[{"issue":"1","article_type":"original","quality_controlled":"1","scopus_import":"1","intvolume":"        16","date_created":"2021-07-19T06:56:45Z","doi":"10.1021/acs.jctc.9b00907","date_published":"2019-01-14T00:00:00Z","extern":"1","arxiv":1,"abstract":[{"lang":"eng","text":"Atomistic modeling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an appropriately chosen set of collective variables can significantly accelerate the exploration of phase space, albeit at the price of distorting the distribution of microstates. Efficient reweighting to recover the unbiased distribution can be nontrivial when employing adaptive sampling techniques such as metadynamics, variationally enhanced sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium manner under a time-dependent bias. We introduce an iterative unbiasing scheme that makes efficient use of all the trajectory data and that does not require the distribution to be evaluated on a grid. The method can thus be used even when the bias has a high dimensionality. We benchmark this approach against some of the existing schemes on model systems with different complexity and dimensionality."}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1549-9618"],"eissn":["1549-9626"]},"article_processing_charge":"No","year":"2019","citation":{"ama":"Giberti F, Cheng B, Tribello GA, Ceriotti M. Iterative unbiasing of quasi-equilibrium sampling. <i>Journal of Chemical Theory and Computation</i>. 2019;16(1):100-107. doi:<a href=\"https://doi.org/10.1021/acs.jctc.9b00907\">10.1021/acs.jctc.9b00907</a>","ieee":"F. Giberti, B. Cheng, G. A. Tribello, and M. Ceriotti, “Iterative unbiasing of quasi-equilibrium sampling,” <i>Journal of Chemical Theory and Computation</i>, vol. 16, no. 1. American Chemical Society, pp. 100–107, 2019.","short":"F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory and Computation 16 (2019) 100–107.","chicago":"Giberti, F., Bingqing Cheng, G. A. Tribello, and M. Ceriotti. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/acs.jctc.9b00907\">https://doi.org/10.1021/acs.jctc.9b00907</a>.","ista":"Giberti F, Cheng B, Tribello GA, Ceriotti M. 2019. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 16(1), 100–107.","mla":"Giberti, F., et al. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” <i>Journal of Chemical Theory and Computation</i>, vol. 16, no. 1, American Chemical Society, 2019, pp. 100–07, doi:<a href=\"https://doi.org/10.1021/acs.jctc.9b00907\">10.1021/acs.jctc.9b00907</a>.","apa":"Giberti, F., Cheng, B., Tribello, G. A., &#38; Ceriotti, M. (2019). Iterative unbiasing of quasi-equilibrium sampling. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.9b00907\">https://doi.org/10.1021/acs.jctc.9b00907</a>"},"title":"Iterative unbiasing of quasi-equilibrium sampling","author":[{"last_name":"Giberti","full_name":"Giberti, F.","first_name":"F."},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","full_name":"Cheng, Bingqing"},{"first_name":"G. A.","full_name":"Tribello, G. A.","last_name":"Tribello"},{"last_name":"Ceriotti","full_name":"Ceriotti, M.","first_name":"M."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2021-08-09T12:37:37Z","external_id":{"arxiv":["1911.01140"],"pmid":["31743021"]},"publisher":"American Chemical Society","main_file_link":[{"url":"https://arxiv.org/abs/1911.01140","open_access":"1"}],"day":"14","publication":"Journal of Chemical Theory and Computation","_id":"9680","oa_version":"Preprint","pmid":1,"volume":16,"month":"01","publication_status":"published","type":"journal_article","page":"100-107","status":"public","oa":1},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Ab initio thermodynamics of liquid and solid water","author":[{"full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"full_name":"Engel, Edgar A.","last_name":"Engel","first_name":"Edgar A."},{"first_name":"Jörg","last_name":"Behler","full_name":"Behler, Jörg"},{"first_name":"Christoph","last_name":"Dellago","full_name":"Dellago, Christoph"},{"first_name":"Michele","full_name":"Ceriotti, Michele","last_name":"Ceriotti"}],"date_updated":"2023-02-23T14:05:08Z","article_processing_charge":"No","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"citation":{"ieee":"B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio thermodynamics of liquid and solid water,” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115, 2019.","ama":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics of liquid and solid water. <i>Proceedings of the National Academy of Sciences</i>. 2019;116(4):1110-1115. doi:<a href=\"https://doi.org/10.1073/pnas.1815117116\">10.1073/pnas.1815117116</a>","apa":"Cheng, B., Engel, E. A., Behler, J., Dellago, C., &#38; Ceriotti, M. (2019). Ab initio thermodynamics of liquid and solid water. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1815117116\">https://doi.org/10.1073/pnas.1815117116</a>","mla":"Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1110–15, doi:<a href=\"https://doi.org/10.1073/pnas.1815117116\">10.1073/pnas.1815117116</a>.","chicago":"Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1815117116\">https://doi.org/10.1073/pnas.1815117116</a>.","short":"B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of the National Academy of Sciences 116 (2019) 1110–1115.","ista":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4), 1110–1115."},"year":"2019","abstract":[{"lang":"eng","text":"A central goal of computational physics and chemistry is to predict material properties by using first-principles methods based on the fundamental laws of quantum mechanics. However, the high computational costs of these methods typically prevent rigorous predictions of macroscopic quantities at finite temperatures, such as heat capacity, density, and chemical potential. Here, we enable such predictions by marrying advanced free-energy methods with data-driven machine-learning interatomic potentials. We show that, for the ubiquitous and technologically essential system of water, a first-principles thermodynamic description not only leads to excellent agreement with experiments, but also reveals the crucial role of nuclear quantum fluctuations in modulating the thermodynamic stabilities of different phases of water."