[{"citation":{"chicago":"Rennella, Enrico, Thomas Cutuil, Paul Schanda, Isabel Ayala, Vincent Forge, and Bernhard Brutscher. “Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja302598j.","ista":"Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. 2012. Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. 134(19), 8066–8069.","mla":"Rennella, Enrico, et al. “Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate.” Journal of the American Chemical Society, vol. 134, no. 19, American Chemical Society, 2012, pp. 8066–69, doi:10.1021/ja302598j.","ama":"Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. 2012;134(19):8066-8069. doi:10.1021/ja302598j","apa":"Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Forge, V., & Brutscher, B. (2012). Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja302598j","ieee":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, and B. Brutscher, “Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate,” Journal of the American Chemical Society, vol. 134, no. 19. American Chemical Society, pp. 8066–8069, 2012.","short":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, B. Brutscher, Journal of the American Chemical Society 134 (2012) 8066–8069."},"date_updated":"2021-01-12T08:19:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"last_name":"Rennella","full_name":"Rennella, Enrico","first_name":"Enrico"},{"first_name":"Thomas","full_name":"Cutuil, Thomas","last_name":"Cutuil"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"Isabel","full_name":"Ayala, Isabel","last_name":"Ayala"},{"last_name":"Forge","full_name":"Forge, Vincent","first_name":"Vincent"},{"first_name":"Bernhard","last_name":"Brutscher","full_name":"Brutscher, Bernhard"}],"title":"Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate","_id":"8466","type":"journal_article","article_type":"original","status":"public","publication_status":"published","year":"2012","publication_identifier":{"issn":["0002-7863","1520-5126"]},"language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","day":"03","page":"8066-8069","date_created":"2020-09-18T10:10:28Z","volume":134,"issue":"19","date_published":"2012-05-03T00:00:00Z","doi":"10.1021/ja302598j","abstract":[{"text":"Recent advances in NMR spectroscopy and the availability of high magnetic field strengths now offer the possibility to record real-time 3D NMR spectra of short-lived protein states, e.g., states that become transiently populated during protein folding. Here we present a strategy for obtaining sequential NMR assignments as well as atom-resolved information on structural and dynamic features within a folding intermediate of the amyloidogenic protein β2-microglobulin that has a half-lifetime of only 20 min.","lang":"eng"}],"oa_version":"None","publisher":"American Chemical Society","quality_controlled":"1","intvolume":" 134","month":"05"},{"_id":"8467","status":"public","type":"journal_article","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"chicago":"Huber, Matthias, Oliver With, Paul Schanda, René Verel, Matthias Ernst, and Beat H. Meier. “A Supplementary Coil for 2H Decoupling with Commercial HCN MAS Probes.” Journal of Magnetic Resonance. Elsevier, 2012. https://doi.org/10.1016/j.jmr.2011.10.010.","ista":"Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. 2012. A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. 214, 76–80.","mla":"Huber, Matthias, et al. “A Supplementary Coil for 2H Decoupling with Commercial HCN MAS Probes.” Journal of Magnetic Resonance, vol. 214, Elsevier, 2012, pp. 76–80, doi:10.1016/j.jmr.2011.10.010.","ama":"Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. 2012;214:76-80. doi:10.1016/j.jmr.2011.10.010","apa":"Huber, M., With, O., Schanda, P., Verel, R., Ernst, M., & Meier, B. H. (2012). A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2011.10.010","ieee":"M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, and B. H. Meier, “A supplementary coil for 2H decoupling with commercial HCN MAS probes,” Journal of Magnetic Resonance, vol. 214. Elsevier, pp. 76–80, 2012.","short":"M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, B.H. Meier, Journal of Magnetic Resonance 214 (2012) 76–80."},"date_updated":"2021-01-12T08:19:28Z","title":"A supplementary coil for 2H decoupling with commercial HCN MAS probes","article_processing_charge":"No","author":[{"first_name":"Matthias","full_name":"Huber, Matthias","last_name":"Huber"},{"full_name":"With, Oliver","last_name":"With","first_name":"Oliver"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"first_name":"René","last_name":"Verel","full_name":"Verel, René"},{"full_name":"Ernst, Matthias","last_name":"Ernst","first_name":"Matthias"},{"full_name":"Meier, Beat H.","last_name":"Meier","first_name":"Beat H."}],"oa_version":"None","abstract":[{"lang":"eng","text":"Partial deuteration is a powerful tool to increase coherence life times and spectral resolution in proton solid-state NMR. The J coupling to deuterium needs, however, to be decoupled to maintain the good resolution in the (usually indirect) 13C dimension(s). We present a simple and reversible way to expand a commercial 1.3 mm HCN MAS probe with a 2H channel with sufficient field strength for J-decoupling of deuterium, namely 2–3 kHz. The coil is placed at the outside of the stator and requires no significant modifications to the probe. The performance and the realizable gains in sensitivity and resolution are demonstrated using perdeuterated ubiquitin, with selectively CHD2-labeled methyl groups."}],"intvolume":" 214","month":"01","quality_controlled":"1","publisher":"Elsevier","publication":"Journal of Magnetic Resonance","language":[{"iso":"eng"}],"day":"01","year":"2012","publication_status":"published","publication_identifier":{"issn":["1090-7807"]},"date_created":"2020-09-18T10:10:36Z","doi":"10.1016/j.jmr.2011.10.010","date_published":"2012-01-01T00:00:00Z","volume":214,"page":"76-80"},{"_id":"8502","article_type":"original","type":"journal_article","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"status":"public","date_updated":"2021-01-12T08:19:44Z","citation":{"mla":"Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” Communications in Mathematical Physics, vol. 315, no. 3, Springer Nature, 2012, pp. 643–97, doi:10.1007/s00220-012-1532-x.","apa":"Kaloshin, V., & Saprykina, M. (2012). An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-012-1532-x","ama":"Kaloshin V, Saprykina M. An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. 