--- _id: '9049' abstract: - lang: eng text: 'Diffusiophoretic motion of colloids and macromolecules under salt gradients exhibits a logarithmic-sensing, i.e. the particle velocity is proportional to the spatial gradient of the logarithm of the salt concentration, as VDP = DDP∇logc. Here we explore experimentally the implications of this log-sensing behavior, on the basis of a hydrogel microfluidic device allowing to build spatially and temporally controlled gradients. We first demonstrate that the non-linearity of the salt-taxis leads to a trapping of particles under concentration gradient oscillations via a rectification of the motion. As an alternative, we make use of the high sensitivity of diffusiophoretic migration to vanishing salt concentration due to the log-sensing: in a counter-intuitive way, a vanishing gradient can lead to measurable velocity provided that the solute concentration is low enough, thus keeping ∇c/c finite. We show that this leads to a strong segregation of particles in osmotic shock configuration, resulting from a step change of the salt concentration at the boundaries. These various phenomena are rationalized on the basis of a theoretical description for the time-dependent Smoluchowski equation for the colloidal density.' article_processing_charge: No article_type: original author: - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Cécile full_name: Cottin-Bizonne, Cécile last_name: Cottin-Bizonne - first_name: Christophe full_name: Ybert, Christophe last_name: Ybert - first_name: Lydéric full_name: Bocquet, Lydéric last_name: Bocquet citation: ama: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 2012;8(4):980-994. doi:10.1039/c1sm06395b apa: Palacci, J. A., Cottin-Bizonne, C., Ybert, C., & Bocquet, L. (2012). Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c1sm06395b chicago: Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter. Royal Society of Chemistry, 2012. https://doi.org/10.1039/c1sm06395b. ieee: J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis,” Soft Matter, vol. 8, no. 4. Royal Society of Chemistry, pp. 980–994, 2012. ista: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2012. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 8(4), 980–994. mla: Palacci, Jérémie A., et al. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter, vol. 8, no. 4, Royal Society of Chemistry, 2012, pp. 980–94, doi:10.1039/c1sm06395b. short: J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Soft Matter 8 (2012) 980–994. date_created: 2021-02-01T13:43:10Z date_published: 2012-01-28T00:00:00Z date_updated: 2023-02-23T13:47:31Z day: '28' doi: 10.1039/c1sm06395b extern: '1' intvolume: ' 8' issue: '4' language: - iso: eng month: '01' oa_version: None page: 980-994 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 8 year: '2012' ... --- _id: '922' abstract: - lang: eng 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.' article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jacques full_name: Prost, Jacques last_name: Prost - first_name: Jean full_name: Joanny, Jean last_name: Joanny 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 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 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. 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. ista: Hannezo EB, Prost J, Joanny J. 2012. Mechanical instabilities of biological tubes. Physical Review Letters. 109(1). 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). date_created: 2018-12-11T11:49:13Z date_published: 2012-07-03T00:00:00Z date_updated: 2021-01-12T08:21:56Z day: '03' doi: 10.1103/PhysRevLett.109.018101 extern: '1' external_id: arxiv: - '1207.1516' intvolume: ' 109' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1207.1516 month: '07' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6519' status: public title: Mechanical instabilities of biological tubes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2012' ... --- _id: '9499' 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. article_number: e1002512 article_processing_charge: No article_type: original author: - first_name: Sang Yeol full_name: Kim, Sang Yeol last_name: Kim - first_name: Jungeun full_name: Lee, Jungeun last_name: Lee - first_name: Leor full_name: Eshed-Williams, Leor last_name: Eshed-Williams - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Z. Renee full_name: Sung, Z. Renee last_name: Sung 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 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. 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. 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. short: S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012). date_created: 2021-06-07T11:07:56Z date_published: 2012-03-22T00:00:00Z date_updated: 2021-12-14T08:31:14Z day: '22' department: - _id: DaZi doi: 10.1371/journal.pgen.1002512 extern: '1' external_id: pmid: - '22457632' intvolume: ' 8' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pgen.1002512 month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: eissn: - 1553-7404 issn: - 1553-7390 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 8 year: '2012' ... --- _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. article_number: e1002988 article_processing_charge: No article_type: original author: - first_name: Devin full_name: Coleman-Derr, Devin last_name: Coleman-Derr - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: 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 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 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. 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. ista: Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988. 