}],"extern":"1","arxiv":1,"date_published":"2019-01-22T00:00:00Z","scopus_import":"1","quality_controlled":"1","issue":"4","article_type":"original","doi":"10.1073/pnas.1815117116","date_created":"2021-07-19T10:17:09Z","intvolume":"       116","page":"1110-1115","status":"public","oa":1,"month":"01","volume":116,"publication_status":"published","type":"journal_article","_id":"9689","publication":"Proceedings of the National Academy of Sciences","day":"22","pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1815117116"}],"publisher":"National Academy of Sciences","external_id":{"arxiv":["1811.08630"],"pmid":["30610171"]}},{"article_processing_charge":"No","month":"12","year":"2019","type":"research_data_reference","citation":{"mla":"Ucar, Mehmet C., and Reinhard Lipowsky. <i>Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding</i>. American Chemical Society , 2019, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>.","short":"M.C. Ucar, R. Lipowsky, (2019).","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">https://doi.org/10.1021/acs.nanolett.9b04445.s001</a>.","ista":"Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>.","apa":"Ucar, M. C., &#38; Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">https://doi.org/10.1021/acs.nanolett.9b04445.s001</a>","ieee":"M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019.","ama":"Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>"},"title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar","full_name":"Ucar, Mehmet C"},{"full_name":"Lipowsky, Reinhard","last_name":"Lipowsky","first_name":"Reinhard"}],"date_updated":"2024-10-09T20:59:07Z","status":"public","related_material":{"record":[{"status":"public","id":"7166","relation":"used_in_publication"}]},"publisher":"American Chemical Society ","date_created":"2021-07-27T09:51:46Z","doi":"10.1021/acs.nanolett.9b04445.s001","day":"19","department":[{"_id":"EdHa"}],"_id":"9726","oa_version":"Published Version","date_published":"2019-12-19T00:00:00Z","abstract":[{"text":"A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)","lang":"eng"}]},{"_id":"9784","day":"09","department":[{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures."}],"oa_version":"Published Version","date_published":"2019-08-09T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9411761.v1"}],"doi":"10.6084/m9.figshare.9411761.v1","date_created":"2021-08-06T08:14:05Z","publisher":"Springer Nature","title":"MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Michael N.","full_name":"Antoniou, Michael N.","last_name":"Antoniou"},{"full_name":"Nicolas, Armel","last_name":"Nicolas","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mesnage","full_name":"Mesnage, Robin","first_name":"Robin"},{"last_name":"Biserni","full_name":"Biserni, Martina","first_name":"Martina"},{"last_name":"Rao","full_name":"Rao, Francesco V.","first_name":"Francesco V."},{"full_name":"Martin, Cristina Vazquez","last_name":"Martin","first_name":"Cristina Vazquez"}],"oa":1,"status":"public","related_material":{"record":[{"status":"public","id":"6819","relation":"used_in_publication"}]},"date_updated":"2023-02-23T12:52:29Z","article_processing_charge":"No","month":"08","citation":{"ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019.","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9411761.v1\">10.6084/m9.figshare.9411761.v1</a>","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., &#38; Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9411761.v1\">https://doi.org/10.6084/m9.figshare.9411761.v1</a>","mla":"Antoniou, Michael N., et al. <i>MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9411761.v1\">10.6084/m9.figshare.9411761.v1</a>.","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9411761.v1\">https://doi.org/10.6084/m9.figshare.9411761.v1</a>.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019).","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9411761.v1\">10.6084/m9.figshare.9411761.v1</a>."},"type":"research_data_reference","year":"2019"},{"date_published":"2019-07-02T00:00:00Z","oa_version":"Published Version","_id":"9786","day":"02","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"doi":"10.1371/journal.pcbi.1007168.s001","date_created":"2021-08-06T08:23:43Z","publisher":"Public Library of Science","status":"public","related_material":{"record":[{"status":"public","id":"6784","relation":"used_in_publication"}]},"date_updated":"2025-04-15T07:33:55Z","title":"Supporting text and results","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Ruess, Jakob","last_name":"Ruess","first_name":"Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pleska, Maros","last_name":"Pleska","orcid":"0000-0001-7460-7479","first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper"}],"citation":{"apa":"Ruess, J., Pleska, M., Guet, C. C., &#38; Tkačik, G. (2019). Supporting text and results. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007168.s001\">https://doi.org/10.1371/journal.pcbi.1007168.s001</a>","mla":"Ruess, Jakob, et al. <i>Supporting Text and Results</i>. Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007168.s001\">10.1371/journal.pcbi.1007168.s001</a>.","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Supporting text and results, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1007168.s001\">10.1371/journal.pcbi.1007168.s001</a>.","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting Text and Results.” Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007168.s001\">https://doi.org/10.1371/journal.pcbi.1007168.s001</a>.","ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.” Public Library of Science, 2019.","ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007168.s001\">10.1371/journal.pcbi.1007168.s001</a>"},"type":"research_data_reference","year":"2019","article_processing_charge":"No","month":"07"},{"publisher":"Public Library of Science","date_created":"2021-08-06T11:34:56Z","doi":"10.1371/journal.pbio.2005902.s006","date_published":"2019-02-07T00:00:00Z","oa_version":"Published Version","day":"07","department":[{"_id":"NiBa"}],"_id":"9801","year":"2019","type":"research_data_reference","citation":{"mla":"Merrill, Richard M., et al. <i>Raw Behavioral Data</i>. Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">10.1371/journal.pbio.2005902.s006</a>.","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">10.1371/journal.pbio.2005902.s006</a>.","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral Data.” Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">https://doi.org/10.1371/journal.pbio.2005902.s006</a>.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, (2019).","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">https://doi.org/10.1371/journal.pbio.2005902.s006</a>","ieee":"R. M. Merrill <i>et al.</i>, “Raw behavioral data.” Public Library of Science, 2019.","ama":"Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">10.1371/journal.pbio.2005902.s006</a>"},"article_processing_charge":"No","month":"02","date_updated":"2023-08-24T14:46:23Z","status":"public","related_material":{"record":[{"id":"6022","relation":"used_in_publication","status":"public"}]},"title":"Raw behavioral data","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Merrill, Richard M.","last_name":"Merrill","first_name":"Richard M."},{"first_name":"Pasi","full_name":"Rastas, Pasi","last_name":"Rastas"},{"first_name":"Simon H.","last_name":"Martin","full_name":"Martin, Simon H."