[{"date_updated":"2021-01-12T06:49:22Z","day":"07","citation":{"apa":"Kabakova, I., De Hoogh, A., Van Der Wel, R., Wulf, M., Le Feber, B., & Kuipers, L. (2016). Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep22665","short":"I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, L. Kuipers, Scientific Reports 6 (2016).","ieee":"I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, and L. Kuipers, “Imaging of electric and magnetic fields near plasmonic nanowires,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","ista":"Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. 2016. Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. 6, 22665.","ama":"Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. 2016;6. doi:10.1038/srep22665","mla":"Kabakova, Irina, et al. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” Scientific Reports, vol. 6, 22665, Nature Publishing Group, 2016, doi:10.1038/srep22665.","chicago":"Kabakova, Irina, Anouk De Hoogh, Ruben Van Der Wel, Matthias Wulf, Boris Le Feber, and Laurens Kuipers. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep22665."},"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5061","creator":"system","file_size":1425165,"date_created":"2018-12-12T10:14:11Z","checksum":"ca76236cb1aae22cb90c65313e2c5e98","date_updated":"2020-07-14T12:44:41Z","file_name":"IST-2016-707-v1+1_srep22665.pdf"}],"volume":6,"has_accepted_license":"1","month":"03","date_created":"2018-12-11T11:50:55Z","license":"https://creativecommons.org/licenses/by/4.0/","date_published":"2016-03-07T00:00:00Z","publication":"Scientific Reports","intvolume":" 6","quality_controlled":"1","publisher":"Nature Publishing Group","status":"public","title":"Imaging of electric and magnetic fields near plasmonic nanowires","article_number":"22665","author":[{"full_name":"Kabakova, Irina","first_name":"Irina","last_name":"Kabakova"},{"full_name":"De Hoogh, Anouk","last_name":"De Hoogh","first_name":"Anouk"},{"full_name":"Van Der Wel, Ruben","first_name":"Ruben","last_name":"Van Der Wel"},{"last_name":"Wulf","orcid":"0000-0001-6613-1378","first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias"},{"full_name":"Le Feber, Boris","last_name":"Le Feber","first_name":"Boris"},{"full_name":"Kuipers, Laurens","first_name":"Laurens","last_name":"Kuipers"}],"oa":1,"type":"journal_article","year":"2016","scopus_import":1,"pubrep_id":"707","doi":"10.1038/srep22665","publist_id":"6082","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","_id":"1246","language":[{"iso":"eng"}],"publication_status":"published","ddc":["539"],"department":[{"_id":"JoFi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Near-field imaging is a powerful tool to investigate the complex structure of light at the nanoscale. Recent advances in near-field imaging have indicated the possibility for the complete reconstruction of both electric and magnetic components of the evanescent field. Here we study the electro-magnetic field structure of surface plasmon polariton waves propagating along subwavelength gold nanowires by performing phase- and polarization-resolved near-field microscopy in collection mode. By applying the optical reciprocity theorem, we describe the signal collected by the probe as an overlap integral of the nanowire's evanescent field and the probe's response function. As a result, we find that the probe's sensitivity to the magnetic field is approximately equal to its sensitivity to the electric field. Through rigorous modeling of the nanowire mode as well as the aperture probe response function, we obtain a good agreement between experimentally measured signals and a numerical model. Our findings provide a better understanding of aperture-based near-field imaging of the nanoscopic plasmonic and photonic structures and are helpful for the interpretation of future near-field experiments.","lang":"eng"}],"acknowledgement":"This work is supported part of the research program of the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO), and part of this work has been funded by the project ‘SPANGL4Q’, which acknowledges the financial support of the Future and Emerging Technologies (FET) program within the Seventh Framework Programme for Research of the European Commission, under FETOpen grant number: FP7-284743. L.K. acknowledges funding from ERC Advanced, Investigator Grant (no. 240438-CONSTANS).","file_date_updated":"2020-07-14T12:44:41Z"},{"oa_version":"Submitted Version","publist_id":"6081","doi":"10.1073/pnas.1501343112","scopus_import":1,"type":"journal_article","year":"2016","acknowledgement":"This work was supported by the Ghent University Special Research Fund (M.K.), the European Research Council (Project ERC-2011-StG-20101109-PSDP) (to J.F.), and the Körber European Science Foun-\r\ndation (J.F.). S.D.G. is indebted to the Agency for Science and Technology for\r\na predoctoral fellowship.","ec_funded":1,"abstract":[{"lang":"eng","text":"The shaping of organs in plants depends on the intercellular flow of the phytohormone auxin, of which the directional signaling is determined by the polar subcellular localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID kinase, which act antagonistically to mediate their apical-basal polar delivery. Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant phenotypes [i.e., reduced apical dominance, primary root length, lateral root emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia; decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems; hypergravitropic root growth and response; increased IAA levels in shoot apices; and reduced auxin accumulation in root meristems] support a role for RON3 in auxin biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3 might act in PIN transporter trafficking. Indeed, pharmacological interference with vesicle trafficking processes revealed that single ron3-2 and double ron3-2 rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our data indicate that RON3 contributes to auxin-mediated development by playing a role in PIN recycling and polarity establishment through regulation of the PP2A complex activity."}],"department":[{"_id":"JiFr"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"publication_status":"published","language":[{"iso":"eng"}],"_id":"1247","month":"03","date_created":"2018-12-11T11:50:56Z","date_published":"2016-03-08T00:00:00Z","volume":113,"date_updated":"2021-01-12T06:49:22Z","day":"08","citation":{"apa":"Karampelias, M., Neyt, P., De Groeve, S., Aesaert, S., Coussens, G., Rolčík, J., … Van Lijsebettens, M. (2016). ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1501343112","short":"M. Karampelias, P. Neyt, S. De Groeve, S. Aesaert, G. Coussens, J. Rolčík, L. Bruno, N. De Winne, A. Van Minnebruggen, M. Van Montagu, M. Ponce, J. Micol, J. Friml, G. De Jaeger, M. Van Lijsebettens, PNAS 113 (2016) 2768–2773.","ieee":"M. Karampelias et al., “ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling,” PNAS, vol. 113, no. 10. National Academy of Sciences, pp. 2768–2773, 2016.","chicago":"Karampelias, Michael, Pia Neyt, Steven De Groeve, Stijn Aesaert, Griet Coussens, Jakub Rolčík, Leonardo Bruno, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1501343112.","ista":"Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce M, Micol J, Friml J, De Jaeger G, Van Lijsebettens M. 2016. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 113(10), 2768–2773.","ama":"Karampelias M, Neyt P, De Groeve S, et al. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 2016;113(10):2768-2773. doi:10.1073/pnas.1501343112","mla":"Karampelias, Michael, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS, vol. 113, no. 10, National Academy of Sciences, 2016, pp. 2768–73, doi:10.1073/pnas.1501343112."},"author":[{"first_name":"Michael","last_name":"Karampelias","full_name":"Karampelias, Michael"},{"full_name":"Neyt, Pia","first_name":"Pia","last_name":"Neyt"},{"full_name":"De Groeve, Steven","last_name":"De Groeve","first_name":"Steven"},{"last_name":"Aesaert","first_name":"Stijn","full_name":"Aesaert, Stijn"},{"last_name":"Coussens","first_name":"Griet","full_name":"Coussens, Griet"},{"last_name":"Rolčík","first_name":"Jakub","full_name":"Rolčík, Jakub"},{"full_name":"Bruno, Leonardo","last_name":"Bruno","first_name":"Leonardo"},{"full_name":"De Winne, Nancy","first_name":"Nancy","last_name":"De Winne"},{"last_name":"Van Minnebruggen","first_name":"Annemie","full_name":"Van Minnebruggen, Annemie"},{"full_name":"Van Montagu, Marc","last_name":"Van Montagu","first_name":"Marc"},{"full_name":"Ponce, Maria","last_name":"Ponce","first_name":"Maria"},{"full_name":"Micol, José","last_name":"Micol","first_name":"José"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"},{"first_name":"Geert","last_name":"De Jaeger","full_name":"De Jaeger, Geert"},{"first_name":"Mieke","last_name":"Van Lijsebettens","full_name":"Van Lijsebettens, Mieke"}],"oa":1,"status":"public","title":"ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling","intvolume":" 113","publication":"PNAS","publisher":"National Academy of Sciences","page":"2768 - 2773","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/"}],"issue":"10"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.8752"}],"quality_controlled":"1","page":"89 - 117","publisher":"Annual Reviews","publication":"Annual Review of Condensed Matter Physics","intvolume":" 7","title":"Information processing in living systems","status":"public","oa":1,"author":[{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William"}],"day":"10","citation":{"short":"G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.","apa":"Tkačik, G., & Bialek, W. (2016). Information processing in living systems. Annual Review of Condensed Matter Physics. Annual Reviews. https://doi.org/10.1146/annurev-conmatphys-031214-014803","ieee":"G. Tkačik and W. Bialek, “Information processing in living systems,” Annual Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016.","ama":"Tkačik G, Bialek W. Information processing in living systems. Annual Review of Condensed Matter Physics. 