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). date_created: 2021-06-07T10:55:27Z date_published: 2012-10-11T00:00:00Z date_updated: 2021-12-14T08:29:57Z day: '11' department: - _id: DaZi doi: 10.1371/journal.pgen.1002988 extern: '1' external_id: pmid: - '23071449' intvolume: ' 8' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pgen.1002988 month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: eissn: - 1553-7404 issn: - 1553-7390 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Deposition of histone variant H2A.Z within gene bodies regulates responsive genes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 8 year: '2012' ... --- _id: '9528' abstract: - lang: eng 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. article_processing_charge: No article_type: review author: - first_name: Jason T. full_name: Huff, Jason T. last_name: Huff - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 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 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 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. 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. 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. 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. short: J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138. date_created: 2021-06-08T08:58:52Z date_published: 2012-04-01T00:00:00Z date_updated: 2021-12-14T08:32:38Z department: - _id: DaZi doi: 10.1016/j.gde.2012.01.007 extern: '1' external_id: pmid: - '22336527' intvolume: ' 22' issue: '2' language: - iso: eng month: '04' oa_version: None page: 132-138 pmid: 1 publication: Current Opinion in Genetics and Development publication_identifier: issn: - 0959-437X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Regulation of biological accuracy, precision, and memory by plant chromatin organization type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 22 year: '2012' ... --- _id: '966' abstract: - lang: eng 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. 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). author: - first_name: Samuel full_name: Bieri, Samuel last_name: Bieri - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Todadri full_name: Senthil, Todadri S last_name: Senthil - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: 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 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 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. 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. 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). 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). date_created: 2018-12-11T11:49:27Z date_published: 2012-12-13T00:00:00Z date_updated: 2021-01-12T08:22:18Z day: '13' doi: 10.1103/PhysRevB.86.224409 extern: 1 intvolume: ' 86' issue: '22' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1208.3231 month: '12' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6431' quality_controlled: 0 status: public title: Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice type: journal_article volume: 86 year: '2012' ... --- _id: '2968' abstract: - lang: eng text: Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and-using triplet alignments of intronic loci-quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. © 2012 Blackwell Publishing Ltd. acknowledgement: "This work was supported by funding from the UK Natural Environment Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1, NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on earlier versions of the manuscript. " author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: George full_name: Melika, George last_name: Melika - first_name: Graham full_name: Stone, Graham last_name: Stone citation: ama: Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 2012;21(18):4605-4617. doi:10.1111/j.1365-294X.2012.05700.x apa: Lohse, K., Barton, N. H., Melika, G., & Stone, G. (2012). A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05700.x chicago: Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05700.x. ieee: K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison of population histories in a parasitoid guild,” Molecular Ecology, vol. 21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012. ista: Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617. mla: Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology, vol. 21, no. 18, Wiley-Blackwell, 2012, pp. 4605–17, doi:10.1111/j.1365-294X.2012.05700.x. short: K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617. date_created: 2018-12-11T12:00:36Z date_published: 2012-09-01T00:00:00Z date_updated: 2023-05-30T13:07:47Z day: '01' ddc: - '570' - '579' department: - _id: NiBa doi: 10.1111/j.1365-294X.2012.05700.x ec_funded: 1 file: - access_level: open_access checksum: c14ee4cb2a8ba9575bfd8a9bb7a883bb content_type: application/pdf creator: system date_created: 2018-12-12T10:17:47Z date_updated: 2020-07-14T12:45:57Z file_id: '5304' file_name: IST-2014-296-v1+1_4_wasps_revised3.pdf file_size: 235820 relation: main_file - access_level: open_access checksum: f00afc5b887c8222014b57375b8caece content_type: application/pdf creator: system date_created: 2018-12-12T10:17:48Z date_updated: 2020-07-14T12:45:57Z file_id: '5305' file_name: IST-2014-296-v1+2_4_wasps_Supporting2.pdf file_size: 41975 relation: main_file file_date_updated: 2020-07-14T12:45:57Z has_accepted_license: '1' intvolume: ' 21' issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 4605 - 4617 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3746' pubrep_id: '296' quality_controlled: '1' related_material: record: - id: '13075' relation: research_data status: public scopus_import: 1 status: public title: A likelihood based comparison of population histories in a parasitoid guild type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2012' ... --- _id: '13075' abstract: - lang: eng text: Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. article_processing_charge: No author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Graham full_name: Stone, Graham last_name: Stone - first_name: George full_name: Melika, George last_name: Melika citation: ama: 'Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:10.5061/DRYAD.0G0FS' apa: 'Lohse, K., Barton, N. H., Stone, G., & Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. https://doi.org/10.5061/DRYAD.0G0FS' chicago: 'Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. https://doi.org/10.5061/DRYAD.0G0FS.' ieee: 'K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012.' ista: 'Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, 10.5061/DRYAD.0G0FS.' mla: 'Lohse, Konrad, et al. Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild. Dryad, 2012, doi:10.5061/DRYAD.0G0FS.' short: K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012). date_created: 2023-05-23T17:01:02Z date_published: 2012-06-08T00:00:00Z date_updated: 2023-05-30T13:07:48Z day: '08' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.0G0FS license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.0g0fs month: '06' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2968' relation: used_in_publication status: public status: public title: 'Data from: A likelihood-based comparison of population histories in a parasitoid guild' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '13407' abstract: - lang: eng text: We show that diamagnetic particles can be remotely manipulated by a magnet by the reversible adsorption of dual-responsive, light-switchable/superparamagnetic nanoparticles down to their surface. Adsorption occurs upon exposure to UV light, and can be reversed thermally or by ambient light. The dynamic self-assembly of thin films of the dual-responsive nanoparticles induces attractive interactions between diamagnetic particles. We demonstrate that catalytic amounts of the dual-responsive nanoparticles are sufficient to magnetically guide and deliver the diamagnetic particles to desired locations, where they can then be released by disassembling the dynamic layers of superparamagnetic nanoparticles with visible light. article_processing_charge: No article_type: original author: - first_name: Olga full_name: Chovnik, Olga last_name: Chovnik - first_name: Renata full_name: Balgley, Renata last_name: Balgley - first_name: Joel R. full_name: Goldman, Joel R. last_name: Goldman - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Chovnik O, Balgley R, Goldman JR, Klajn R. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. 2012;134(48):19564-19567. doi:10.1021/ja309633v apa: Chovnik, O., Balgley, R., Goldman, J. R., & Klajn, R. (2012). Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja309633v chicago: Chovnik, Olga, Renata Balgley, Joel R. Goldman, and Rafal Klajn. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja309633v. ieee: O. Chovnik, R. Balgley, J. R. Goldman, and R. Klajn, “Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets,” Journal of the American Chemical Society, vol. 134, no. 48. American Chemical Society, pp. 19564–19567, 2012. ista: Chovnik O, Balgley R, Goldman JR, Klajn R. 2012. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. 134(48), 19564–19567. mla: Chovnik, Olga, et al. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” Journal of the American Chemical Society, vol. 134, no. 48, American Chemical Society, 2012, pp. 19564–67, doi:10.1021/ja309633v. short: O. Chovnik, R. Balgley, J.R. Goldman, R. Klajn, Journal of the American Chemical Society 134 (2012) 19564–19567. date_created: 2023-08-01T09:47:42Z date_published: 2012-11-26T00:00:00Z date_updated: 2023-08-08T07:51:10Z day: '26' doi: 10.1021/ja309633v extern: '1' external_id: pmid: - '23181449' intvolume: ' 134' issue: '48' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '11' oa_version: Published Version page: 19564-19567 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '13408' abstract: - lang: eng text: Well-defined metallic nanobowls can be prepared by extending the concept of a protecting group to colloidal synthesis. Magnetic nanoparticles are employed as “protecting groups” during the galvanic replacement of silver with gold. The replacement reaction is accompanied by spontantous dissociation of the protecting groups, leaving behind metallic nanobowls. article_processing_charge: No article_type: original author: - first_name: Yonatan full_name: Ridelman, Yonatan last_name: Ridelman - first_name: Gurvinder full_name: Singh, Gurvinder last_name: Singh - first_name: Ronit full_name: Popovitz-Biro, Ronit last_name: Popovitz-Biro - first_name: Sharon G. full_name: Wolf, Sharon G. last_name: Wolf - first_name: Sanjib full_name: Das, Sanjib last_name: Das - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 2012;8(5):654-660. doi:10.1002/smll.201101882 apa: Ridelman, Y., Singh, G., Popovitz-Biro, R., Wolf, S. G., Das, S., & Klajn, R. (2012). Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. Wiley. https://doi.org/10.1002/smll.201101882 chicago: Ridelman, Yonatan, Gurvinder Singh, Ronit Popovitz-Biro, Sharon G. Wolf, Sanjib Das, and Rafal Klajn. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small. Wiley, 2012. https://doi.org/10.1002/smll.201101882. ieee: Y. Ridelman, G. Singh, R. Popovitz-Biro, S. G. Wolf, S. Das, and R. Klajn, “Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles,” Small, vol. 8, no. 5. Wiley, pp. 654–660, 2012. ista: Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. 2012. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 8(5), 654–660. mla: Ridelman, Yonatan, et al. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small, vol. 8, no. 5, Wiley, 2012, pp. 654–60, doi:10.1002/smll.201101882. short: Y. Ridelman, G. Singh, R. Popovitz-Biro, S.G. Wolf, S. Das, R. Klajn, Small 8 (2012) 654–660. date_created: 2023-08-01T09:47:55Z date_published: 2012-03-12T00:00:00Z date_updated: 2023-08-08T07:55:10Z day: '12' doi: 10.1002/smll.201101882 extern: '1' external_id: pmid: - '22392681' intvolume: ' 8' issue: '5' keyword: - Biomaterials - Biotechnology - General Materials Science - General Chemistry language: - iso: eng month: '03' oa_version: None page: 654-660 pmid: 1 publication: Small publication_identifier: eissn: - 1613-6829 issn: - 1613-6810 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2012' ...