},{"first_name":"Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87","full_name":"Melo Hurtado, Maria C","last_name":"Melo Hurtado"},{"first_name":"Sarah","last_name":"Barker","full_name":"Barker, Sarah"},{"first_name":"John","last_name":"Davey","full_name":"Davey, John"},{"first_name":"W. Owen","last_name":"Mcmillan","full_name":"Mcmillan, W. Owen"},{"last_name":"Jiggins","full_name":"Jiggins, Chris D.","first_name":"Chris D."}]},{"date_published":"2019-07-16T00:00:00Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed."}],"department":[{"_id":"NiBa"}],"day":"16","_id":"9802","publisher":"Dryad","date_created":"2021-08-06T11:45:11Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.8tp0900"}],"doi":"10.5061/dryad.8tp0900","date_updated":"2024-10-09T20:58:56Z","oa":1,"status":"public","related_material":{"record":[{"relation":"used_in_publication","id":"6680","status":"public"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","author":[{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","last_name":"Sachdeva"}],"year":"2019","type":"research_data_reference","citation":{"short":"H. Sachdeva, (2019).","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, <a href=\"https://doi.org/10.5061/dryad.8tp0900\">10.5061/dryad.8tp0900</a>.","chicago":"Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.8tp0900\">https://doi.org/10.5061/dryad.8tp0900</a>.","mla":"Sachdeva, Himani. <i>Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.8tp0900\">10.5061/dryad.8tp0900</a>.","apa":"Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. <a href=\"https://doi.org/10.5061/dryad.8tp0900\">https://doi.org/10.5061/dryad.8tp0900</a>","ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.8tp0900\">10.5061/dryad.8tp0900</a>","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019."},"month":"07","article_processing_charge":"No"},{"date_updated":"2023-08-29T06:41:51Z","oa":1,"status":"public","related_material":{"record":[{"relation":"used_in_publication","id":"6713","status":"public"}]},"title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"João Pl","full_name":"Castro, João Pl","last_name":"Castro"},{"first_name":"Michelle N.","last_name":"Yancoskie","full_name":"Yancoskie, Michelle N."},{"first_name":"Marta","full_name":"Marchini, Marta","last_name":"Marchini"},{"full_name":"Belohlavy, Stefanie","last_name":"Belohlavy","first_name":"Stefanie","orcid":"0000-0002-9849-498X","id":"43FE426A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Layla","last_name":"Hiramatsu","full_name":"Hiramatsu, Layla"},{"first_name":"Marek","full_name":"Kučka, Marek","last_name":"Kučka"},{"last_name":"Beluch","full_name":"Beluch, William H.","first_name":"William H."},{"first_name":"Ronald","last_name":"Naumann","full_name":"Naumann, Ronald"},{"last_name":"Skuplik","full_name":"Skuplik, Isabella","first_name":"Isabella"},{"first_name":"John","full_name":"Cobb, John","last_name":"Cobb"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Campbell","last_name":"Rolian","full_name":"Rolian, Campbell"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"}],"year":"2019","citation":{"short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019).","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">https://doi.org/10.5061/dryad.0q2h6tk</a>.","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, <a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">10.5061/dryad.0q2h6tk</a>.","mla":"Castro, João Pl, et al. <i>Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">10.5061/dryad.0q2h6tk</a>.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. <a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">https://doi.org/10.5061/dryad.0q2h6tk</a>","ama":"Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">10.5061/dryad.0q2h6tk</a>","ieee":"J. P. Castro <i>et al.</i>, “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019."},"type":"research_data_reference","month":"06","article_processing_charge":"No","oa_version":"Published Version","date_published":"2019-06-06T00:00:00Z","abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}],"department":[{"_id":"NiBa"}],"day":"06","_id":"9804","date_created":"2021-08-06T11:52:54Z","publisher":"Dryad","doi":"10.5061/dryad.0q2h6tk","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0q2h6tk"}]},{"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: The consequences of an introgression event","status":"public","oa":1,"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"40"}]},"date_updated":"2025-07-10T11:52:34Z","article_processing_charge":"No","month":"01","citation":{"apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. <a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">https://doi.org/10.5061/dryad.2kb6fh4</a>","mla":"Barton, Nicholas H. <i>Data from: The Consequences of an Introgression Event</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">10.5061/dryad.2kb6fh4</a>.","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">https://doi.org/10.5061/dryad.2kb6fh4</a>.","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, <a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">10.5061/dryad.2kb6fh4</a>.","short":"N.H. Barton, (2019).","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">10.5061/dryad.2kb6fh4</a>"},"type":"research_data_reference","year":"2019","_id":"9805","day":"09","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?"}],"oa_version":"Published Version","date_published":"2019-01-09T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.2kb6fh4"}],"doi":"10.5061/dryad.2kb6fh4","publisher":"Dryad","date_created":"2021-08-06T12:03:50Z"},{"year":"2019","type":"research_data_reference","citation":{"chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.9kj41f0\">https://doi.org/10.5061/dryad.9kj41f0</a>.","ista":"Kutzer M, Kurtz J, Armitage SAO. 2019. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance, Dryad, <a href=\"https://doi.org/10.5061/dryad.9kj41f0\">10.5061/dryad.9kj41f0</a>.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, (2019).","mla":"Kutzer, Megan, et al. <i>Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.9kj41f0\">10.5061/dryad.9kj41f0</a>.","apa":"Kutzer, M., Kurtz, J., &#38; Armitage, S. A. O. (2019). Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Dryad. <a href=\"https://doi.org/10.5061/dryad.9kj41f0\">https://doi.org/10.5061/dryad.9kj41f0</a>","ama":"Kutzer M, Kurtz J, Armitage SAO. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.9kj41f0\">10.5061/dryad.9kj41f0</a>","ieee":"M. Kutzer, J. Kurtz, and S. A. O. Armitage, “Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance.” Dryad, 2019."