2016;7:89-117. doi:10.1146/annurev-conmatphys-031214-014803","ista":"Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117.","mla":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” Annual Review of Condensed Matter Physics, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803.","chicago":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” Annual Review of Condensed Matter Physics. Annual Reviews, 2016. https://doi.org/10.1146/annurev-conmatphys-031214-014803."},"date_updated":"2021-01-12T06:49:23Z","volume":7,"date_published":"2016-03-10T00:00:00Z","date_created":"2018-12-11T11:50:56Z","month":"03","language":[{"iso":"eng"}],"_id":"1248","publication_status":"published","project":[{"name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","call_identifier":"FWF"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"abstract":[{"text":"Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information-theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales.","lang":"eng"}],"acknowledgement":"Our work was supported in part by the US\r\nNational Science Foundation (PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651), by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations.","type":"journal_article","year":"2016","scopus_import":1,"doi":"10.1146/annurev-conmatphys-031214-014803","publist_id":"6080","oa_version":"Preprint"},{"oa":1,"author":[{"full_name":"Saha, Arnab","first_name":"Arnab","last_name":"Saha"},{"last_name":"Nishikawa","first_name":"Masatoshi","full_name":"Nishikawa, Masatoshi"},{"last_name":"Behrndt","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Julicher","first_name":"Frank","full_name":"Julicher, Frank"},{"full_name":"Grill, Stephan","last_name":"Grill","first_name":"Stephan"}],"title":"Determining physical properties of the cell cortex","status":"public","publisher":"Biophysical Society","quality_controlled":"1","page":"1421 - 1429","intvolume":" 110","publication":"Biophysical Journal","issue":"6","date_created":"2018-12-11T11:50:56Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_published":"2016-03-29T00:00:00Z","month":"03","has_accepted_license":"1","volume":110,"file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:10:54Z","file_size":1965645,"relation":"main_file","file_id":"4845","creator":"system","checksum":"c408cf2e25a25c8d711cffea524bda55","file_name":"IST-2016-706-v1+1_1-s2.0-S0006349516001582-main.pdf","date_updated":"2020-07-14T12:44:41Z"}],"day":"29","citation":{"apa":"Saha, A., Nishikawa, M., Behrndt, M., Heisenberg, C.-P. J., Julicher, F., & Grill, S. (2016). Determining physical properties of the cell cortex. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2016.02.013","short":"A. Saha, M. Nishikawa, M. Behrndt, C.-P.J. Heisenberg, F. Julicher, S. Grill, Biophysical Journal 110 (2016) 1421–1429.","ieee":"A. Saha, M. Nishikawa, M. Behrndt, C.-P. J. Heisenberg, F. Julicher, and S. Grill, “Determining physical properties of the cell cortex,” Biophysical Journal, vol. 110, no. 6. Biophysical Society, pp. 1421–1429, 2016.","chicago":"Saha, Arnab, Masatoshi Nishikawa, Martin Behrndt, Carl-Philipp J Heisenberg, Frank Julicher, and Stephan Grill. “Determining Physical Properties of the Cell Cortex.” Biophysical Journal. Biophysical Society, 2016. https://doi.org/10.1016/j.bpj.2016.02.013.","ama":"Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. Determining physical properties of the cell cortex. Biophysical Journal. 2016;110(6):1421-1429. doi:10.1016/j.bpj.2016.02.013","ista":"Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. 2016. Determining physical properties of the cell cortex. Biophysical Journal. 110(6), 1421–1429.","mla":"Saha, Arnab, et al. “Determining Physical Properties of the Cell Cortex.” Biophysical Journal, vol. 110, no. 6, Biophysical Society, 2016, pp. 1421–29, doi:10.1016/j.bpj.2016.02.013."},"date_updated":"2021-01-12T06:49:23Z","file_date_updated":"2020-07-14T12:44:41Z","acknowledgement":"S.W.G. acknowledges support by grant no. 281903 from the European Research Council and by grant No. GR-7271/2-1 from the Deutsche Forschungsgemeinschaft. S.W.G. and C.-P.H. acknowledge support through a grant from the Fonds zur Förderung der Wissenschaftlichen Forschung and the Deutsche Forschungsgemeinschaft (No. I930-B20). We are grateful to Daniel Dickinson for providing the LP133 C. elegans strain. We thank G. Salbreux, V. K. Krishnamurthy, and J. S. Bois for fruitful discussions.","abstract":[{"text":"Actin and myosin assemble into a thin layer of a highly dynamic network underneath the membrane of eukaryotic cells. This network generates the forces that drive cell- and tissue-scale morphogenetic processes. The effective material properties of this active network determine large-scale deformations and other morphogenetic events. For example, the characteristic time of stress relaxation (the Maxwell time τM) in the actomyosin sets the timescale of large-scale deformation of the cortex. Similarly, the characteristic length of stress propagation (the hydrodynamic length λ) sets the length scale of slow deformations, and a large hydrodynamic length is a prerequisite for long-ranged cortical flows. Here we introduce a method to determine physical parameters of the actomyosin cortical layer in vivo directly from laser ablation experiments. For this we investigate the cortical response to laser ablation in the one-cell-stage Caenorhabditis elegans embryo and in the gastrulating zebrafish embryo. These responses can be interpreted using a coarse-grained physical description of the cortex in terms of a two-dimensional thin film of an active viscoelastic gel. To determine the Maxwell time τM, the hydrodynamic length λ, the ratio of active stress ζΔμ, and per-area friction γ, we evaluated the response to laser ablation in two different ways: by quantifying flow and density fields as a function of space and time, and by determining the time evolution of the shape of the ablated region. Importantly, both methods provide best-fit physical parameters that are in close agreement with each other and that are similar to previous estimates in the two systems. Our method provides an accurate and robust means for measuring physical parameters of the actomyosin cortical layer. It can be useful for investigations of actomyosin mechanics at the cellular-scale, but also for providing insights into the active mechanics processes that govern tissue-scale morphogenesis.","lang":"eng"}],"project":[{"call_identifier":"FWF","grant_number":"I 930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","name":"Control of Epithelial Cell Layer Spreading in Zebrafish"}],"department":[{"_id":"CaHe"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","ddc":["572","576"],"_id":"1249","language":[{"iso":"eng"}],"oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"publist_id":"6079","doi":"10.1016/j.bpj.2016.02.013","pubrep_id":"706","scopus_import":1,"year":"2016","type":"journal_article"},{"department":[{"_id":"CaGu"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1250","language":[{"iso":"eng"}],"ddc":["576","579"],"publication_status":"published","file_date_updated":"2020-07-14T12:44:41Z","acknowledgement":"This manuscript is dedicated to the memory of Alex Böhm, who was a great friend and a passionate biologist. Alex passed away after the initial submission of this manuscript. We thank Vesna Olivera and Ursula Sauder from the Zentrum für Mikroskopie Uni Basel for excellent service, and Olin Silander, Nikki Freed, and Nela Nikolic for helpful discussions. This work was supported by the Swiss National Science Foundation grants to M. Ackermann and Urs Jenal (supporting AB).","abstract":[{"text":"In bacteria, replicative aging manifests as a difference in growth or survival between the two cells emerging from division. One cell can be regarded as an aging mother with a decreased potential for future survival and division, the other as a rejuvenated daughter. Here, we aimed at investigating some of the processes involved in aging in the bacterium Escherichia coli, where the two types of cells can be distinguished by the age of their cell poles. We found that certain changes in the regulation of the carbohydrate metabolism can affect aging. A mutation in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative lifespan; csrA mutants stop dividing once their pole exceeds an age of about five divisions. These old-pole cells accumulate glycogen at their old cell poles; after their last division, they do not contain a chromosome, presumably because of spatial exclusion by the glycogen aggregates. The new-pole daughters produced by these aging mothers are born young; they only express the deleterious phenotype once their pole is old. These results demonstrate how manipulations of nutrient allocation can lead to the