2012;315(3):643-697. doi:10.1007/s00220-012-1532-x","ieee":"V. Kaloshin and M. Saprykina, “An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension,” Communications in Mathematical Physics, vol. 315, no. 3. Springer Nature, pp. 643–697, 2012.","short":"V. Kaloshin, M. Saprykina, Communications in Mathematical Physics 315 (2012) 643–697.","chicago":"Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” Communications in Mathematical Physics. Springer Nature, 2012. https://doi.org/10.1007/s00220-012-1532-x.","ista":"Kaloshin V, Saprykina M. 2012. An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. 315(3), 643–697."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"full_name":"Saprykina, Maria","last_name":"Saprykina","first_name":"Maria"}],"title":"An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension","abstract":[{"lang":"eng","text":"The famous ergodic hypothesis suggests that for a typical Hamiltonian on a typical energy surface nearly all trajectories are dense. KAM theory disproves it. Ehrenfest (The Conceptual Foundations of the Statistical Approach in Mechanics. Ithaca, NY: Cornell University Press, 1959) and Birkhoff (Collected Math Papers. Vol 2, New York: Dover, pp 462–465, 1968) stated the quasi-ergodic hypothesis claiming that a typical Hamiltonian on a typical energy surface has a dense orbit. This question is wide open. Herman (Proceedings of the International Congress of Mathematicians, Vol II (Berlin, 1998). Doc Math 1998, Extra Vol II, Berlin: Int Math Union, pp 797–808, 1998) proposed to look for an example of a Hamiltonian near H0(I)=⟨I,I⟩2 with a dense orbit on the unit energy surface. In this paper we construct a Hamiltonian H0(I)+εH1(θ,I,ε) which has an orbit dense in a set of maximal Hausdorff dimension equal to 5 on the unit energy surface."}],"oa_version":"None","publisher":"Springer Nature","quality_controlled":"1","intvolume":" 315","month":"11","publication_status":"published","year":"2012","publication_identifier":{"issn":["0010-3616","1432-0916"]},"language":[{"iso":"eng"}],"publication":"Communications in Mathematical Physics","day":"01","page":"643-697","date_created":"2020-09-18T10:47:16Z","issue":"3","volume":315,"date_published":"2012-11-01T00:00:00Z","doi":"10.1007/s00220-012-1532-x"},{"abstract":[{"text":"ackground: The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes.Results: We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates the relationship between TAG and nucleotide content. For biologically plausible rates of mutations we show that, in bacteria, TAG stop codon is universally associated with lower fitness, with TAA being the optimal for G-content < 16% while for G-content > 16% TGA has a higher fitness than TAG.Conclusions: Our data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications.Reviewers: This article was reviewed by Michail Gelfand, Arcady Mushegian and Shamil Sunyaev. For the full reviews, please go to the Reviewers' Comments section.","lang":"eng"}],"acknowledgement":"We thank Elena Alkalaeva and Peter Kolosov for insightful discussion and Brian Charlesworth for a critical reading of our manuscript. The work has been supported by a Plan Nacional grant from the Spanish Ministry of Science and Innovation, EMBO Young Investigator and Howard Hughes Medical Institute International Early Career Scientist awards.\n","quality_controlled":0,"publisher":"BioMed Central","month":"09","intvolume":" 7","year":"2012","publication_status":"published","day":"01","publication":"Biology Direct","doi":"10.1186/1745-6150-7-30","date_published":"2012-09-01T00:00:00Z","volume":7,"date_created":"2018-12-11T11:48:52Z","license":"https://creativecommons.org/licenses/by/4.0/","_id":"858","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","citation":{"ista":"Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria are not selectively equivalent. Biology Direct. 7.","chicago":"Povolotskaya, Inna, Fyodor Kondrashov, Alice Ledda, and Peter Vlasov. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-30.","apa":"Povolotskaya, I., Kondrashov, F., Ledda, A., & Vlasov, P. (2012). Stop codons in bacteria are not selectively equivalent. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-30","ama":"Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. Stop codons in bacteria are not selectively equivalent. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-30","short":"I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012).","ieee":"I. Povolotskaya, F. Kondrashov, A. Ledda, and P. Vlasov, “Stop codons in bacteria are not selectively equivalent,” Biology Direct, vol. 7. BioMed Central, 2012.","mla":"Povolotskaya, Inna, et al. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct, vol. 7, BioMed Central, 2012, doi:10.1186/1745-6150-7-30."},"date_updated":"2021-01-12T08:20:08Z","extern":1,"publist_id":"6792","author":[{"first_name":"Inna","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"full_name":"Ledda, Alice","last_name":"Ledda","first_name":"Alice"},{"full_name":"Vlasov, Peter K","last_name":"Vlasov","first_name":"Peter"}],"title":"Stop codons in bacteria are not selectively equivalent"},{"_id":"900","type":"journal_article","status":"public","date_updated":"2021-01-12T08:21:45Z","citation":{"chicago":"Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Epistasis as the Primary Factor in Molecular Evolution.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11510.","ista":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2012. Epistasis as the primary factor in molecular evolution. Nature. 490(7421), 535–538.","mla":"Breen, Michael, et al. “Epistasis as the Primary Factor in Molecular Evolution.” Nature, vol. 490, no. 7421, Nature Publishing Group, 2012, pp. 535–38, doi:10.1038/nature11510.","ama":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Epistasis as the primary factor in molecular evolution. Nature. 2012;490(7421):535-538. doi:10.1038/nature11510","apa":"Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2012). Epistasis as the primary factor in molecular evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11510","short":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 490 (2012) 535–538.","ieee":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Epistasis as the primary factor in molecular evolution,” Nature, vol. 490, no. 7421. Nature Publishing Group, pp. 535–538, 2012."