},"article_processing_charge":"No","month":"02","date_updated":"2025-07-10T11:53:11Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6105"}]},"status":"public","oa":1,"author":[{"full_name":"Kutzer, Megan","last_name":"Kutzer","first_name":"Megan","orcid":"0000-0002-8696-6978","id":"29D0B332-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kurtz","full_name":"Kurtz, Joachim","first_name":"Joachim"},{"first_name":"Sophie A.O.","last_name":"Armitage","full_name":"Armitage, Sophie A.O."}],"title":"Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-06T12:06:40Z","publisher":"Dryad","doi":"10.5061/dryad.9kj41f0","main_file_link":[{"url":"https://doi.org/10.5061/dryad.9kj41f0","open_access":"1"}],"date_published":"2019-02-05T00:00:00Z","oa_version":"Published Version","abstract":[{"text":"1. Hosts can alter their strategy towards pathogens during their lifetime, i.e., they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e. resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fitness consequences that result from a high pathogen load. Finally, previous exposure may also lead to life history adjustments, such as terminal investment into reproduction. 2. Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested if previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute-phase infection (one day post-challenge). We then asked if previous pathogen exposure affects chronic-phase pathogen persistence and longer-term survival (28 days post-challenge). 3. We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long-term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses. 4. We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection. 5. To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi-faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host-pathogen system and that infection persistence may be bacterium-specific.","lang":"eng"}],"day":"05","department":[{"_id":"SyCr"}],"_id":"9806"},{"has_accepted_license":"1","publisher":"Wiley","external_id":{"isi":["000470025900008"]},"_id":"5","day":"01","publication":"Journal of the London Mathematical Society","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"06","file":[{"file_id":"7238","date_created":"2020-01-07T13:31:53Z","file_size":431754,"checksum":"1be56239b2cd740a0e9a084f773c22f6","file_name":"2019_Wiley_Ganev.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:35Z","creator":"kschuh"}],"volume":99,"type":"journal_article","publication_status":"published","page":"778-806","oa":1,"ddc":["510"],"status":"public","scopus_import":"1","quality_controlled":"1","issue":"3","file_date_updated":"2020-07-14T12:46:35Z","doi":"10.1112/jlms.12193","date_created":"2018-12-11T11:44:06Z","intvolume":"        99","department":[{"_id":"TaHa"}],"license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"text":"In this paper, we introduce a quantum version of the wonderful compactification of a group as a certain noncommutative projective scheme. Our approach stems from the fact that the wonderful compactification encodes the asymptotics of matrix coefficients, and from its realization as a GIT quotient of the Vinberg semigroup. In order to define the wonderful compactification for a quantum group, we adopt a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key to our construction is a quantum version of the Vinberg semigroup, which we define as a q-deformation of a certain Rees algebra, compatible with a standard Poisson structure. Furthermore, we discuss quantum analogues of the stratification of the wonderful compactification by orbits for a certain group action, and provide explicit computations in the case of SL2.","lang":"eng"}],"date_published":"2019-06-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","publist_id":"8052","language":[{"iso":"eng"}],"citation":{"ista":"Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806.","chicago":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” <i>Journal of the London Mathematical Society</i>. Wiley, 2019. <a href=\"https://doi.org/10.1112/jlms.12193\">https://doi.org/10.1112/jlms.12193</a>.","short":"I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806.","mla":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3, Wiley, 2019, pp. 778–806, doi:<a href=\"https://doi.org/10.1112/jlms.12193\">10.1112/jlms.12193</a>.","apa":"Ganev, I. V. (2019). The wonderful compactification for quantum groups. <i>Journal of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/jlms.12193\">https://doi.org/10.1112/jlms.12193</a>","ama":"Ganev IV. The wonderful compactification for quantum groups. <i>Journal of the London Mathematical Society</i>. 2019;99(3):778-806. doi:<a href=\"https://doi.org/10.1112/jlms.12193\">10.1112/jlms.12193</a>","ieee":"I. V. Ganev, “The wonderful compactification for quantum groups,” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3. Wiley, pp. 778–806, 2019."},"year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The wonderful compactification for quantum groups","author":[{"first_name":"Iordan V","id":"447491B8-F248-11E8-B48F-1D18A9856A87","full_name":"Ganev, Iordan V","last_name":"Ganev"}],"date_updated":"2023-09-19T10:13:08Z","isi":1},{"scopus_import":"1","quality_controlled":"1","issue":"1","doi":"10.1080/23818107.2018.1545142","intvolume":"       166","date_created":"2018-12-16T22:59:20Z","department":[{"_id":"NiBa"}],"abstract":[{"text":"Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones.","lang":"eng"}],"date_published":"2019-01-01T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2381-8107"],"eissn":["2381-8115"]},"citation":{"ieee":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” <i>Botany Letters</i>, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019.","ama":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. <i>Botany Letters</i>. 2019;166(1):80-92. doi:<a href=\"https://doi.org/10.1080/23818107.2018.1545142\">10.1080/23818107.2018.1545142</a>","mla":"Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” <i>Botany Letters</i>, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:<a href=\"https://doi.org/10.1080/23818107.2018.1545142\">10.1080/23818107.2018.1545142</a>.","chicago":"Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” <i>Botany Letters</i>. Taylor and Francis, 2019. <a href=\"https://doi.org/10.1080/23818107.2018.1545142\">https://doi.org/10.1080/23818107.2018.1545142</a>.","short":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92.","ista":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92.","apa":"Andalo, C., Burrus, M., Paute, S., Lauzeral, C., &#38; Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. <i>Botany Letters</i>. Taylor and Francis. <a