exclusion of the chromosome and limit replicative lifespan in E. coli, and illustrate how mutations can have phenotypic effects that are specific for cells with old poles. This raises the question how bacteria can avoid the accumulation of such mutations in their genomes over evolutionary times, and how they can achieve the long replicative lifespans that have recently been reported.","lang":"eng"}],"pubrep_id":"705","type":"journal_article","year":"2016","scopus_import":1,"oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publist_id":"6077","doi":"10.1371/journal.pgen.1005974","quality_controlled":"1","publisher":"Public Library of Science","publication":"PLoS Genetics","intvolume":" 12","issue":"4","oa":1,"author":[{"last_name":"Boehm","first_name":"Alex","full_name":"Boehm, Alex"},{"first_name":"Markus","last_name":"Arnoldini","full_name":"Arnoldini, Markus"},{"last_name":"Bergmiller","orcid":"0000-0001-5396-4346","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"first_name":"Thomas","last_name":"Röösli","full_name":"Röösli, Thomas"},{"full_name":"Bigosch, Colette","last_name":"Bigosch","first_name":"Colette"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"title":"Genetic manipulation of glycogen allocation affects replicative lifespan in E coli","article_number":"e1005974","status":"public","day":"19","citation":{"chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” PLoS Genetics. Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1005974.","mla":"Boehm, Alex, et al. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” PLoS Genetics, vol. 12, no. 4, e1005974, Public Library of Science, 2016, doi:10.1371/journal.pgen.1005974.","ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 12(4), e1005974.","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 2016;12(4). doi:10.1371/journal.pgen.1005974","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Genetic manipulation of glycogen allocation affects replicative lifespan in E coli,” PLoS Genetics, vol. 12, no. 4. Public Library of Science, 2016.","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, PLoS Genetics 12 (2016).","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann, M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974"},"file":[{"date_updated":"2020-07-14T12:44:41Z","file_name":"IST-2016-705-v1+1_journal.pgen.1005974.PDF","checksum":"53d22b2b39e5adc243d34f18b2615a85","file_size":6273249,"creator":"system","file_id":"5067","relation":"main_file","date_created":"2018-12-12T10:14:17Z","content_type":"application/pdf","access_level":"open_access"}],"date_updated":"2023-02-23T14:11:39Z","related_material":{"record":[{"id":"9873","relation":"research_data","status":"public"}]},"date_created":"2018-12-11T11:50:56Z","date_published":"2016-04-19T00:00:00Z","month":"04","has_accepted_license":"1","volume":12},{"month":"04","date_published":"2016-04-01T00:00:00Z","date_created":"2018-12-11T11:50:57Z","volume":28,"date_updated":"2021-01-12T06:49:24Z","day":"01","citation":{"ama":"Zhu J, Bailly A, Zwiewka M, et al. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 2016;28(4):930-948. doi:10.1105/tpc.15.00726","ista":"Zhu J, Bailly A, Zwiewka M, Sovero V, Di Donato M, Ge P, Oehri J, Aryal B, Hao P, Linnert M, Burgardt N, Lücke C, Weiwad M, Michel M, Weiergräber O, Pollmann S, Azzarello E, Mancuso S, Ferro N, Fukao Y, Hoffmann C, Wedlich Söldner R, Friml J, Thomas C, Geisler M. 2016. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 28(4), 930–948.","mla":"Zhu, Jinsheng, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell, vol. 28, no. 4, American Society of Plant Biologists, 2016, pp. 930–48, doi:10.1105/tpc.15.00726.","chicago":"Zhu, Jinsheng, Aurélien Bailly, Marta Zwiewka, Valpuri Sovero, Martin Di Donato, Pei Ge, Jacqueline Oehri, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00726.","apa":"Zhu, J., Bailly, A., Zwiewka, M., Sovero, V., Di Donato, M., Ge, P., … Geisler, M. (2016). TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.15.00726","short":"J. Zhu, A. Bailly, M. Zwiewka, V. Sovero, M. Di Donato, P. Ge, J. Oehri, B. Aryal, P. Hao, M. Linnert, N. Burgardt, C. Lücke, M. Weiwad, M. Michel, O. Weiergräber, S. Pollmann, E. Azzarello, S. Mancuso, N. Ferro, Y. Fukao, C. Hoffmann, R. Wedlich Söldner, J. Friml, C. Thomas, M. Geisler, Plant Cell 28 (2016) 930–948.","ieee":"J. Zhu et al., “TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics,” Plant Cell, vol. 28, no. 4. American Society of Plant Biologists, pp. 930–948, 2016."},"author":[{"last_name":"Zhu","first_name":"Jinsheng","full_name":"Zhu, Jinsheng"},{"last_name":"Bailly","first_name":"Aurélien","full_name":"Bailly, Aurélien"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"last_name":"Sovero","first_name":"Valpuri","full_name":"Sovero, Valpuri"},{"last_name":"Di Donato","first_name":"Martin","full_name":"Di Donato, Martin"},{"full_name":"Ge, Pei","first_name":"Pei","last_name":"Ge"},{"full_name":"Oehri, Jacqueline","last_name":"Oehri","first_name":"Jacqueline"},{"last_name":"Aryal","first_name":"Bibek","full_name":"Aryal, Bibek"},{"last_name":"Hao","first_name":"Pengchao","full_name":"Hao, Pengchao"},{"full_name":"Linnert, Miriam","first_name":"Miriam","last_name":"Linnert"},{"first_name":"Noelia","last_name":"Burgardt","full_name":"Burgardt, Noelia"},{"first_name":"Christian","last_name":"Lücke","full_name":"Lücke, Christian"},{"full_name":"Weiwad, Matthias","first_name":"Matthias","last_name":"Weiwad"},{"last_name":"Michel","first_name":"Max","full_name":"Michel, Max"},{"full_name":"Weiergräber, Oliver","last_name":"Weiergräber","first_name":"Oliver"},{"first_name":"Stephan","last_name":"Pollmann","full_name":"Pollmann, Stephan"},{"first_name":"Elisa","last_name":"Azzarello","full_name":"Azzarello, Elisa"},{"first_name":"Stefano","last_name":"Mancuso","full_name":"Mancuso, Stefano"},{"full_name":"Ferro, Noel","first_name":"Noel","last_name":"Ferro"},{"full_name":"Fukao, Yoichiro","first_name":"Yoichiro","last_name":"Fukao"},{"first_name":"Céline","last_name":"Hoffmann","full_name":"Hoffmann, Céline"},{"first_name":"Roland","last_name":"Wedlich Söldner","full_name":"Wedlich Söldner, Roland"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"},{"full_name":"Thomas, Clément","first_name":"Clément","last_name":"Thomas"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"}],"oa":1,"status":"public","title":"TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics","intvolume":" 28","publication":"Plant Cell","publisher":"American Society of Plant Biologists","quality_controlled":"1","page":"930 - 948","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863381/"}],"issue":"4","oa_version":"Submitted Version","doi":"10.1105/tpc.15.00726","publist_id":"6078","scopus_import":1,"year":"2016","type":"journal_article","acknowledgement":" This work was supported by grants from the European Social Fund (CZ.1.07/2.3.00/20.0043), the Czech Science Foundation GAČR (GA13-40637S) to J.F. and M.Z., the Ministry of Education, Youth, and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) to M.Z., the Ministry for Higher Education and Research of Luxembourg (REC-LOCM-20140703) to C.T., the Partial Funding Program for Short Stays Abroad of CONICET Argentina (to N.I.B.), Swiss National Funds, the Pool de Recherche of the University of Fribourg, and the Novartis Foundation (all to M.G.). ","abstract":[{"lang":"eng","text":"Plant growth and architecture is regulated by the polar distribution of the hormone auxin. Polarity and flexibility of this process is provided by constant cycling of auxin transporter vesicles along actin filaments, coordinated by a positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic acid (NPA), counteracting the effect of auxin; however, underlying targets and mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis thaliana ABCB chaperone TWISTED DWARF1 (TWD1).We identify ACTIN7 as a relevant, although likely indirect, TWD1 interactor, and show TWD1-dependent regulation of actin filament organization and dynamics and that TWD1 is required for NPA-mediated actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence of efflux transporters, and as a consequence act7 and twd1 share developmental and physiological phenotypes indicative of defects in auxin transport. These can be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide evidence that TWD1 determines downstreamlocations of auxin efflux transporters by adjusting actin filament debundling and dynamizing processes and mediating NPA action on the latter. This function appears to be evolutionary conserved since TWD1 expression in budding yeast alters actin polarization and cell polarity and provides NPA sensitivity."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"publication_status":"published","language":[{"iso":"eng"}],"_id":"1251"},{"oa":1,"author":[{"full_name":"Harker, Shaun","first_name":"Shaun","last_name":"Harker"},{"full_name":"Kokubu, Hiroshi","last_name":"Kokubu","first_name":"Hiroshi"},{"full_name":"Mischaikow, Konstantin","first_name":"Konstantin","last_name":"Mischaikow"},{"last_name":"Pilarczyk","first_name":"Pawel","full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"}],"title":"Inducing a map on homology from a correspondence","status":"public","quality_controlled":"1","page":"1787 - 1801","main_file_link":[{"url":"https://arxiv.org/abs/1411.7563","open_access":"1"}],"publisher":"American Mathematical Society","publication":"Proceedings of the American Mathematical Society","intvolume":" 144","issue":"4","date_published":"2016-04-01T00:00:00Z","date_created":"2018-12-11T11:50:57Z","month":"04","volume":144,"article_type":"original","citation":{"ieee":"S. Harker, H. Kokubu, K. Mischaikow, and P. Pilarczyk, “Inducing a map on homology from a correspondence,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1787–1801, 2016.","apa":"Harker, S., Kokubu, H., Mischaikow, K., & Pilarczyk, P. (2016). Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12812","short":"S. Harker, H. Kokubu, K. Mischaikow, P. Pilarczyk, Proceedings of the American Mathematical Society 144 (2016) 1787–1801.","chicago":"Harker, Shaun, Hiroshi Kokubu, Konstantin Mischaikow, and Pawel Pilarczyk. “Inducing a Map on Homology from a Correspondence.” Proceedings of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/12812.","mla":"Harker, Shaun, et al. “Inducing a Map on Homology from a Correspondence.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2016, pp. 1787–801, doi:10.1090/proc/12812.","ista":"Harker S, Kokubu H, Mischaikow K, Pilarczyk P. 2016. Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. 144(4), 1787–1801.","ama":"Harker S, Kokubu H, Mischaikow K, Pilarczyk P. Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. 2016;144(4):1787-1801. doi:10.1090/proc/12812"},"day":"01","date_updated":"2022-05-24T09:35:58Z","publication_identifier":{"issn":["1088-6826"]},"acknowledgement":"The authors gratefully acknowledge the support of the Lorenz Center which\r\nprovided an opportunity for us to discuss in depth the work of this paper. Research leading to these results has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Funda¸c˜ao para a Ciˆencia e a Tecnologia (FCT) in the framework of the research\r\nproject FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008),\r\nas well as from the People Programme (Marie Curie Actions) of the European\r\nUnion’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033 (supporting PP). The work of the first and third author has\r\nbeen partially supported by NSF grants NSF-DMS-0835621, 0915019, 1125174,\r\n1248071, and contracts from AFOSR and DARPA. The work of the second author\r\nwas supported by Grant-in-Aid for Scientific Research (No. 25287029), Ministry of\r\nEducation, Science, Technology, Culture and Sports, Japan.","article_processing_charge":"No","abstract":[{"text":"We study the homomorphism induced in homology by a closed correspondence between topological spaces, using projections from the graph of the correspondence to its domain and codomain. We provide assumptions under which the homomorphism induced by an outer approximation of a continuous map coincides with the homomorphism induced in homology by the map. In contrast to more classical results we do not require that the projection to the domain have acyclic preimages. Moreover, we show that it is possible to retrieve correct homological information from a correspondence even if some data is missing or perturbed. Finally, we describe an application to combinatorial maps that are either outer approximations of continuous maps or reconstructions of such maps from a finite set of data points.","lang":"eng"}],"ec_funded":1,"project":[{"call_identifier":"FP7","grant_number":"622033","_id":"255F06BE-B435-11E9-9278-68D0E5697425","name":"Persistent Homology - Images, Data and Maps"}],"external_id":{"arxiv":["1411.7563"]},"department":[{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"1252","publication_status":"published","oa_version":"Preprint","publist_id":"6075","doi":"10.1090/proc/12812","arxiv":1,"type":"journal_article","year":"2016","scopus_import":"1"},{"file":[{"content_type":"application/pdf","access_level":"open_access","file_size":601679,"relation":"main_file","creator":"system","file_id":"5278","date_created":"2018-12-12T10:17:24Z","checksum":"649aee381f30f7ef7e9efa912d41c2e3","date_updated":"2020-07-14T12:44:41Z","file_name":"IST-2018-981-v1+1_YNP150011_annotatedproof_FINAL.pdf"}],"day":"01","citation":{"chicago":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” JAMA Psychiatry. American Medical Association, 2016. https://doi.org/10.1001/jamapsychiatry.2015.3144.","ama":"Tsai L, Siegert S. How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. 2016;73(4):409-410. doi:10.1001/jamapsychiatry.2015.3144","ista":"Tsai L, Siegert S. 2016. How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. 73(4), 409–410.","mla":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” JAMA Psychiatry, vol. 73, no. 4, American Medical Association, 2016, pp. 409–10, doi:10.1001/jamapsychiatry.2015.3144.","short":"L. Tsai, S. Siegert, JAMA Psychiatry 73 (2016) 409–410.","apa":"Tsai, L., & Siegert, S. (2016). How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. American Medical Association. https://doi.org/10.1001/jamapsychiatry.2015.3144","ieee":"L. Tsai and S. Siegert, “How MicroRNAs Are involved in splitting the mind,” JAMA Psychiatry, vol. 73, no. 4. American Medical Association, pp. 409–410, 2016."},"date_updated":"2024-02-14T12:07:22Z","has_accepted_license":"1","volume":73,"date_created":"2018-12-11T11:50:58Z","date_published":"2016-04-01T00:00:00Z","month":"04","issue":"4","publisher":"American Medical Association","page":"409 - 410","quality_controlled":"1","intvolume":" 73","publication":"JAMA Psychiatry","title":"How MicroRNAs Are involved in splitting the mind","status":"public","oa":1,"author":[{"full_name":"Tsai, Lihuei","last_name":"Tsai","first_name":"Lihuei"},{"full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra"}],"scopus_import":"1","year":"2016","type":"journal_article","pubrep_id":"981","doi":"10.1001/jamapsychiatry.2015.3144","publist_id":"6074","oa_version":"Submitted Version","pmid":1,"publication_status":"published","ddc":["576","610"],"language":[{"iso":"eng"}],"_id":"1253","external_id":{"pmid":["26963490"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SaSi"}],"abstract":[{"lang":"eng","text":"This article provides an introduction to the role of microRNAs in the nervous system and outlines their potential involvement in the pathophysiology of schizophrenia, which is hypothesized to arise owing to environmental factors and genetic predisposition."}],"publication_identifier":{"issn":["2168-622X"]},"file_date_updated":"2020-07-14T12:44:41Z","article_processing_charge":"No"},{"author":[{"full_name":"Golmakani, Ali","first_name":"Ali","last_name":"Golmakani"},{"full_name":"Luzzatto, Stefano","first_name":"Stefano","last_name":"Luzzatto"},{"last_name":"Pilarczyk","first_name":"Pawel","full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"status":"public","title":"Uniform expansivity outside a critical neighborhood in the quadratic family","intvolume":" 25","publication":"Experimental Mathematics","publisher":"Taylor and Francis","quality_controlled":"1","page":"116 - 124","main_file_link":[{"url":"https://arxiv.org/abs/1504.00116","open_access":"1"}],"issue":"2","month":"04","date_published":"2016-04-02T00:00:00Z","date_created":"2018-12-11T11:50:58Z","volume":25,"date_updated":"2021-01-12T06:49:25Z","citation":{"chicago":"Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics. Taylor and Francis, 2016. https://doi.org/10.1080/10586458.2015.1048011.","mla":"Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics, vol. 25, no. 2, Taylor and Francis, 2016, pp. 116–24, doi:10.1080/10586458.2015.1048011.","ama":"Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 2016;25(2):116-124. doi:10.1080/10586458.2015.1048011","ista":"Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 25(2), 116–124.","ieee":"A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside a critical neighborhood in the quadratic family,” Experimental Mathematics, vol. 25, no. 2. Taylor and Francis, pp. 116–124, 2016.","apa":"Golmakani, A., Luzzatto, S., & Pilarczyk, P. (2016). Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. Taylor and Francis. https://doi.org/10.1080/10586458.2015.1048011","short":"A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016) 116–124."},"day":"02","acknowledgement":"AG and PP were partially supported by Abdus Salam International Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS, and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033. The authors gratefully acknowledge the Department of\r\nMathematics of Kyoto University for providing access\r\nto their server for conducting computations for this\r\nproject.","ec_funded":1,"abstract":[{"lang":"eng","text":"We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"project":[{"name":"Persistent Homology - Images, Data and Maps","_id":"255F06BE-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"622033"}],"publication_status":"published","language":[{"iso":"eng"}],"_id":"1254","oa_version":"Preprint","doi":"10.1080/10586458.2015.1048011","publist_id":"6071","scopus_import":1,"year":"2016","type":"journal_article"},{"issue":"4","intvolume":" 3","publication":"Royal Society Open Science","publisher":"Royal Society, The","quality_controlled":"1","status":"public","article_number":"160138","title":"Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction","author":[{"first_name":"Robert","last_name":"Peuß","full_name":"Peuß, Robert"},{"full_name":"Wensing, Kristina","last_name":"Wensing","first_name":"Kristina"},{"first_name":"Luisa","last_name":"Woestmann","full_name":"Woestmann, Luisa"},{"first_name":"Hendrik","last_name":"Eggert","full_name":"Eggert, Hendrik"},{"orcid":"0000-0002-8214-4758","last_name":"Milutinovic","first_name":"Barbara","full_name":"Milutinovic, Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sroka","first_name":"Marlene","full_name":"Sroka, Marlene"},{"full_name":"Scharsack, Jörn","first_name":"Jörn","last_name":"Scharsack"},{"last_name":"Kurtz","first_name":"Joachim","full_name":"Kurtz, Joachim"},{"last_name":"Armitage","first_name":"Sophie","full_name":"Armitage, Sophie"}],"oa":1,"date_updated":"2021-01-12T06:49:25Z","file":[{"file_name":"IST-2016-704-v1+1_160138.full.pdf","date_updated":"2020-07-14T12:44:41Z","checksum":"c3cd84666c8dc0ce6a784f1c82c1cf68","date_created":"2018-12-12T10:14:01Z","file_size":627377,"relation":"main_file","creator":"system","file_id":"5049","access_level":"open_access","content_type":"application/pdf"}],"citation":{"chicago":"Peuß, Robert, Kristina Wensing, Luisa Woestmann, Hendrik Eggert, Barbara Milutinovic, Marlene Sroka, Jörn Scharsack, Joachim Kurtz, and Sophie Armitage. “Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity, Behaviour and Reproduction.” Royal Society Open Science. Royal Society, The, 2016. https://doi.org/10.1098/rsos.160138.","ista":"Peuß R, Wensing K, Woestmann L, Eggert H, Milutinovic B, Sroka M, Scharsack J, Kurtz J, Armitage S. 2016. Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. Royal Society Open Science. 3(4), 160138.","ama":"Peuß R, Wensing K, Woestmann L, et al. Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. Royal Society Open Science. 2016;3(4). doi:10.1098/rsos.160138","mla":"Peuß, Robert, et al. “Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity, Behaviour and Reproduction.” Royal Society Open Science, vol. 3, no. 4, 160138, Royal Society, The, 2016, doi:10.1098/rsos.160138.","apa":"Peuß, R., Wensing, K., Woestmann, L., Eggert, H., Milutinovic, B., Sroka, M., … Armitage, S. (2016). Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.160138","short":"R. Peuß, K. Wensing, L. Woestmann, H. Eggert, B. Milutinovic, M. Sroka, J. Scharsack, J. Kurtz, S. Armitage, Royal Society Open Science 3 (2016).","ieee":"R. Peuß et al., “Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction,” Royal Society Open Science, vol. 3, no. 4. Royal Society, The, 2016."},"day":"01","volume":3,"has_accepted_license":"1","month":"04","date_created":"2018-12-11T11:50:58Z","date_published":"2016-04-01T00:00:00Z","publication_status":"published","ddc":["576","592"],"_id":"1255","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Down syndrome cell adhesion molecule 1 (Dscam1) has widereaching and vital neuronal functions although the role it plays in insect and crustacean immunity is less well understood. In this study, we combine different approaches to understand the roles that Dscam1 plays in fitness-related contexts in two model insect species. Contrary to our expectations, we found no short-term modulation of Dscam1 gene expression after haemocoelic or oral bacterial exposure in Tribolium castaneum, or after haemocoelic bacterial exposure in Drosophila melanogaster. Furthermore, RNAi-mediated Dscam1 knockdown and subsequent bacterial exposure did not reduce T. castaneum survival. However, Dscam1 knockdown in larvae resulted in adult locomotion defects, as well as dramatically reduced fecundity in males and females. We suggest that Dscam1 does not always play a straightforward role in immunity, but strongly influences behaviour and fecundity. This study takes a step towards understanding more about the role of this intriguing gene from different phenotypic perspectives.","lang":"eng"}],"acknowledgement":"We thank Dietmar Schmucker for reading a draft of this manuscript and thank him and his group for\r\nhelpful discussions. We thank Barbara Hasert, Kevin Ferro and Manuel F. Talarico for technical support and helpful\r\ndiscussions. We also thank two anonymous reviewers for their comments. This study was supported by grants from the Volkswagen Stiftung (1/83 516 and AZ 86020: both to S.A.O.A.) and from the DFG priority programme 1399 ‘Host parasite coevolution’ (KU 1929/4-2 to R.P. and J.K.).","file_date_updated":"2020-07-14T12:44:41Z","scopus_import":1,"year":"2016","type":"journal_article","pubrep_id":"704","doi":"10.1098/rsos.160138","publist_id":"6070","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version"},{"publisher":"IEEE","quality_controlled":"1","status":"public","article_number":"7461337","title":"From stateflow simulation to verified implementation: A verification approach and a real-time train controller design","author":[{"full_name":"Jiang, Yu","first_name":"Yu","last_name":"Jiang"},{"last_name":"Yang","first_name":"Yixiao","full_name":"Yang, Yixiao"},{"full_name":"Liu, Han","first_name":"Han","last_name":"Liu"},{"full_name":"Kong, Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui","orcid":"0000-0002-3066-6941","last_name":"Kong"},{"first_name":"Ming","last_name":"Gu","full_name":"Gu, Ming"},{"full_name":"Sun, Jiaguang","last_name":"Sun","first_name":"Jiaguang"},{"full_name":"Sha, Lui","first_name":"Lui","last_name":"Sha"}],"oa":1,"conference":{"end_date":"2016-04-14","start_date":"2016-04-11","location":"Vienna, Austria","name":"RTAS: Real-time and Embedded Technology and Applications Symposium"},"date_updated":"2021-01-12T06:49:26Z","file":[{"file_name":"IST-2017-780-v1+1_RTAS-42-Camera-Ready.pdf","date_updated":"2020-07-14T12:44:41Z","checksum":"42f0462911cc9957f2356b12fb33b4b6","date_created":"2018-12-12T10:12:31Z","creator":"system","relation":"main_file","file_id":"4949","file_size":1293599,"access_level":"open_access","content_type":"application/pdf"}],"day":"27","citation":{"chicago":"Jiang, Yu, Yixiao Yang, Han Liu, Hui Kong, Ming Gu, Jiaguang Sun, and Lui Sha. “From Stateflow Simulation to Verified Implementation: A Verification Approach and a Real-Time Train Controller Design.” IEEE, 2016. https://doi.org/10.1109/RTAS.2016.7461337.","mla":"Jiang, Yu, et al. From Stateflow Simulation to Verified Implementation: A Verification Approach and a Real-Time Train Controller Design. 7461337, IEEE, 2016, doi:10.1109/RTAS.2016.7461337.","ama":"Jiang Y, Yang Y, Liu H, et al. From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. In: IEEE; 2016. doi:10.1109/RTAS.2016.7461337","ista":"Jiang Y, Yang Y, Liu H, Kong H, Gu M, Sun J, Sha L. 2016. From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. RTAS: Real-time and Embedded Technology and Applications Symposium, 7461337.","ieee":"Y. Jiang et al., “From stateflow simulation to verified implementation: A verification approach and a real-time train controller design,” presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, Vienna, Austria, 2016.","apa":"Jiang, Y., Yang, Y., Liu, H., Kong, H., Gu, M., Sun, J., & Sha, L. (2016). From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. Presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, Vienna, Austria: IEEE. https://doi.org/10.1109/RTAS.2016.7461337","short":"Y. Jiang, Y. Yang, H. Liu, H. Kong, M. Gu, J. Sun, L. Sha, in:, IEEE, 2016."},"has_accepted_license":"1","month":"04","date_published":"2016-04-27T00:00:00Z","date_created":"2018-12-11T11:50:58Z","publication_status":"published","ddc":["005"],"language":[{"iso":"eng"}],"_id":"1256","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"Simulink is widely used for model driven development (MDD) of industrial software systems. Typically, the Simulink based development is initiated from Stateflow modeling, followed by simulation, validation and code generation mapped to physical execution platforms. However, recent industrial trends have raised the demands of rigorous verification on safety-critical applications, which is unfortunately challenging for Simulink. In this paper, we present an approach to bridge the Stateflow based model driven development and a well- defined rigorous verification. First, we develop a self- contained toolkit to translate Stateflow model into timed automata, where major advanced modeling features in Stateflow are supported. Taking advantage of the strong verification capability of Uppaal, we can not only find bugs in Stateflow models which are missed by Simulink Design Verifier, but also check more important temporal properties. Next, we customize a runtime verifier for the generated nonintrusive VHDL and C code of Stateflow model for monitoring. The major strength of the customization is the flexibility to collect and analyze runtime properties with a pure software monitor, which opens more opportunities for engineers to achieve high reliability of the target system compared with the traditional act that only relies on Simulink Polyspace. We incorporate these two parts into original Stateflow based MDD seamlessly. In this way, safety-critical properties are both verified at the model level, and at the consistent system implementation level with physical execution environment in consideration. We apply our approach on a train controller design, and the verified implementation is tested and deployed on a real hardware platform."