:00Z","language":[{"iso":"eng"}],"publication":"Physical Review Letters","citation":{"ama":"Hannezo EB, Prost J, Joanny J. Mechanical instabilities of biological tubes. Physical Review Letters. 2012;109(1). doi:10.1103/PhysRevLett.109.018101","ista":"Hannezo EB, Prost J, Joanny J. 2012. Mechanical instabilities of biological tubes. Physical Review Letters. 109(1).","apa":"Hannezo, E. B., Prost, J., & Joanny, J. (2012). Mechanical instabilities of biological tubes. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.018101","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Mechanical instabilities of biological tubes,” Physical Review Letters, vol. 109, no. 1. American Physical Society, 2012.","mla":"Hannezo, Edouard B., et al. “Mechanical Instabilities of Biological Tubes.” Physical Review Letters, vol. 109, no. 1, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.018101.","short":"E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 109 (2012).","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Mechanical Instabilities of Biological Tubes.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.018101."},"oa":1,"external_id":{"arxiv":["1207.1516"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1207.1516"}]},{"type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9499","intvolume":" 8","title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","status":"public","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"22","citation":{"ama":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3). doi:10.1371/journal.pgen.1002512","apa":"Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., & Sung, Z. R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002512","ieee":"S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development,” PLoS Genetics, vol. 8, no. 3. Public Library of Science, 2012.","ista":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 8(3), e1002512.","short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012).","mla":"Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics, vol. 8, no. 3, e1002512, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002512.","chicago":"Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512."},"publication":"PLoS Genetics","article_type":"original","date_published":"2012-03-22T00:00:00Z","article_number":"e1002512","extern":"1","pmid":1,"year":"2012","department":[{"_id":"DaZi"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"last_name":"Kim","first_name":"Sang Yeol","full_name":"Kim, Sang Yeol"},{"full_name":"Lee, Jungeun","first_name":"Jungeun","last_name":"Lee"},{"last_name":"Eshed-Williams","first_name":"Leor","full_name":"Eshed-Williams, Leor"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"},{"full_name":"Sung, Z. Renee","last_name":"Sung","first_name":"Z. Renee"}],"volume":8,"date_updated":"2021-12-14T08:31:14Z","date_created":"2021-06-07T11:07:56Z","publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"month":"03","oa":1,"external_id":{"pmid":["22457632"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1002512"}],"quality_controlled":"1","doi":"10.1371/journal.pgen.1002512","language":[{"iso":"eng"}]},{"oa_version":"Published Version","status":"public","title":"Deposition of histone variant H2A.Z within gene bodies regulates responsive genes","intvolume":" 8","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9497","abstract":[{"lang":"eng","text":"The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes."}],"issue":"10","type":"journal_article","date_published":"2012-10-11T00:00:00Z","article_type":"original","publication":"PLoS Genetics","citation":{"mla":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002988.","short":"D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).","chicago":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988.","ama":"Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988","ista":"Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988.","apa":"Coleman-Derr, D., & Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002988","ieee":"D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” PLoS Genetics, vol. 8, no. 10. Public Library of Science, 2012."},"day":"11","article_processing_charge":"No","scopus_import":"1","date_created":"2021-06-07T10:55:27Z","date_updated":"2021-12-14T08:29:57Z","volume":8,"author":[{"full_name":"Coleman-Derr, Devin","first_name":"Devin","last_name":"Coleman-Derr"},{"last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"publication_status":"published","department":[{"_id":"DaZi"}],"publisher":"Public Library of Science","year":"2012","pmid":1,"extern":"1","article_number":"e1002988","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1002988","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1002988"}],"external_id":{"pmid":["23071449"]},"oa":1,"month":"10","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]}},{"author":[{"full_name":"Huff, Jason