href=\"https://doi.org/10.1080/23818107.2018.1545142\">https://doi.org/10.1080/23818107.2018.1545142</a>"},"year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","author":[{"first_name":"Christophe","last_name":"Andalo","full_name":"Andalo, Christophe"},{"first_name":"Monique","last_name":"Burrus","full_name":"Burrus, Monique"},{"full_name":"Paute, Sandrine","last_name":"Paute","first_name":"Sandrine"},{"last_name":"Lauzeral","full_name":"Lauzeral, Christine","first_name":"Christine"},{"last_name":"Field","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478"}],"isi":1,"date_updated":"2025-07-10T11:52:54Z","external_id":{"isi":["000463802800009"]},"publisher":"Taylor and Francis","_id":"5680","publication":"Botany Letters","day":"01","oa_version":"None","month":"01","volume":166,"publication_status":"published","type":"journal_article","page":"80-92","status":"public"},{"type":"journal_article","publication_status":"published","file":[{"content_type":"application/pdf","date_updated":"2020-10-21T07:18:35Z","creator":"dernst","relation":"main_file","access_level":"open_access","file_size":71590590,"date_created":"2020-10-21T07:18:35Z","checksum":"e38523787b3bc84006f2793de99ad70f","file_name":"2018_NatureCellBio_Petridou_accepted.pdf","file_id":"8685","success":1}],"month":"02","volume":21,"ddc":["570"],"status":"public","oa":1,"page":"169–178","acknowledged_ssus":[{"_id":"Bio"}],"publisher":"Nature Publishing Group","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["30559456"],"isi":["000457468300011"]},"has_accepted_license":"1","pmid":1,"oa_version":"Submitted Version","ec_funded":1,"_id":"5789","publication":"Nature Cell Biology","day":"01","citation":{"ieee":"N. Petridou, S. Grigolon, G. Salbreux, E. B. Hannezo, and C.-P. J. Heisenberg, “Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling,” <i>Nature Cell Biology</i>, vol. 21. Nature Publishing Group, pp. 169–178, 2019.","ama":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. <i>Nature Cell Biology</i>. 2019;21:169–178. doi:<a href=\"https://doi.org/10.1038/s41556-018-0247-4\">10.1038/s41556-018-0247-4</a>","mla":"Petridou, Nicoletta, et al. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” <i>Nature Cell Biology</i>, vol. 21, Nature Publishing Group, 2019, pp. 169–178, doi:<a href=\"https://doi.org/10.1038/s41556-018-0247-4\">10.1038/s41556-018-0247-4</a>.","ista":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. 2019. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 21, 169–178.","chicago":"Petridou, Nicoletta, Silvia Grigolon, Guillaume Salbreux, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41556-018-0247-4\">https://doi.org/10.1038/s41556-018-0247-4</a>.","short":"N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 169–178.","apa":"Petridou, N., Grigolon, S., Salbreux, G., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2019). Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41556-018-0247-4\">https://doi.org/10.1038/s41556-018-0247-4</a>"},"year":"2019","article_processing_charge":"No","publication_identifier":{"issn":["1465-7392"]},"language":[{"iso":"eng"}],"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/","relation":"press_release"}]},"date_updated":"2025-07-10T11:52:59Z","isi":1,"author":[{"last_name":"Petridou","full_name":"Petridou, Nicoletta","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8451-1195","first_name":"Nicoletta"},{"first_name":"Silvia","last_name":"Grigolon","full_name":"Grigolon, Silvia"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","doi":"10.1038/s41556-018-0247-4","date_created":"2018-12-30T22:59:15Z","intvolume":"        21","quality_controlled":"1","scopus_import":"1","article_type":"original","file_date_updated":"2020-10-21T07:18:35Z","abstract":[{"lang":"eng","text":"Tissue morphogenesis is driven by mechanical forces that elicit changes in cell size, shape and motion. The extent by which forces deform tissues critically depends on the rheological properties of the recipient tissue. Yet, whether and how dynamic changes in tissue rheology affect tissue morphogenesis and how they are regulated within the developing organism remain unclear. Here, we show that blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid, pronounced and spatially patterned tissue fluidization. Blastoderm fluidization is temporally controlled by mitotic cell rounding-dependent cell–cell contact disassembly during the last rounds of cell cleavages. Moreover, fluidization is spatially restricted to the central blastoderm by local activation of non-canonical Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby counteracting the effect of mitotic rounding on contact disassembly. Overall, our results identify a fluidity transition mediated by loss of cell cohesion as a critical regulator of embryo morphogenesis."}],"date_published":"2019-02-01T00:00:00Z","department":[{"_id":"CaHe"},{"_id":"EdHa"}]},{"publication_status":"published","type":"book_chapter","citation":{"apa":"Asaoka, Y., Morita, H., Furumoto, H., Heisenberg, C.-P. J., &#38; Furutani-Seiki, M. (2019). Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In A. Hergovich (Ed.), <i>The hippo pathway</i> (Vol. 1893, pp. 167–181). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-8910-2_14\">https://doi.org/10.1007/978-1-4939-8910-2_14</a>","mla":"Asaoka, Yoichi, et al. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” <i>The Hippo Pathway</i>, edited by Alexander Hergovich, vol. 1893, Springer, 2019, pp. 167–81, doi:<a href=\"https://doi.org/10.1007/978-1-4939-8910-2_14\">10.1007/978-1-4939-8910-2_14</a>.","short":"Y. Asaoka, H. Morita, H. Furumoto, C.-P.J. Heisenberg, M. Furutani-Seiki, in:, A. Hergovich (Ed.), The Hippo Pathway, Springer, 2019, pp. 167–181.","chicago":"Asaoka, Yoichi, Hitoshi Morita, Hiroko Furumoto, Carl-Philipp J Heisenberg, and Makoto Furutani-Seiki. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” In <i>The Hippo Pathway</i>, edited by Alexander Hergovich, 1893:167–81. Methods in Molecular Biology. Springer, 2019. <a href=\"https://doi.org/10.1007/978-1-4939-8910-2_14\">https://doi.org/10.1007/978-1-4939-8910-2_14</a>.","ista":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. 2019.Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: The hippo pathway. MIMB, vol. 1893, 167–181.","ieee":"Y. Asaoka, H. Morita, H. Furumoto, C.