}],"acknowledgement":"This work is supported in part by NSF CNS 13-30077, NSF CNS 13-29886, NSF CNS 15-45002, NSFC 61303014, NSFC 61202010, and NSFC 91218302.","file_date_updated":"2020-07-14T12:44:41Z","scopus_import":1,"year":"2016","type":"conference","pubrep_id":"780","publist_id":"6069","doi":"10.1109/RTAS.2016.7461337","oa_version":"Submitted Version"},{"file":[{"date_updated":"2020-07-14T12:44:42Z","file_name":"IST-2016-703-v1+1_s00220-016-2600-4.pdf","checksum":"4fb2411d9c2f56676123165aad46c828","creator":"system","relation":"main_file","file_id":"5119","file_size":800792,"date_created":"2018-12-12T10:15:02Z","content_type":"application/pdf","access_level":"open_access"}],"citation":{"short":"C. Sadel, B. Virág, Communications in Mathematical Physics 343 (2016) 881–919.","apa":"Sadel, C., & Virág, B. (2016). A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-016-2600-4","ieee":"C. Sadel and B. Virág, “A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes,” Communications in Mathematical Physics, vol. 343, no. 3. Springer, pp. 881–919, 2016.","chicago":"Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products of Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” Communications in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-016-2600-4.","ista":"Sadel C, Virág B. 2016. A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. Communications in Mathematical Physics. 343(3), 881–919.","ama":"Sadel C, Virág B. A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. Communications in Mathematical Physics. 2016;343(3):881-919. doi:10.1007/s00220-016-2600-4","mla":"Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products of Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” Communications in Mathematical Physics, vol. 343, no. 3, Springer, 2016, pp. 881–919, doi:10.1007/s00220-016-2600-4."},"day":"01","date_updated":"2021-01-12T06:49:26Z","has_accepted_license":"1","volume":343,"date_created":"2018-12-11T11:50:59Z","date_published":"2016-05-01T00:00:00Z","month":"05","issue":"3","publisher":"Springer","quality_controlled":"1","page":"881 - 919","intvolume":" 343","publication":"Communications in Mathematical Physics","title":"A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes","status":"public","oa":1,"author":[{"orcid":"0000-0001-8255-3968","last_name":"Sadel","first_name":"Christian","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","full_name":"Sadel, Christian"},{"last_name":"Virág","first_name":"Bálint","full_name":"Virág, Bálint"}],"scopus_import":1,"year":"2016","type":"journal_article","pubrep_id":"703","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publist_id":"6067","doi":"10.1007/s00220-016-2600-4","oa_version":"Published Version","ddc":["510","539"],"publication_status":"published","language":[{"iso":"eng"}],"_id":"1257","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LaEr"}],"abstract":[{"lang":"eng","text":"We consider products of random matrices that are small, independent identically distributed perturbations of a fixed matrix (Formula presented.). Focusing on the eigenvalues of (Formula presented.) of a particular size we obtain a limit to a SDE in a critical scaling. Previous results required (Formula presented.) to be a (conjugated) unitary matrix so it could not have eigenvalues of different modulus. From the result we can also obtain a limit SDE for the Markov process given by the action of the random products on the flag manifold. Applying the result to random Schrödinger operators we can improve some results by Valko and Virag showing GOE statistics for the rescaled eigenvalue process of a sequence of Anderson models on long boxes. In particular, we solve a problem posed in their work."}],"ec_funded":1,"file_date_updated":"2020-07-14T12:44:42Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The work of C. Sadel was supported by NSERC Discovery Grant 92997-2010 RGPIN and by the People Programme (Marie Curie Actions) of the EU 7th Framework Programme FP7/2007-2013, REA Grant 291734.","article_processing_charge":"Yes (via OA deal)"},{"publist_id":"6068","doi":"10.1242/dev.130211","volume":143,"month":"05","date_created":"2018-12-11T11:50:59Z","date_published":"2016-05-03T00:00:00Z","oa_version":"None","type":"journal_article","year":"2016","scopus_import":1,"date_updated":"2021-01-12T06:49:27Z","citation":{"short":"M. Gallemi, A. Galstyan, S. Paulišić, C. Then, A. Ferrández Ayela, L. Lorenzo Orts, I. Roig Villanova, X. Wang, J. Micol, M. Ponce, P. Devlin, J. Martínez García, Development 143 (2016) 1623–1631.","apa":"Gallemi, M., Galstyan, A., Paulišić, S., Then, C., Ferrández Ayela, A., Lorenzo Orts, L., … Martínez García, J. (2016). DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. Company of Biologists. https://doi.org/10.1242/dev.130211","ieee":"M. Gallemi et al., “DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis,” Development, vol. 143, no. 9. Company of Biologists, pp. 1623–1631, 2016.","chicago":"Gallemi, Marçal, Anahit Galstyan, Sandi Paulišić, Christiane Then, Almudena Ferrández Ayela, Laura Lorenzo Orts, Irma Roig Villanova, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in Arabidopsis.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.130211.","ama":"Gallemi M, Galstyan A, Paulišić S, et al. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. 2016;143(9):1623-1631. doi:10.1242/dev.130211","ista":"Gallemi M, Galstyan A, Paulišić S, Then C, Ferrández Ayela A, Lorenzo Orts L, Roig Villanova I, Wang X, Micol J, Ponce M, Devlin P, Martínez García J. 2016. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. 143(9), 1623–1631.","mla":"Gallemi, Marçal, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in Arabidopsis.” Development, vol. 143, no. 9, Company of Biologists, 2016, pp. 1623–31, doi:10.1242/dev.130211."},"day":"03","status":"public","abstract":[{"text":"When plants grow in close proximity basic resources such as light can become limiting. Under such conditions plants respond to anticipate and/or adapt to the light shortage, a process known as the shade avoidance syndrome (SAS). Following genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC), we identified DRACULA2 (DRA2), which encodes an Arabidopsis homolog of mammalian nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together with other nucleoporins, participates positively in the control of the hypocotyl elongation response to plant proximity, a role that can be considered dependent on the nucleocytoplasmic transport of macromolecules (i.e. is transport dependent). In addition, our results reveal a specific role for DRA2 in controlling shade-induced gene expression. We suggest that this novel regulatory role of DRA2 is transport independent and that it might rely on its dynamic localization within and outside of the NPC. These results provide mechanistic insights in to how SAS responses are rapidly established by light conditions. They also indicate that nucleoporins have an active role in plant signaling.","lang":"eng"}],"title":"DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis","author":[{"full_name":"Gallemi Rovira, Marcal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi Rovira","first_name":"Marcal"},{"last_name":"Galstyan","first_name":"Anahit","full_name":"Galstyan, Anahit"},{"first_name":"Sandi","last_name":"Paulišić","full_name":"Paulišić, Sandi"},{"full_name":"Then, Christiane","last_name":"Then","first_name":"Christiane"},{"last_name":"Ferrández Ayela","first_name":"Almudena","full_name":"Ferrández Ayela, Almudena"},{"full_name":"Lorenzo Orts, Laura","first_name":"Laura","last_name":"Lorenzo Orts"},{"first_name":"Irma","last_name":"Roig Villanova","full_name":"Roig Villanova, Irma"},{"full_name":"Wang, Xuewen","last_name":"Wang","first_name":"Xuewen"},{"full_name":"Micol, José","first_name":"José","last_name":"Micol"},{"full_name":"Ponce, Maria","last_name":"Ponce","first_name":"Maria"},{"full_name":"Devlin, Paul","first_name":"Paul","last_name":"Devlin"},{"last_name":"Martínez García","first_name":"Jaime","full_name":"Martínez García, Jaime"}],"acknowledgement":"M.G. received an FPI fellowship from the Spanish Ministerio de Economía y Competitividad (MINECO). A.G. and A.F.-A. received FPU fellowships from the Spanish Ministerio de Educación. S.P. received an FI fellowship from the Agència de Gestió D'ajuts Universitaris i de Recerca (AGAUR - Generalitat de Catalunya). C.T. received a Marie Curie IEF postdoctoral contract funded by the European Commission. I.R.-V. received initially an FPI fellowship from the Spanish MINECO and later a Beatriu de Pinós contract from AGAUR. Our research is supported by grants from the Spanish MINECO-FEDER [BIO2008-00169, BIO2011-23489 and BIO2014-59895-P] and Generalitat de Catalunya [2011-SGR447 and Xarba] to J.F.M.