},"extern":1,"publist_id":"6748","author":[{"last_name":"Breen","full_name":"Breen, Michael S","first_name":"Michael"},{"full_name":"Kemena, Carsten","last_name":"Kemena","first_name":"Carsten"},{"last_name":"Vlasov","full_name":"Vlasov, Peter K","first_name":"Peter"},{"last_name":"Notredame","full_name":"Notredame, Cédric","first_name":"Cédric"},{"last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"title":"Epistasis as the primary factor in molecular evolution","abstract":[{"lang":"eng","text":"The main forces directing long-term molecular evolution remain obscure. A sizable fraction of amino-acid substitutions seem to be fixed by positive selection, but it is unclear to what degree long-term protein evolution is constrained by epistasis, that is, instances when substitutions that are accepted in one genotype are deleterious in another. Here we obtain a quantitative estimate of the prevalence of epistasis in long-term protein evolution by relating data on amino-acid usage in 14 organelle proteins and 2 nuclear-encoded proteins to their rates of short-term evolution. We studied multiple alignments of at least 1,000 orthologues for each of these 16 proteins from species from a diverse phylogenetic background and found that an average site contained approximately eight different amino acids. Thus, without epistasis an average site should accept two-fifths of all possible amino acids, and the average rate of amino-acid substitutions should therefore be about three-fifths lower than the rate of neutral evolution. However, we found that the measured rate of amino-acid substitution in recent evolution is 20 times lower than the rate of neutral evolution and an order of magnitude lower than that expected in the absence of epistasis. These data indicate that epistasis is pervasive throughout protein evolution: about 90 per cent of all amino-acid substitutions have a neutral or beneficial impact only in the genetic backgrounds in which they occur, and must therefore be deleterious in a different background of other species. Our findings show that most amino-acid substitutions have different fitness effects in different species and that epistasis provides the primary conceptual framework to describe the tempo and mode of long-term protein evolution."}],"acknowledgement":"The work was supported by Plan Nacional grants from the Spanish Ministry of Science and Innovation, to F.A.K. and C.N. C.K. was supported by the European Union FP7 project Quantomics (KBBE2A222664). F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. We thank B. Lehner and T. Warnecke for input and a critical reading of the manuscript.\n","quality_controlled":0,"publisher":"Nature Publishing Group","intvolume":" 490","month":"10","year":"2012","publication_status":"published","publication":"Nature","day":"25","page":"535 - 538","date_created":"2018-12-11T11:49:06Z","date_published":"2012-10-25T00:00:00Z","issue":"7421","volume":490,"doi":"10.1038/nature11510"},{"month":"06","intvolume":" 108","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1202.6264"}],"pmid":1,"oa_version":"Preprint","abstract":[{"text":"In this Letter, we explore experimentally the phase behavior of a dense active suspension of self-propelled colloids. In addition to a solidlike and gaslike phase observed for high and low densities, a novel cluster phase is reported at intermediate densities. This takes the form of a stationary assembly of dense aggregates—resulting from a permanent dynamical merging and separation of active colloids—whose average size grows with activity as a linear function of the self-propelling velocity. While different possible scenarios can be considered to account for these observations—such as a generic velocity weakening instability recently put forward—we show that the experimental results are reproduced mathematically by a chemotactic aggregation mechanism, originally introduced to account for bacterial aggregation and accounting here for diffusiophoretic chemical interaction between colloidal swimmers.","lang":"eng"}],"issue":"26","volume":108,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"publication_status":"published","status":"public","article_type":"letter_note","type":"journal_article","_id":"9014","extern":"1","date_updated":"2023-02-23T13:46:45Z","quality_controlled":"1","publisher":"American Physical Society ","oa":1,"doi":"10.1103/physrevlett.108.268303","date_published":"2012-06-29T00:00:00Z","date_created":"2021-01-19T10:26:59Z","day":"29","publication":"Physical Review Letters","year":"2012","article_number":"268303","title":"Dynamic clustering in active colloidal suspensions with chemical signaling","author":[{"last_name":"Theurkauff","full_name":"Theurkauff, I.","first_name":"I."},{"last_name":"Cottin-Bizonne","full_name":"Cottin-Bizonne, C.","first_name":"C."},{"first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci"},{"full_name":"Ybert, C.","last_name":"Ybert","first_name":"C."},{"first_name":"L.","full_name":"Bocquet, L.","last_name":"Bocquet"}],"external_id":{"pmid":["23005020"],"arxiv":["1202.6264"]},"article_processing_charge":"No","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"chicago":"Theurkauff, I., C. Cottin-Bizonne, Jérémie A Palacci, C. Ybert, and L. Bocquet. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” Physical Review Letters. American Physical Society , 2012. https://doi.org/10.1103/physrevlett.108.268303.","ista":"Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. 2012. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 108(26), 268303.","mla":"Theurkauff, I., et al. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” Physical Review Letters, vol. 108, no. 26, 268303, American Physical Society , 2012, doi:10.1103/physrevlett.108.268303.","short":"I. Theurkauff, C. Cottin-Bizonne, J.A. Palacci, C. Ybert, L. Bocquet, Physical Review Letters 108 (2012).","ieee":"I. Theurkauff, C. Cottin-Bizonne, J. A. Palacci, C. Ybert, and L. Bocquet, “Dynamic clustering in active colloidal suspensions with chemical signaling,” Physical Review Letters, vol. 108, no. 26. American Physical Society , 2012.","ama":"Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 2012;108(26). doi:10.1103/physrevlett.108.268303","apa":"Theurkauff, I., Cottin-Bizonne, C., Palacci, J. A., Ybert, C., & Bocquet, L. (2012). Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. American Physical Society . https://doi.org/10.1103/physrevlett.108.268303"}},{"author":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"},{"first_name":"Jacqueline","full_name":"Cole, Jacqueline","last_name":"Cole"},{"first_name":"Martin","last_name":"Blood Forsythe","full_name":"Blood Forsythe, Martin"},{"last_name":"Hickstein","full_name":"Hickstein, Daniel","first_name":"Daniel"}],"publist_id":"7963","title":"Identifying and evaluating organic nonlinear optical materials via molecular moments","date_updated":"2021-01-12T08:21:50Z","citation":{"mla":"Higginbotham, Andrew P., et al. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” Journal of Applied Physics, vol. 111, no. 3, 033512, American Institute of Physics, 2012, doi:10.1063/1.3678593.","ieee":"A. P. Higginbotham, J. Cole, M. Blood Forsythe, and D. Hickstein, “Identifying and evaluating organic nonlinear optical materials via molecular moments,” Journal of Applied Physics, vol. 111, no. 3. American Institute of Physics, 2012.","short":"A.P. Higginbotham, J. Cole, M. Blood Forsythe, D. Hickstein, Journal of Applied Physics 111 (2012).","apa":"Higginbotham, A. P., Cole, J., Blood Forsythe, M., & Hickstein, D. (2012). Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. American Institute of Physics. https://doi.org/10.1063/1.3678593","ama":"Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. 2012;111(3). doi:10.1063/1.3678593","chicago":"Higginbotham, Andrew P, Jacqueline Cole, Martin Blood Forsythe, and Daniel Hickstein. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” Journal of Applied Physics. American Institute of Physics, 2012. https://doi.org/10.1063/1.3678593.","ista":"Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. 2012. Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. 111(3), 033512."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"journal_article","status":"public","_id":"91","article_number":"033512","date_created":"2018-12-11T11:44:35Z","doi":"10.1063/1.3678593","date_published":"2012-02-07T00:00:00Z","volume":111,"issue":"3","year":"2012","publication_status":"published","language":[{"iso":"eng"}],"publication":"Journal of Applied Physics","day":"07","publisher":"American Institute of Physics","quality_controlled":"1","intvolume":" 111","month":"02","abstract":[{"text":"We demonstrate how to appropriately estimate the zero-frequency (static) hyperpolarizability of an organic molecule from its charge distribution, and we explore applications of these estimates for identifying and evaluating new organic nonlinear optical (NLO) materials. First, we calculate hyperpolarizabilities from Hartree-Fock-derived charge distributions and find order-of-magnitude agreement with experimental values. We show that these simple arithmetic calculations will enable systematic searches for new organic NLO molecules. Second, we derive hyperpolarizabilities from crystallographic data using a multipolar charge-density analysis and find good agreement with empirical calculations. This demonstrates an experimental determination of the full static hyperpolarizability tensor in a solid-state sample. ","lang":"eng"}],"acknowledgement":"This work was supported by The Winston Churchill Foundation of the United States (A.P.H., M.A.B.F., D.D.H.), The Royal Society via a University Research Fellowship (J.M.C.), and the University of New Brunswick via The Vice-Chancellor’s Research Chair (J.M.C.).","oa_version":"None"},{"extern":"1","date_updated":"2022-01-24T13:49:41Z","status":"public","keyword":["Atmospheric Science"],"type":"journal_article","article_type":"original","_id":"9142","issue":"8","volume":69,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-4928","1520-0469"]},"publication_status":"published","month":"08","intvolume":" 69","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1175/JAS-D-11-0257.1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In models of radiative–convective equilibrium it is known that convection can spontaneously aggregate into one single localized moist region if the domain is large enough. The large changes in the mean climate state and radiative fluxes accompanying this self-aggregation raise questions as to what simulations at lower resolutions with parameterized convection, in similar homogeneous geometries, should be expected to produce to be considered successful in mimicking a cloud-resolving model.\r\nThe authors investigate this self-aggregation in a nonrotating, three-dimensional cloud-resolving model on a square domain without large-scale forcing. It is found that self-aggregation is sensitive not only to the domain size, but also to the horizontal resolution. With horizontally homogeneous initial conditions, convective aggregation only occurs on domains larger than about 200km and with resolutions coarser than about 2km in the model examined. The system exhibits hysteresis, so that with aggregated initial conditions, convection remains aggregated even at our finest resolution, 500m, as long as the domain is greater than 200–300km.\r\nThe sensitivity of self-aggregation to resolution and domain size in this model is due to the sensitivity of the distribution of low clouds to these two parameters. Indeed, the mechanism responsible for the aggregation of convection is the dynamical response to the longwave radiative cooling from low clouds. Strong longwave cooling near cloud top in dry regions forces downward motion, which by continuity generates inflow near cloud top and near-surface outflow from dry regions. This circulation results in the net export of moist static energy from regions with low moist static energy, yielding a positive feedback."}],"title":"Detailed investigation of the self-aggregation of convection in cloud-resolving simulations","author":[{"last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J"},{"full_name":"Held, Isaac M.","last_name":"Held","first_name":"Isaac M."}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Muller, C. J., & Held, I. M. (2012). Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. American Meteorological Society. https://doi.org/10.1175/jas-d-11-0257.1","ama":"Muller CJ, Held IM. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 2012;69(8):2551-2565. doi:10.1175/jas-d-11-0257.1","ieee":"C. J. Muller and I. M. Held, “Detailed investigation of the self-aggregation of convection in cloud-resolving simulations,” Journal of the Atmospheric Sciences, vol. 69, no. 8. American Meteorological Society, pp. 2551–2565, 2012.","short":"C.J. Muller, I.M. Held, Journal of the Atmospheric Sciences 69 (2012) 2551–2565.","mla":"Muller, Caroline J., and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences, vol. 69, no. 8, American Meteorological Society, 2012, pp. 2551–65, doi:10.1175/jas-d-11-0257.1.","ista":"Muller CJ, Held IM. 2012. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 69(8), 2551–2565.","chicago":"Muller, Caroline J, and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences. American Meteorological Society, 2012. https://doi.org/10.1175/jas-d-11-0257.1."},"doi":"10.1175/jas-d-11-0257.1","date_published":"2012-08-01T00:00:00Z","date_created":"2021-02-15T14:39:03Z","page":"2551-2565","day":"01","publication":"Journal of the Atmospheric Sciences","year":"2012","quality_controlled":"1","publisher":"American Meteorological Society","oa":1},{"_id":"9451","status":"public","type":"journal_article","article_type":"original","ddc":["580"],"extern":"1","date_updated":"2021-12-14T08:28:51Z","department":[{"_id":"DaZi"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.","lang":"eng"}],"intvolume":" 337","month":"09","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"volume":337,"issue":"6100","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.","ista":"Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364.","mla":"Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839.","apa":"Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224839","ama":"Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364. doi:10.1126/science.1224839","short":"C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.","ieee":"C. A. Ibarra et al., “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012."},"title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","external_id":{"pmid":["22984074"]},"article_processing_charge":"No","author":[{"last_name":"Ibarra","full_name":"Ibarra, Christian A.","first_name":"Christian A."},{"first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi"},{"first_name":"Vera K.","last_name":"Schoft","full_name":"Schoft, Vera K."},{"full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh","first_name":"Tzung-Fu"},{"full_name":"Uzawa, Rie","last_name":"Uzawa","first_name":"Rie"},{"first_name":"Jessica A.","full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues"},{"first_name":"Assaf","full_name":"Zemach, Assaf","last_name":"Zemach"},{"full_name":"Chumak, Nina","last_name":"Chumak","first_name":"Nina"},{"first_name":"Adriana","last_name":"Machlicova","full_name":"Machlicova, Adriana"},{"first_name":"Toshiro","last_name":"Nishimura","full_name":"Nishimura, Toshiro"},{"first_name":"Denisse","full_name":"Rojas, Denisse","last_name":"Rojas"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"full_name":"Tamaru, Hisashi","last_name":"Tamaru","first_name":"Hisashi"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","publication":"Science","day":"14","year":"2012","has_accepted_license":"1","date_created":"2021-06-04T07:51:31Z","date_published":"2012-09-14T00:00:00Z","doi":"10.1126/science.1224839","page":"1360-1364"},{"quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory Press","oa":1,"page":"147-154","date_published":"2012-12-18T00:00:00Z","doi":"10.1101/sqb.2012.77.014944","date_created":"2021-06-08T13:01:23Z","year":"2012","day":"18","publication":"Cold Spring Harbor Symposia on Quantitative Biology","author":[{"full_name":"Coleman-Derr, D.","last_name":"Coleman-Derr","first_name":"D."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"article_processing_charge":"No","external_id":{"pmid":["23250988"]},"title":"DNA methylation, H2A.Z, and the regulation of constitutive expression","citation":{"mla":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology, vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:10.1101/sqb.2012.77.014944.","ieee":"D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation of constitutive expression,” Cold Spring Harbor Symposia on Quantitative Biology, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.","short":"D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154.","ama":"Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 2012;77:147-154. doi:10.1101/sqb.2012.77.014944","apa":"Coleman-Derr, D., & Zilberman, D. (2012). DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2012.77.014944","chicago":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press, 2012. https://doi.org/10.1101/sqb.2012.77.014944.","ista":"Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 77, 147–154."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/sqb.2012.77.014944"}],"month":"12","intvolume":" 77","abstract":[{"lang":"eng","text":"The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies."}],"oa_version":"Published Version","pmid":1,"volume":77,"publication_identifier":{"issn":["0091-7451"],"eissn":["1943-4456"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"review","type":"journal_article","status":"public","_id":"9535","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:33:09Z","extern":"1"},{"ec_funded":1,"issue":"4","related_material":{"record":[{"relation":"research_data","id":"9755","status":"public"}]},"volume":10,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4689","checksum":"4ebacefd9fbab5c68adf829124115fd1","creator":"system","date_updated":"2020-07-14T12:46:04Z","file_size":674228,"date_created":"2018-12-12T10:08:28Z","file_name":"IST-2012-96-v1+1_journal.pbio.1001300.pdf"}],"publication_status":"published","intvolume":" 10","month":"04","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”).","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:04Z","department":[{"_id":"SyCr"}],"ddc":["570","579"],"date_updated":"2023-02-23T14:07:11Z","pubrep_id":"96","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"3242","date_created":"2018-12-11T12:02:13Z","doi":"10.1371/journal.pbio.1001300","date_published":"2012-04-03T00:00:00Z","publication":"PLoS Biology","day":"03","year":"2012","has_accepted_license":"1","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","acknowledgement":"Funding for this project was obtained by the German Research Foundation DFG (http://www.dfg.de/en/index.jsp) as an Individual Research Grant (CR118/2-1 to SC) and the European Research Council (http://erc.europa.eu/) in form of two ERC Starting Grants (ERC-2009-StG240371-SocialVaccines to SC and ERC-2010-StG259294-LatentCauses to FJT). In addition, the Junge Akademie (Young Academy of the Berlin-Brandenburg Academy of Sciences and Humanities and the National Academy of Sciences Leopoldina (http://www.diejungeakademie.de/english/index.html) funded this joint Antnet project of SC and