-P. J. Heisenberg, and M. Furutani-Seiki, “Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids,” in <i>The hippo pathway</i>, vol. 1893, A. Hergovich, Ed. Springer, 2019, pp. 167–181.","ama":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: Hergovich A, ed. <i>The Hippo Pathway</i>. Vol 1893. Methods in Molecular Biology. Springer; 2019:167-181. doi:<a href=\"https://doi.org/10.1007/978-1-4939-8910-2_14\">10.1007/978-1-4939-8910-2_14</a>"},"year":"2019","series_title":"Methods in Molecular Biology","month":"01","publication_identifier":{"isbn":["978-1-4939-8909-6"]},"language":[{"iso":"eng"}],"volume":1893,"status":"public","date_updated":"2021-01-12T08:03:30Z","page":"167-181","editor":[{"last_name":"Hergovich","full_name":"Hergovich, Alexander","first_name":"Alexander"}],"title":"Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Asaoka","full_name":"Asaoka, Yoichi","first_name":"Yoichi"},{"full_name":"Morita, Hitoshi","last_name":"Morita","first_name":"Hitoshi"},{"first_name":"Hiroko","last_name":"Furumoto","full_name":"Furumoto, Hiroko"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"first_name":"Makoto","last_name":"Furutani-Seiki","full_name":"Furutani-Seiki, Makoto"}],"doi":"10.1007/978-1-4939-8910-2_14","publisher":"Springer","date_created":"2019-01-06T22:59:11Z","intvolume":"      1893","scopus_import":1,"quality_controlled":"1","abstract":[{"text":"The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis.","lang":"eng"}],"date_published":"2019-01-01T00:00:00Z","oa_version":"None","_id":"5793","alternative_title":["MIMB"],"department":[{"_id":"CaHe"}],"day":"01","publication":"The hippo pathway"},{"status":"public","oa":1,"ddc":["530"],"page":"602-614","type":"journal_article","publication_status":"published","corr_author":"1","file":[{"access_level":"open_access","relation":"main_file","creator":"bkavcic","date_updated":"2020-10-09T11:00:05Z","content_type":"application/pdf","success":1,"file_id":"8641","file_name":"lmt_sftmtr_V8.pdf","checksum":"614c337d6424ccd3d48d1b1f9513510d","date_created":"2020-10-09T11:00:05Z","file_size":5370762}],"month":"01","volume":15,"pmid":1,"oa_version":"Submitted Version","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode"},"_id":"5817","day":"10","publication":"Soft Matter","external_id":{"pmid":["30629082"],"isi":["000457329700003"]},"publisher":"Royal Society of Chemistry","has_accepted_license":"1","date_updated":"2024-10-09T20:58:29Z","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-6041-254X","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor","last_name":"Kavcic"},{"last_name":"Sakashita","full_name":"Sakashita, A.","first_name":"A."},{"first_name":"H.","full_name":"Noguchi, H.","last_name":"Noguchi"},{"full_name":"Ziherl, P.","last_name":"Ziherl","first_name":"P."}],"title":"Limiting shapes of confined lipid vesicles","citation":{"apa":"Kavcic, B., Sakashita, A., Noguchi, H., &#38; Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c8sm01956h\">https://doi.org/10.1039/c8sm01956h</a>","mla":"Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” <i>Soft Matter</i>, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:<a href=\"https://doi.org/10.1039/c8sm01956h\">10.1039/c8sm01956h</a>.","chicago":"Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” <i>Soft Matter</i>. Royal Society of Chemistry, 2019. <a href=\"https://doi.org/10.1039/c8sm01956h\">https://doi.org/10.1039/c8sm01956h</a>.","ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614.","short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.","ieee":"B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” <i>Soft Matter</i>, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019.","ama":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. <i>Soft Matter</i>. 2019;15(4):602-614. doi:<a href=\"https://doi.org/10.1039/c8sm01956h\">10.1039/c8sm01956h</a>"},"year":"2019","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"abstract":[{"lang":"eng","text":"We theoretically study the shapes of lipid vesicles confined to a spherical cavity, elaborating a framework based on the so-called limiting shapes constructed from geometrically simple structural elements such as double-membrane walls and edges. Partly inspired by numerical results, the proposed non-compartmentalized and compartmentalized limiting shapes are arranged in the bilayer-couple phase diagram which is then compared to its free-vesicle counterpart. We also compute the area-difference-elasticity phase diagram of the limiting shapes and we use it to interpret shape transitions experimentally observed in vesicles confined within another vesicle. The limiting-shape framework may be generalized to theoretically investigate the structure of certain cell organelles such as the mitochondrion."}],"date_published":"2019-01-10T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","department":[{"_id":"GaTk"}],"doi":"10.1039/c8sm01956h","intvolume":"        15","date_created":"2019-01-11T07:37:47Z","scopus_import":"1","quality_controlled":"1","file_date_updated":"2020-10-09T11:00:05Z","article_type":"original","issue":"4"},{"external_id":{"isi":["000457409100028"],"arxiv":["1812.09011"]},"publisher":"AIP Publishing","main_file_link":[{"url":"https://arxiv.org/abs/1812.09011","open_access":"1"}],"oa_version":"Preprint","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","day":"22","article_number":"013122","_id":"5878","publication_status":"published","type":"journal_article","volume":29,"month":"01","oa":1,"status":"public","intvolume":"        29","date_created":"2019-01-23T08:35:09Z","doi":"10.1063/1.5058279","issue":"1","article_type":"original","quality_controlled":"1","scopus_import":"1","date_published":"2019-01-22T00:00:00Z","arxiv":1,"abstract":[{"text":"We consider the motion of a droplet bouncing on a vibrating bath of the same fluid in the presence of a central potential. We formulate a rotation symmetry-reduced description of this system, which allows for the straightforward application of dynamical systems theory tools. As an illustration of the utility of the symmetry reduction, we apply it to a model of the pilot-wave system with a central harmonic force. We begin our analysis by identifying local bifurcations and the onset of chaos. We then describe the emergence of chaotic regions and their merging bifurcations, which lead to the formation of a global attractor. In this final regime, the droplet’s angular momentum spontaneously changes its sign as observed in the experiments of Perrard et al.","lang":"eng"}],"department":[{"_id":"BjHo"}],"year":"2019","citation":{"ieee":"N. B. Budanur and M. Fleury, “State space geometry of the chaotic pilot-wave hydrodynamics,” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 29, no. 1. AIP Publishing, 2019.","ama":"Budanur NB, Fleury M. State space geometry of the chaotic pilot-wave hydrodynamics. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. 2019;29(1). doi:<a href=\"https://doi.org/10.1063/1.5058279\">10.1063/1.5058279</a>","apa":"Budanur, N. B., &#38; Fleury, M. (2019). State space geometry of the chaotic pilot-wave hydrodynamics. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5058279\">https://doi.org/10.1063/1.5058279</a>","mla":"Budanur, Nazmi B., and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 29, no. 1, 013122, AIP Publishing, 2019, doi:<a href=\"https://doi.org/10.1063/1.5058279\">10.1063/1.5058279</a>.","chicago":"Budanur, Nazmi B, and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing, 2019. <a href=\"https://doi.org/10.1063/1.5058279\">https://doi.org/10.1063/1.5058279</a>.","short":"N.B. Budanur, M. Fleury, Chaos: An Interdisciplinary Journal of Nonlinear Science 29 (2019).","ista":"Budanur NB, Fleury M. 2019. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 29(1), 013122."},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"article_processing_charge":"No","date_updated":"2023-08-25T10:16:11Z","isi":1,"related_material":{"link":[{"url":"https://aip.scitation.org/doi/abs/10.1063/1.5097157","relation":"erratum"}]},"title":"State space geometry of the chaotic pilot-wave hydrodynamics","author":[{"last_name":"Budanur","full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","orcid":"0000-0003-0423-5010"},{"first_name":"Marc","full_name":"Fleury, Marc","last_name":"Fleury"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"external_id":{"isi":["000456783700001"],"arxiv":["1807.04285"]},"publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.04285"}],"article_number":"040601","publication":"Physical Review Letters","day":"01","_id":"5906","oa_version":"Preprint","volume":122,"month":"02","type":"journal_article","publication_status":"published","status":"public","oa":1,"article_type":"original","issue":"4","quality_controlled":"1","scopus_import":"1","intvolume":"       122","date_created":"2019-02-01T08:22:28Z","doi":"10.1103/physrevlett.122.040601","department":[{"_id":"MaSe"}],"date_published":"2019-02-01T00:00:00Z","arxiv":1,"abstract":[{"text":"We introduce a simple, exactly solvable strong-randomness renormalization group (RG) model for the many-body localization (MBL) transition in one dimension. Our approach relies on a family of RG flows parametrized by the asymmetry between thermal and localized phases. We identify the physical MBL transition in the limit of maximal asymmetry, reflecting the instability of MBL against rare thermal inclusions. We find a critical point that is localized with power-law distributed thermal inclusions. The typical size of critical inclusions remains finite at the transition, while the average size is logarithmically diverging. We propose a two-parameter scaling theory for the many-body localization transition that falls into the Kosterlitz-Thouless universality class, with the MBL phase corresponding to a stable line of fixed points with multifractal behavior.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"article_processing_charge":"No","year":"2019","citation":{"ieee":"A. Goremykina, R. Vasseur, and M. Serbyn, “Analytically solvable renormalization group for the many-body localization transition,” <i>Physical Review Letters</i>, vol. 122, no. 4. American Physical Society, 2019.","ama":"Goremykina A, Vasseur R, Serbyn M. Analytically solvable renormalization group for the many-body localization transition. <i>Physical Review Letters</i>. 2019;122(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.122.040601\">10.1103/physrevlett.122.040601</a>","apa":"Goremykina, A., Vasseur, R., &#38; Serbyn, M. (2019). Analytically solvable renormalization group for the many-body localization transition. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.122.040601\">https://doi.org/10.1103/physrevlett.122.040601</a>","mla":"Goremykina, Anna, et al. “Analytically Solvable Renormalization Group for the Many-Body Localization Transition.” <i>Physical Review Letters</i>, vol. 122, no. 4, 040601, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevlett.122.040601\">10.1103/physrevlett.122.040601</a>.","ista":"Goremykina A, Vasseur R, Serbyn M. 2019. Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. 122(4), 040601.","chicago":"Goremykina, Anna, Romain Vasseur, and Maksym Serbyn. “Analytically Solvable Renormalization Group for the Many-Body Localization Transition.” <i>Physical Review Letters</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevlett.122.040601\">https://doi.org/10.1103/physrevlett.122.040601</a>.","short":"A. Goremykina, R. Vasseur, M. Serbyn, Physical Review Letters 122 (2019)."},"author":[{"first_name":"Anna","last_name":"Goremykina","full_name":"Goremykina, Anna"},{"last_name":"Vasseur","full_name":"Vasseur, Romain","first_name":"Romain"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","last_name":"Serbyn"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Analytically solvable renormalization group for the many-body localization transition","isi":1,"date_updated":"2024-02-28T13:13:38Z"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","_id":"5907","article_number":"331","publication":"Scientific Reports","day":"23","publisher":"Nature Publishing Group","external_id":{"isi":["000456392400012"]},"has_accepted_license":"1","ddc":["580"],"oa":1,"status":"public","publication_status":"published","type":"journal_article","month":"01","file":[{"date_created":"2019-02-05T13:10:02Z","checksum":"4129c7d7663d1f8a1edf8c4232372f66","file_size":2124292,"file_name":"2019_ScientificReports_Mocsai.pdf","file_id":"5923","content_type":"application/pdf","date_updated":"2020-07-14T12:47:13Z","creator":"dernst","relation":"main_file","access_level":"open_access"}],"volume":9,"abstract":[{"text":"Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins.","lang":"eng"}],"date_published":"2019-01-23T00:00:00Z","department":[{"_id":"FlSc"}],"doi":"10.1038/s41598-018-36884-1","date_created":"2019-02-03T22:59:13Z","intvolume":"         9","scopus_import":"1","quality_controlled":"1","issue":"1","file_date_updated":"2020-07-14T12:47:13Z","date_updated":"2023-08-24T14:33:16Z","isi":1,"author":[{"first_name":"Réka","last_name":"Mócsai","full_name":"Mócsai, Réka"},{"full_name":"Figl, Rudolf","last_name":"Figl","first_name":"Rudolf"},{"first_name":"Clemens","full_name":"Troschl, Clemens","last_name":"Troschl"},{"first_name":"Richard","full_name":"Strasser, Richard","last_name":"Strasser"},{"first_name":"Elisabeth","full_name":"Svehla, Elisabeth","last_name":"Svehla"},{"first_name":"Markus","full_name":"Windwarder, Markus","last_name":"Windwarder"},{"full_name":"Thader, Andreas","last_name":"Thader","first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Friedrich","full_name":"Altmann, Friedrich","last_name":"Altmann"}],"title":"N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” <i>Scientific Reports</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41598-018-36884-1\">https://doi.org/10.1038/s41598-018-36884-1</a>.","short":"R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (2019).","ista":"Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A, Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 9(1), 331.","mla":"Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” <i>Scientific Reports</i>, vol. 9, no. 1, 331, Nature Publishing Group, 2019, doi:<a href=\"https://doi.org/10.1038/s41598-018-36884-1\">10.1038/s41598-018-36884-1</a>.","apa":"Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M., … Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-36884-1\">https://doi.org/10.1038/s41598-018-36884-1</a>","ama":"Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. <i>Scientific Reports</i>. 