T.","first_name":"Jason T.","last_name":"Huff"},{"last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"volume":22,"date_updated":"2021-12-14T08:32:38Z","date_created":"2021-06-08T08:58:52Z","pmid":1,"year":"2012","publisher":"Elsevier","department":[{"_id":"DaZi"}],"publication_status":"published","extern":"1","doi":"10.1016/j.gde.2012.01.007","language":[{"iso":"eng"}],"external_id":{"pmid":["22336527"]},"quality_controlled":"1","publication_identifier":{"issn":["0959-437X"]},"month":"04","oa_version":"None","_id":"9528","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 22","status":"public","title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization","issue":"2","abstract":[{"text":"Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory.","lang":"eng"}],"type":"journal_article","date_published":"2012-04-01T00:00:00Z","citation":{"ama":"Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007","ieee":"J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” Current Opinion in Genetics and Development, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.","apa":"Huff, J. T., & Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2012.01.007","ista":"Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 22(2), 132–138.","short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138.","mla":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:10.1016/j.gde.2012.01.007.","chicago":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007."},"publication":"Current Opinion in Genetics and Development","page":"132-138","article_type":"review","article_processing_charge":"No","scopus_import":"1"},{"month":"12","day":"13","date_published":"2012-12-13T00:00:00Z","doi":"10.1103/PhysRevB.86.224409","quality_controlled":0,"citation":{"chicago":"Bieri, Samuel, Maksym Serbyn, Todadri Senthil, and Patrick Lee. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2012. https://doi.org/10.1103/PhysRevB.86.224409.","mla":"Bieri, Samuel, et al. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22, American Physical Society, 2012, doi:10.1103/PhysRevB.86.224409.","short":"S. Bieri, M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 86 (2012).","ista":"Bieri S, Serbyn M, Senthil T, Lee P. 2012. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 86(22).","ieee":"S. Bieri, M. Serbyn, T. Senthil, and P. Lee, “Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice,” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22. American Physical Society, 2012.","apa":"Bieri, S., Serbyn, M., Senthil, T., & Lee, P. (2012). Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.86.224409","ama":"Bieri S, Serbyn M, Senthil T, Lee P. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 2012;86(22). doi:10.1103/PhysRevB.86.224409"},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1208.3231","open_access":"1"}],"publication":"Physical Review B - Condensed Matter and Materials Physics","extern":1,"issue":"22","publist_id":"6431","abstract":[{"text":"Motivated by recent experiments on Ba3NiSb2O 9, we investigate possible quantum spin liquid ground states for spin S=1 Heisenberg models on the triangular lattice. We use variational Monte Carlo techniques to calculate the energies of microscopic spin liquid wave functions where spin is represented by three flavors of fermionic spinon operators. These energies are compared with the energies of various competing three-sublattice ordered states. Our approach shows that the antiferromagnetic Heisenberg model with biquadratic term and single-ion anisotropy does not have a low-temperature spin liquid phase. However, for an SU(3)-invariant model with sufficiently strong ring-exchange terms, we find a paired chiral quantum spin liquid with a Fermi surface of deconfined spinons that is stable against all types of ordering patterns we considered. We discuss the physics of this exotic spin liquid state in relation to the recent experiment and suggest new ways to test this scenario.","lang":"eng"}],"type":"journal_article","volume":86,"date_updated":"2021-01-12T08:22:18Z","date_created":"2018-12-11T11:49:27Z","author":[{"full_name":"Bieri, Samuel","first_name":"Samuel","last_name":"Bieri"},{"full_name":"Maksym Serbyn","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"full_name":"Senthil, Todadri S","first_name":"Todadri","last_name":"Senthil"},{"last_name":"Lee","first_name":"Patrick","full_name":"Lee, Patrick"}],"publisher":"American Physical Society","intvolume":" 86","publication_status":"published","title":"Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice","status":"public","_id":"966","year":"2012","acknowledgement":"We thank Kuang-Ting Chen, Rebecca Flint, Dmitri Ivanov, Z.-X. Liu, Tai-Kai Ng, Lara Thompson, Tamás Tóth, and Fa Wang for helpful discussions. T.S. is supported by NSF DMR 1005434. P.A.L. is supported by NSF DMR 1104498. S.B. acknowledges support from the Swiss National Science Foundation (SNSF)."}]