FJT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","title":"Social transfer of pathogenic fungus promotes active immunisation in ant colonies","publist_id":"3434","author":[{"first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","full_name":"Konrad, Matthias"},{"last_name":"Vyleta","full_name":"Vyleta, Meghan","first_name":"Meghan","id":"418901AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Theis","full_name":"Theis, Fabian","first_name":"Fabian"},{"id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","full_name":"Stock, Miriam","last_name":"Stock"},{"first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","full_name":"Tragust, Simon","last_name":"Tragust"},{"full_name":"Klatt, Martina","last_name":"Klatt","first_name":"Martina","id":"E60F29C6-E9AE-11E9-AF6E-D190C7302F38"},{"first_name":"Verena","full_name":"Drescher, Verena","last_name":"Drescher"},{"first_name":"Carsten","full_name":"Marr, Carsten","last_name":"Marr"},{"last_name":"Ugelvig","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Simon Tragust, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001300.","ista":"Konrad M, Vyleta M, Theis F, Stock M, Tragust S, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. 10(4), e1001300.","mla":"Konrad, Matthias, et al. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” PLoS Biology, vol. 10, no. 4, e1001300, Public Library of Science, 2012, doi:10.1371/journal.pbio.1001300.","ieee":"M. Konrad et al., “Social transfer of pathogenic fungus promotes active immunisation in ant colonies,” PLoS Biology, vol. 10, no. 4. Public Library of Science, 2012.","short":"M. Konrad, M. Vyleta, F. Theis, M. Stock, S. Tragust, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, PLoS Biology 10 (2012).","apa":"Konrad, M., Vyleta, M., Theis, F., Stock, M., Tragust, S., Klatt, M., … Cremer, S. (2012). Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001300","ama":"Konrad M, Vyleta M, Theis F, et al. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. 2012;10(4). doi:10.1371/journal.pbio.1001300"},"project":[{"name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"},{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425"},{"name":"Antnet","_id":"25E0E184-B435-11E9-9278-68D0E5697425"}],"article_number":"e1001300"},{"publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.sv37s","open_access":"1"}],"oa":1,"month":"09","abstract":[{"lang":"eng","text":"Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”)."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","id":"3242","status":"public"}]},"date_published":"2012-09-27T00:00:00Z","doi":"10.5061/dryad.sv37s","date_created":"2021-07-30T08:39:13Z","year":"2012","day":"27","type":"research_data_reference","status":"public","_id":"9755","author":[{"last_name":"Konrad","full_name":"Konrad, Matthias","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vyleta","full_name":"Vyleta, Meghan","id":"418901AA-F248-11E8-B48F-1D18A9856A87","first_name":"Meghan"},{"full_name":"Theis, Fabian","last_name":"Theis","first_name":"Fabian"},{"first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","full_name":"Stock, Miriam","last_name":"Stock"},{"last_name":"Klatt","full_name":"Klatt, Martina","id":"E60F29C6-E9AE-11E9-AF6E-D190C7302F38","first_name":"Martina"},{"first_name":"Verena","last_name":"Drescher","full_name":"Drescher, Verena"},{"first_name":"Carsten","full_name":"Marr, Carsten","last_name":"Marr"},{"first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","last_name":"Ugelvig"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"article_processing_charge":"No","department":[{"_id":"SyCr"}],"title":"Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies","citation":{"mla":"Konrad, Matthias, et al. Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies. Dryad, 2012, doi:10.5061/dryad.sv37s.","ama":"Konrad M, Vyleta M, Theis F, et al. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. 2012. doi:10.5061/dryad.sv37s","apa":"Konrad, M., Vyleta, M., Theis, F., Stock, M., Klatt, M., Drescher, V., … Cremer, S. (2012). Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. Dryad. https://doi.org/10.5061/dryad.sv37s","short":"M. Konrad, M. Vyleta, F. Theis, M. Stock, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, (2012).","ieee":"M. Konrad et al., “Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies.” Dryad, 2012.","chicago":"Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” Dryad, 2012. https://doi.org/10.5061/dryad.sv37s.","ista":"Konrad M, Vyleta M, Theis F, Stock M, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies, Dryad, 10.5061/dryad.sv37s."},"date_updated":"2023-02-23T11:18:41Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"abstract":[{"lang":"eng","text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction."}],"oa_version":"Published Version","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.274b1"}],"month":"11","year":"2012","day":"14","date_published":"2012-11-14T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2944"}]},"doi":"10.5061/dryad.274b1","date_created":"2021-07-30T12:36:39Z","_id":"9758","type":"research_data_reference","status":"public","citation":{"ista":"Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates, Dryad, 10.5061/dryad.274b1.","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates.” Dryad, 2012. https://doi.org/10.5061/dryad.274b1.","apa":"Aeschbacher, S., Futschik, A., & Beaumont, M. (2012). Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. Dryad. https://doi.org/10.5061/dryad.274b1","ama":"Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. 2012. doi:10.5061/dryad.274b1","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates.” Dryad, 2012.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, (2012).","mla":"Aeschbacher, Simon, et al. Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. Dryad, 2012, doi:10.5061/dryad.274b1."