2019;9(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-36884-1\">10.1038/s41598-018-36884-1</a>","ieee":"R. Mócsai <i>et al.</i>, “N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated,” <i>Scientific Reports</i>, vol. 9, no. 1. Nature Publishing Group, 2019."},"year":"2019","article_processing_charge":"No","language":[{"iso":"eng"}]},{"year":"2019","citation":{"mla":"Lee, Eunkyoung, et al. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1420–29, doi:<a href=\"https://doi.org/10.1073/pnas.1818099116\">10.1073/pnas.1818099116</a>.","chicago":"Lee, Eunkyoung, Steffen Vanneste, Jessica Pérez-Sancho, Francisco Benitez-Fuente, Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiří Friml, and Abel Rosado. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1818099116\">https://doi.org/10.1073/pnas.1818099116</a>.","short":"E. Lee, S. Vanneste, J. Pérez-Sancho, F. Benitez-Fuente, M. Strelau, A.P. Macho, M.A. Botella, J. Friml, A. Rosado, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 1420–1429.","ista":"Lee E, Vanneste S, Pérez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP, Botella MA, Friml J, Rosado A. 2019. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 116(4), 1420–1429.","apa":"Lee, E., Vanneste, S., Pérez-Sancho, J., Benitez-Fuente, F., Strelau, M., Macho, A. P., … Rosado, A. (2019). Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1818099116\">https://doi.org/10.1073/pnas.1818099116</a>","ieee":"E. Lee <i>et al.</i>, “Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 4. National Academy of Sciences, pp. 1420–1429, 2019.","ama":"Lee E, Vanneste S, Pérez-Sancho J, et al. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2019;116(4):1420-1429. doi:<a href=\"https://doi.org/10.1073/pnas.1818099116\">10.1073/pnas.1818099116</a>"},"language":[{"iso":"eng"}],"article_processing_charge":"No","date_updated":"2023-08-24T14:31:09Z","isi":1,"author":[{"first_name":"Eunkyoung","full_name":"Lee, Eunkyoung","last_name":"Lee"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Jessica","last_name":"Pérez-Sancho","full_name":"Pérez-Sancho, Jessica"},{"first_name":"Francisco","last_name":"Benitez-Fuente","full_name":"Benitez-Fuente, Francisco"},{"first_name":"Matthew","last_name":"Strelau","full_name":"Strelau, Matthew"},{"full_name":"Macho, Alberto P.","last_name":"Macho","first_name":"Alberto P."},{"first_name":"Miguel A.","full_name":"Botella, Miguel A.","last_name":"Botella"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"full_name":"Rosado, Abel","last_name":"Rosado","first_name":"Abel"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis","date_created":"2019-02-03T22:59:14Z","intvolume":"       116","doi":"10.1073/pnas.1818099116","article_type":"original","issue":"4","scopus_import":"1","quality_controlled":"1","date_published":"2019-01-22T00:00:00Z","abstract":[{"text":"The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants.","lang":"eng"}],"department":[{"_id":"JiFr"}],"publication_status":"published","type":"journal_article","volume":116,"month":"01","oa":1,"status":"public","page":"1420-1429","publisher":"National Academy of Sciences","external_id":{"isi":["000456336100050"],"pmid":["30610176"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1818099116"}],"oa_version":"Published Version","pmid":1,"day":"22","publication":"Proceedings of the National Academy of Sciences of the United States of America","_id":"5908"},{"title":"Experiments on a jet in a crossflow in the low-velocity-ratio regime","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0003-1740-7635","first_name":"Lukasz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","full_name":"Klotz, Lukasz","last_name":"Klotz"},{"first_name":"Konrad","last_name":"Gumowski","full_name":"Gumowski, Konrad"},{"last_name":"Wesfreid","full_name":"Wesfreid, José Eduardo","first_name":"José Eduardo"}],"isi":1,"date_updated":"2025-04-14T07:43:59Z","language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2019","citation":{"ieee":"L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow in the low-velocity-ratio regime,” <i>Journal of Fluid Mechanics</i>, vol. 863. Cambridge University Press, pp. 386–406, 2019.","ama":"Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the low-velocity-ratio regime. <i>Journal of Fluid Mechanics</i>. 2019;863:386-406. doi:<a href=\"https://doi.org/10.1017/jfm.2018.974\">10.1017/jfm.2018.974</a>","apa":"Klotz, L., Gumowski, K., &#38; Wesfreid, J. E. (2019). Experiments on a jet in a crossflow in the low-velocity-ratio regime. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2018.974\">https://doi.org/10.1017/jfm.2018.974</a>","mla":"Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” <i>Journal of Fluid Mechanics</i>, vol. 863, Cambridge University Press, 2019, pp. 386–406, doi:<a href=\"https://doi.org/10.1017/jfm.2018.974\">10.1017/jfm.2018.974</a>.","ista":"Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406.","short":"L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019) 386–406.","chicago":"Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2019. <a href=\"https://doi.org/10.1017/jfm.2018.974\">https://doi.org/10.1017/jfm.2018.974</a>."},"department":[{"_id":"BjHo"}],"arxiv":1,"date_published":"2019-03-25T00:00:00Z","abstract":[{"lang":"eng","text":"The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow velocity ratio is investigated experimentally for a velocity ratio range of R ∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral analysis we characterize the Strouhal number and amplitude of the hairpin instability as a function of R and ReD. We demonstrate that the dynamics of the hairpins is well described by the Landau model, and, hence, that the instability occurs through Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind different bluff bodies. Using the Landau model, we determine the precise threshold values of hairpin shedding. We also study the spatial dependence of this hydrodynamical instability, which shows a global behaviour."}],"article_type":"original","scopus_import":"1","quality_controlled":"1","date_created":"2019-02-10T22:59:15Z","intvolume":"       863","doi":"10.1017/jfm.2018.974","page":"386-406","oa":1,"status":"public","volume":863,"month":"03","publication_status":"published","type":"journal_article","day":"25","publication":"Journal of Fluid Mechanics","_id":"5943","ec_funded":1,"oa_version":"Preprint","publisher":"Cambridge University Press","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"external_id":{"arxiv":["1902.07931"],"isi":["000526029100016"]},"main_file_link":[{"url":"https://arxiv.org/abs/1902.07931","open_access":"1"}]}]