-G., and Generalitat Valenciana [PROMETEO/2009/112, PROMETEOII/2014/006] to M.R.P. and J.L.M. We acknowledge the support of the Spanish MINECO for the ‘Centro de Excelencia Severo Ochoa 2016-2019’ [award SEV-2015-0533]. We thank the CRAG greenhouse service for plant care; Chus Burillo for technical help; Sergi Portolés and Carles Rentero for assistance with mutagenesis; Mark Estelle (UCSD, USA) for providing sar1-4, sar3-1 and sar3-3 seeds; Juanjo López-Moya (CRAG, Barcelona; 35S:HcPro plasmid) and Dolors Ludevid (CRAG; C307 plasmid) for providing DNA plasmids; and Manuel Rodríguez-Concepción (CRAG) and Miguel Blázquez (IBMCP, Valencia, Spain) for comments on the manuscript.","language":[{"iso":"eng"}],"_id":"1258","publication_status":"published","issue":"9","publication":"Development","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"EvBe"}],"intvolume":" 143","quality_controlled":"1","page":"1623 - 1631","publisher":"Company of Biologists"},{"issue":"2","intvolume":" 19","publication":"Mathematical Physics, Analysis and Geometry","publisher":"Springer","quality_controlled":"1","status":"public","article_number":"13","title":"Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit","author":[{"full_name":"Bräunlich, Gerhard","last_name":"Bräunlich","first_name":"Gerhard"},{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"date_updated":"2021-01-12T06:49:27Z","file":[{"checksum":"9954f685cc25c58d7f1712c67b47ad8d","date_updated":"2020-07-14T12:44:42Z","file_name":"IST-2016-702-v1+1_s11040-016-9209-x.pdf","content_type":"application/pdf","access_level":"open_access","creator":"system","relation":"main_file","file_id":"4736","file_size":506242,"date_created":"2018-12-12T10:09:13Z"}],"citation":{"chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Bogolubov–Hartree–Fock Theory for Strongly Interacting Fermions in the Low Density Limit.” Mathematical Physics, Analysis and Geometry. Springer, 2016. https://doi.org/10.1007/s11040-016-9209-x.","mla":"Bräunlich, Gerhard, et al. “Bogolubov–Hartree–Fock Theory for Strongly Interacting Fermions in the Low Density Limit.” Mathematical Physics, Analysis and Geometry, vol. 19, no. 2, 13, Springer, 2016, doi:10.1007/s11040-016-9209-x.","ista":"Bräunlich G, Hainzl C, Seiringer R. 2016. Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. Mathematical Physics, Analysis and Geometry. 19(2), 13.","ama":"Bräunlich G, Hainzl C, Seiringer R. Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. Mathematical Physics, Analysis and Geometry. 2016;19(2). doi:10.1007/s11040-016-9209-x","ieee":"G. Bräunlich, C. Hainzl, and R. Seiringer, “Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit,” Mathematical Physics, Analysis and Geometry, vol. 19, no. 2. Springer, 2016.","apa":"Bräunlich, G., Hainzl, C., & Seiringer, R. (2016). Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-016-9209-x","short":"G. Bräunlich, C. Hainzl, R. Seiringer, Mathematical Physics, Analysis and Geometry 19 (2016)."},"day":"01","volume":19,"has_accepted_license":"1","month":"06","date_published":"2016-06-01T00:00:00Z","date_created":"2018-12-11T11:50:59Z","publication_status":"published","ddc":["510","539"],"language":[{"iso":"eng"}],"_id":"1259","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"We consider the Bogolubov–Hartree–Fock functional for a fermionic many-body system with two-body interactions. For suitable interaction potentials that have a strong enough attractive tail in order to allow for two-body bound states, but are otherwise sufficiently repulsive to guarantee stability of the system, we show that in the low-density limit the ground state of this model consists of a Bose–Einstein condensate of fermion pairs. The latter can be described by means of the Gross–Pitaevskii energy functional."}],"article_processing_charge":"Yes (via OA deal)","acknowledgement":"Partial financial support from the DFG grant GRK 1838, as well as the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R.S.), is gratefully acknowledged.","file_date_updated":"2020-07-14T12:44:42Z","scopus_import":1,"type":"journal_article","year":"2016","pubrep_id":"702","doi":"10.1007/s11040-016-9209-x","publist_id":"6066","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version"},{"issue":"6","intvolume":" 27","publication":"International Journal of Modern Physics C","publisher":"World Scientific Publishing","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.02963"}],"quality_controlled":"1","status":"public","article_number":"1650067","title":"The dual of the space of interactions in neural network models","author":[{"first_name":"Daniele","last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"date_updated":"2021-01-12T06:49:28Z","day":"01","citation":{"chicago":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” International Journal of Modern Physics C. World Scientific Publishing, 2016. https://doi.org/10.1142/S0129183116500674.","ista":"De Martino D. 2016. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 27(6), 1650067.","ama":"De Martino D. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 2016;27(6). doi:10.1142/S0129183116500674","mla":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” International Journal of Modern Physics C, vol. 27, no. 6, 1650067, World Scientific Publishing, 2016, doi:10.1142/S0129183116500674.","apa":"De Martino, D. (2016). The dual of the space of interactions in neural network models. International Journal of Modern Physics C. World Scientific Publishing. https://doi.org/10.1142/S0129183116500674","short":"D. De Martino, International Journal of Modern Physics C 27 (2016).","ieee":"D. De Martino, “The dual of the space of interactions in neural network models,” International Journal of Modern Physics C, vol. 27, no. 6. World Scientific Publishing, 2016."},"article_type":"original","volume":27,"month":"06","date_published":"2016-06-01T00:00:00Z","date_created":"2018-12-11T11:51:00Z","publication_status":"published","_id":"1260","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"external_id":{"arxiv":["1505.02963"]},"abstract":[{"text":"In this work, the Gardner problem of inferring interactions and fields for an Ising neural network from given patterns under a local stability hypothesis is addressed under a dual perspective. By means of duality arguments, an integer linear system is defined whose solution space is the dual of the Gardner space and whose solutions represent mutually unstable patterns. We propose and discuss Monte Carlo methods in order to find and remove unstable patterns and uniformly sample the space of interactions thereafter. We illustrate the problem on a set of real data and perform ensemble calculation that shows how the emergence of phase dominated by unstable patterns can be triggered in a nonlinear discontinuous way.","lang":"eng"}],"article_processing_charge":"No","scopus_import":1,"year":"2016","type":"journal_article","arxiv":1,"doi":"10.1142/S0129183116500674","publist_id":"6065","oa_version":"Preprint"},{"title":"Long-time behavior of a finite volume discretization for a fourth order diffusion equation","status":"public","oa":1,"author":[{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","orcid":"0000-0002-0845-1338","first_name":"Jan"},{"last_name":"Matthes","first_name":"Daniel","full_name":"Matthes, Daniel"}],"issue":"7","publisher":"IOP Publishing Ltd.","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1505.03178","open_access":"1"}],"page":"1992 - 2023","intvolume":" 29","publication":"Nonlinearity","volume":29,"date_created":"2018-12-11T11:51:00Z","date_published":"2016-06-10T00:00:00Z","month":"06","day":"10","citation":{"chicago":"Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization for a Fourth Order Diffusion Equation.” Nonlinearity. IOP Publishing Ltd., 2016. https://doi.org/10.1088/0951-7715/29/7/1992.","ama":"Maas J, Matthes D. Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. 2016;29(7):1992-2023. doi:10.1088/0951-7715/29/7/1992","ista":"Maas J, Matthes D. 2016. Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. 29(7), 1992–2023.","mla":"Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization for a Fourth Order Diffusion Equation.” Nonlinearity, vol. 29, no. 7, IOP Publishing Ltd., 2016, pp. 1992–2023, doi:10.1088/0951-7715/29/7/1992.","short":"J. Maas, D. Matthes, Nonlinearity 29 (2016) 1992–2023.","apa":"Maas, J., & Matthes, D. (2016). Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. IOP Publishing Ltd. https://doi.org/10.1088/0951-7715/29/7/1992","ieee":"J. Maas and D. Matthes, “Long-time behavior of a finite volume discretization for a fourth order diffusion equation,” Nonlinearity, vol. 29, no. 7. IOP Publishing Ltd., pp. 1992–2023, 2016."},"date_updated":"2021-01-12T06:49:28Z","abstract":[{"lang":"eng","text":"We consider a non-standard finite-volume discretization of a strongly non-linear fourth order diffusion equation on the d-dimensional cube, for arbitrary . The scheme preserves two important structural properties of the equation: the first is the interpretation as a gradient flow in a mass transportation metric, and the second is an intimate relation to a linear Fokker-Planck equation. Thanks to these structural properties, the scheme possesses two discrete Lyapunov functionals. These functionals approximate the entropy and the Fisher information, respectively, and their dissipation rates converge to the optimal ones in the discrete-to-continuous limit. Using the dissipation, we derive estimates on the long-time asymptotics of the discrete solutions. Finally, we present results from numerical experiments which indicate that our discretization is able to capture significant features of the complex original dynamics, even with a rather coarse spatial resolution."