},"date_updated":"2023-02-23T11:05:19Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Aeschbacher","full_name":"Aeschbacher, Simon","first_name":"Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Futschik","full_name":"Futschik, Andreas","first_name":"Andreas"},{"first_name":"Mark","full_name":"Beaumont, Mark","last_name":"Beaumont"}],"article_processing_charge":"No","title":"Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates","department":[{"_id":"NiBa"}]},{"department":[{"_id":"SyCr"}],"title":"Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison","article_processing_charge":"No","author":[{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Tragust, Simon","last_name":"Tragust"},{"last_name":"Mitteregger","full_name":"Mitteregger, Barbara","first_name":"Barbara","id":"479DDAAC-E9CD-11E9-9B5F-82450873F7A1"},{"full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","last_name":"Barone","first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Konrad, Matthias","last_name":"Konrad","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"short":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, (2012).","ieee":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison.” Dryad, 2012.","ama":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. 2012. doi:10.5061/dryad.61649","apa":"Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., & Cremer, S. (2012). Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Dryad. https://doi.org/10.5061/dryad.61649","mla":"Tragust, Simon, et al. Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison. Dryad, 2012, doi:10.5061/dryad.61649.","ista":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2012. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison, Dryad, 10.5061/dryad.61649.","chicago":"Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” Dryad, 2012. https://doi.org/10.5061/dryad.61649."},"date_updated":"2023-02-23T11:04:28Z","status":"public","type":"research_data_reference","_id":"9757","date_created":"2021-07-30T12:31:31Z","related_material":{"record":[{"status":"public","id":"2926","relation":"used_in_publication"}]},"date_published":"2012-12-14T00:00:00Z","doi":"10.5061/dryad.61649","day":"14","year":"2012","month":"12","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.61649"}],"publisher":"Dryad","oa_version":"Published Version","abstract":[{"lang":"eng","text":"To fight infectious diseases, host immune defences are employed at multiple levels. Sanitary behaviour, such as pathogen avoidance and removal, acts as a first line of defence to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care towards pathogen-exposed group members [2]. One of the most common behaviours is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores as it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behaviour extends current understanding of grooming and the establishment of social immunity in insect societies."}]},{"oa_version":"None","abstract":[{"lang":"eng","text":"In this paper we present a surprising example of a Cr unimodal map of an interval f:I→I whose number of periodic points Pn(f)=∣{x∈I:fnx=x}∣ grows faster than any ahead given sequence along a subsequence nk=3k. This example also shows that ‘non-flatness’ of critical points is necessary for the Martens–de Melo–van Strien theorem [M. Martens, W. de Melo and S. van Strien. Julia–Fatou–Sullivan theory for real one-dimensional dynamics. Acta Math.168(3–4) (1992), 273–318] to hold."}],"intvolume":" 32","month":"02","publisher":"Cambridge University Press","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Ergodic Theory and Dynamical Systems","day":"01","publication_status":"published","year":"2012","publication_identifier":{"issn":["0143-3857","1469-4417"]},"date_created":"2020-09-18T10:47:33Z","date_published":"2012-02-01T00:00:00Z","doi":"10.1017/s0143385710000817","issue":"1","volume":32,"page":"159-165","_id":"8504","keyword":["Applied Mathematics","General Mathematics"],"status":"public","article_type":"original","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"ieee":"V. Kaloshin and O. S. KOZLOVSKI, “A Cr unimodal map with an arbitrary fast growth of the number of periodic points,” Ergodic Theory and Dynamical Systems, vol. 32, no. 1. Cambridge University Press, pp. 159–165, 2012.","short":"V. Kaloshin, O.S. KOZLOVSKI, Ergodic Theory and Dynamical Systems 32 (2012) 159–165.","ama":"Kaloshin V, KOZLOVSKI OS. A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. 2012;32(1):159-165. doi:10.1017/s0143385710000817","apa":"Kaloshin, V., & KOZLOVSKI, O. S. (2012). A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/s0143385710000817","mla":"Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical Systems, vol. 32, no. 1, Cambridge University Press, 2012, pp. 159–65, doi:10.1017/s0143385710000817.","ista":"Kaloshin V, KOZLOVSKI OS. 2012. A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. 32(1), 159–165.","chicago":"Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2012. https://doi.org/10.1017/s0143385710000817."},"date_updated":"2021-01-12T08:19:44Z","title":"A Cr unimodal map with an arbitrary fast growth of the number of periodic points","article_processing_charge":"No","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","last_name":"Kaloshin"},{"first_name":"O. S.","full_name":"KOZLOVSKI, O. S.","last_name":"KOZLOVSKI"}]},{"month":"07","intvolume":" 176","publisher":"Princeton University Press","quality_controlled":"1","oa_version":"None","abstract":[{"text":"We prove there are finitely many isometry classes of planar central configurations (also called relative equilibria) in the Newtonian 5-body problem, except perhaps if the 5-tuple of positive masses belongs to a given codimension 2 subvariety of the mass space.","lang":"eng"}],"doi":"10.4007/annals.2012.176.1.10","volume":176,"issue":"1","date_published":"2012-07-01T00:00:00Z","date_created":"2020-09-18T10:47:24Z","page":"535-588","day":"01","publication":"Annals of Mathematics","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0003-486X"]},"year":"2012","publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"8503","title":"Finiteness of central configurations of five bodies in the plane","author":[{"first_name":"Alain","full_name":"Albouy, Alain","last_name":"Albouy"},{"last_name":"Kaloshin","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:44Z","citation":{"ama":"Albouy A, Kaloshin V. Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. 2012;176(1):535-588. doi:10.4007/annals.2012.176.1.10","apa":"Albouy, A., & Kaloshin, V. (2012). Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. Princeton University Press. https://doi.org/10.4007/annals.2012.176.1.10","ieee":"A. Albouy and V. Kaloshin, “Finiteness of central configurations of five bodies in the plane,” Annals of Mathematics, vol. 176, no. 1. Princeton University Press, pp. 535–588, 2012.","short":"A. Albouy, V. Kaloshin, Annals of Mathematics 176 (2012) 535–588.","mla":"Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of Five Bodies in the Plane.” Annals of Mathematics, vol. 176, no. 1, Princeton University Press, 2012, pp. 535–88, doi:10.4007/annals.2012.176.1.10.","ista":"Albouy A, Kaloshin V. 2012. Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. 176(1), 535–588.","chicago":"Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of Five Bodies in the Plane.” Annals of Mathematics. Princeton University Press, 2012. https://doi.org/10.4007/annals.2012.176.1.10."}},{"date_published":"2012-01-01T00:00:00Z","volume":279,"doi":"10.1098/rspb.2012.1108","issue":"1749","date_created":"2018-12-11T11:49:01Z","page":"5048 - 5057","day":"01","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","publication_status":"published","year":"2012","month":"01","intvolume":" 279","quality_controlled":0,"publisher":"Royal Society, The","acknowledgement":"The work was supported by a Plan Nacional grant no. BFU2009-09271 from the Spanish Ministry of Science and Innovation. The author is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist.","abstract":[{"text":"A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications.","lang":"eng"}],"title":"Gene duplication as a mechanism of genomic adaptation to a changing environment","publist_id":"6765","author":[{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"extern":1,"date_updated":"2021-01-12T08:21:16Z","citation":{"chicago":"Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2012. https://doi.org/10.1098/rspb.2012.1108.","ista":"Kondrashov F. 2012. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 279(1749), 5048–5057.","mla":"Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749, Royal Society, The, 2012, pp. 5048–57, doi:10.1098/rspb.2012.1108.","short":"F. Kondrashov, Proceedings of the Royal Society of London Series B Biological Sciences 279 (2012) 5048–5057.","ieee":"F. Kondrashov, “Gene duplication as a mechanism of genomic adaptation to a changing environment,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749. Royal Society, The, pp. 5048–5057, 2012.","ama":"Kondrashov F. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 2012;279(1749):5048-5057. doi:10.1098/rspb.2012.1108","apa":"Kondrashov, F. (2012). Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.1108"},"status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"887"},{"intvolume":" 8","month":"01","quality_controlled":"1","publisher":"Royal Society of Chemistry","scopus_import":"1","oa_version":"None","abstract":[{"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.","lang":"eng"}],"date_created":"2021-02-01T13:43:10Z","volume":8,"doi":"10.1039/c1sm06395b","date_published":"2012-01-28T00:00:00Z","issue":"4","page":"980-994","publication":"Soft Matter","language":[{"iso":"eng"}],"day":"28","publication_status":"published","year":"2012","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"status":"public","type":"journal_article","article_type":"original","_id":"9049","title":"Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis","article_processing_charge":"No","author":[{"last_name":"Palacci","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A"},{"last_name":"Cottin-Bizonne","full_name":"Cottin-Bizonne, Cécile","first_name":"Cécile"},{"first_name":"Christophe","full_name":"Ybert, Christophe","last_name":"Ybert"},{"first_name":"Lydéric","last_name":"Bocquet","full_name":"Bocquet, Lydéric"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","extern":"1","date_updated":"2023-02-23T13:47:31Z","citation":{"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.","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.","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","short":"J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Soft Matter 8 (2012) 980–994.","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.","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."}},{"month":"07","intvolume":" 109","publisher":"American Physical Society","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1207.1516"}],"oa_version":"Preprint","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."}],"volume":109,"doi":"10.1103/PhysRevLett.109.018101","date_published":"2012-07-03T00:00:00Z","issue":"1","date_created":"2018-12-11T11:49:13Z","day":"03","language":[{"iso":"eng"}],"publication":"Physical Review Letters","publication_status":"published","year":"2012","status":"public","type":"journal_article","_id":"922","title":"Mechanical instabilities of biological tubes","author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"full_name":"Prost, Jacques","last_name":"Prost","first_name":"Jacques"},{"first_name":"Jean","last_name":"Joanny","full_name":"Joanny, Jean"}],"publist_id":"6519","article_processing_charge":"No","external_id":{"arxiv":["1207.1516"]},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:21:56Z","citation":{"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).","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.","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.","ista":"Hannezo EB, Prost J, Joanny J. 2012. Mechanical instabilities of biological tubes. Physical Review Letters. 109(1)."}},{"article_number":"e1002512","citation":{"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.","short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012).","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","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","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.","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.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Kim","full_name":"Kim, Sang Yeol","first_name":"Sang Yeol"},{"full_name":"Lee, Jungeun","last_name":"Lee","first_name":"Jungeun"},{"first_name":"Leor","full_name":"Eshed-Williams, Leor","last_name":"Eshed-Williams"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"first_name":"Z. Renee","full_name":"Sung, Z. Renee","last_name":"Sung"}],"external_id":{"pmid":["22457632"]},"article_processing_charge":"No","title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"year":"2012","day":"22","publication":"PLoS Genetics","doi":"10.1371/journal.pgen.1002512","date_published":"2012-03-22T00:00:00Z","date_created":"2021-06-07T11:07:56Z","_id":"9499","article_type":"original","type":"journal_article","status":"public","date_updated":"2021-12-14T08:31:14Z","extern":"1","department":[{"_id":"DaZi"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002512","open_access":"1"}],"month":"03","intvolume":" 8","publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":8,"issue":"3"}]