}],"acknowledgement":"This research was supported by the DFG Collaborative Research Centers TRR 109, ‘ Discretization in Geometry and Dynamics ’ and 1060 ‘ The Mathematics of Emergent Effects ’ .","publication_status":"published","_id":"1261","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JaMa"}],"doi":"10.1088/0951-7715/29/7/1992","publist_id":"6062","oa_version":"Preprint","scopus_import":1,"year":"2016","type":"journal_article"},{"acknowledgement":"This work was supported by the Federal Ministry of Food, Agriculture and Consumer Protection (Germany): Fit Bee project (grant 511-06.01-28-1-71.007-10), the EU: BeeDoc (grant 244956), iDiv (2013 NGS-Fast Track grant W47004118) and the Insect Pollinators Initiative (IPI grant BB/I000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, the Scottish Government and the Wellcome Trust, under the Living with Environmental Change Partnership. We thank A. Abrahams, M. Husemann and A. Soro\r\nfor support in obtaining\r\nV. destructor\r\n-free honeybees; and BBKA\r\nPresident D. Aston for access to records of colony overwinter\r\n2011–2012 mortality in the UK. We also thank the anonymous refe-\r\nrees and Stephen Martin for comments that led to substantial\r\nimprovement of the manuscript.","file_date_updated":"2020-07-14T12:44:42Z","abstract":[{"lang":"eng","text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SyCr"}],"publication_status":"published","ddc":["576","592"],"_id":"1262","language":[{"iso":"eng"}],"oa_version":"Published Version","publist_id":"6060","doi":"10.1098/rspb.2016.0811","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"701","scopus_import":1,"type":"journal_article","year":"2016","author":[{"full_name":"Mcmahon, Dino","first_name":"Dino","last_name":"Mcmahon"},{"full_name":"Natsopoulou, Myrsini","first_name":"Myrsini","last_name":"Natsopoulou"},{"first_name":"Vincent","last_name":"Doublet","full_name":"Doublet, Vincent"},{"full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Fürst","orcid":"0000-0002-3712-925X"},{"full_name":"Weging, Silvio","first_name":"Silvio","last_name":"Weging"},{"last_name":"Brown","first_name":"Mark","full_name":"Brown, Mark"},{"full_name":"Gogol Döring, Andreas","last_name":"Gogol Döring","first_name":"Andreas"},{"full_name":"Paxton, Robert","first_name":"Robert","last_name":"Paxton"}],"oa":1,"status":"public","article_number":"20160811","title":"Elevated virulence of an emerging viral genotype as a driver of honeybee loss","intvolume":" 283","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","publisher":"Royal Society, The","quality_controlled":"1","issue":"1833","month":"06","date_published":"2016-06-29T00:00:00Z","date_created":"2018-12-11T11:51:00Z","volume":283,"has_accepted_license":"1","date_updated":"2023-02-23T14:05:30Z","file":[{"date_created":"2018-12-12T10:08:46Z","creator":"system","file_id":"4708","relation":"main_file","file_size":796872,"access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-701-v1+1_20160811.full.pdf","date_updated":"2020-07-14T12:44:42Z","checksum":"0b0d1be38b497d004064650acb3baced"}],"citation":{"ieee":"D. Mcmahon et al., “Elevated virulence of an emerging viral genotype as a driver of honeybee loss,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1833. Royal Society, The, 2016.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, Proceedings of the Royal Society of London Series B Biological Sciences 283 (2016).","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.0811","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2016. https://doi.org/10.1098/rspb.2016.0811.","mla":"Mcmahon, Dino, et al. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1833, 20160811, Royal Society, The, 2016, doi:10.1098/rspb.2016.0811.","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. 2016;283(1833). doi:10.1098/rspb.2016.0811","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. 283(1833), 20160811."},"day":"29","related_material":{"record":[{"status":"public","id":"9704","relation":"research_data"}]}},{"date_updated":"2023-10-17T12:17:15Z","day":"20","citation":{"mla":"Rueda, Alfredo, et al. “Efficient Microwave to Optical Photon Conversion: An Electro-Optical Realization.” Optica, vol. 3, no. 6, Optica Publishing Group, 2016, pp. 597–604, doi:10.1364/OPTICA.3.000597.","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Efficient microwave to optical photon conversion: An electro-optical realization. Optica. 2016;3(6):597-604. doi:10.1364/OPTICA.3.000597","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient microwave to optical photon conversion: An electro-optical realization. Optica. 3(6), 597–604.","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Gerhard Schunk, Dmitry Strekalov, et al. “Efficient Microwave to Optical Photon Conversion: An Electro-Optical Realization.” Optica. Optica Publishing Group, 2016. https://doi.org/10.1364/OPTICA.3.000597.","ieee":"A. Rueda et al., “Efficient microwave to optical photon conversion: An electro-optical realization,” Optica, vol. 3, no. 6. Optica Publishing Group, pp. 597–604, 2016.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, Optica 3 (2016) 597–604.","apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Efficient microwave to optical photon conversion: An electro-optical realization. Optica. Optica Publishing Group. https://doi.org/10.1364/OPTICA.3.000597"},"volume":3,"month":"06","date_published":"2016-06-20T00:00:00Z","date_created":"2018-12-11T11:51:01Z","issue":"6","publication":"Optica","intvolume":" 3","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1364/OPTICA.3.000597"}],"page":"597 - 604","quality_controlled":"1","publisher":"Optica Publishing Group","status":"public","title":"Efficient microwave to optical photon conversion: An electro-optical realization","author":[{"first_name":"Alfredo","last_name":"Rueda","full_name":"Rueda, Alfredo"},{"full_name":"Sedlmeir, Florian","first_name":"Florian","last_name":"Sedlmeir"},{"full_name":"Collodo, Michele","last_name":"Collodo","first_name":"Michele"},{"first_name":"Ulrich","last_name":"Vogl","full_name":"Vogl, Ulrich"},{"full_name":"Stiller, Birgit","first_name":"Birgit","last_name":"Stiller"},{"last_name":"Schunk","first_name":"Gerhard","full_name":"Schunk, Gerhard"},{"full_name":"Strekalov, Dmitry","last_name":"Strekalov","first_name":"Dmitry"},{"last_name":"Marquardt","first_name":"Christoph","full_name":"Marquardt, Christoph"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X"},{"first_name":"Oskar","last_name":"Painter","full_name":"Painter, Oskar"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"first_name":"Harald","last_name":"Schwefel","full_name":"Schwefel, Harald"}],"oa":1,"type":"journal_article","year":"2016","scopus_import":"1","publist_id":"6061","doi":"10.1364/OPTICA.3.000597","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"1263","publication_status":"published","department":[{"_id":"JoFi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Linking classical microwave electrical circuits to the optical telecommunication band is at the core of modern communication. Future quantum information networks will require coherent microwave-to-optical conversion to link electronic quantum processors and memories via low-loss optical telecommunication networks. Efficient conversion can be achieved with electro-optical modulators operating at the single microwave photon level. In the standard electro-optic modulation scheme, this is impossible because both up- and down-converted sidebands are necessarily present. Here, we demonstrate true single-sideband up- or down-conversion in a triply resonant whispering gallery mode resonator by explicitly addressing modes with asymmetric free spectral range. Compared to previous experiments, we show a 3 orders of magnitude improvement of the electro-optical conversion efficiency, reaching 0.1% photon number conversion for a 10 GHz microwave tone at 0.42 mW of optical pump power. The presented scheme is fully compatible with existing superconducting 3D circuit quantum electrodynamics technology and can be used for nonclassical state conversion and communication. Our conversion bandwidth is larger than 1 MHz and is not fundamentally limited.","lang":"eng"}],"article_processing_charge":"No","acknowledgement":"Alexander von Humboldt Foundation; Studienstiftung des Deutschen Volkes. We would like to acknowledge our stimulating discussions with Konrad Lehnert and Alessandro Pitanti."},{"publication":"Plant Physiology","intvolume":" 171","page":"1965 - 1982","quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936568/","open_access":"1"}],"publisher":"American Society of Plant Biologists","issue":"3","author":[{"last_name":"Sancho Andrés","first_name":"Gloria","full_name":"Sancho Andrés, Gloria"},{"last_name":"Soriano Ortega","first_name":"Esther","full_name":"Soriano Ortega, Esther"},{"full_name":"Gao, Caiji","last_name":"Gao","first_name":"Caiji"},{"full_name":"Bernabé Orts, Joan","last_name":"Bernabé Orts","first_name":"Joan"},{"first_name":"Madhumitha","last_name":"Narasimhan","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","last_name":"Müller","id":"420AB15A-F248-11E8-B48F-1D18A9856A87","full_name":"Müller, Anna"},{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"},{"full_name":"Jiang, Liwen","first_name":"Liwen","last_name":"Jiang"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Fernando","last_name":"Aniento","full_name":"Aniento, Fernando"},{"last_name":"Marcote","first_name":"Maria","full_name":"Marcote, Maria"}],"oa":1,"status":"public","title":"Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier","date_updated":"2021-01-12T06:49:29Z","citation":{"chicago":"Sancho Andrés, Gloria, Esther Soriano Ortega, Caiji Gao, Joan Bernabé Orts, Madhumitha Narasimhan, Anna Müller, Ricardo Tejos, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00373.","ista":"Sancho Andrés G, Soriano Ortega E, Gao C, Bernabé Orts J, Narasimhan M, Müller A, Tejos R, Jiang L, Friml J, Aniento F, Marcote M. 2016. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 171(3), 1965–1982.","ama":"Sancho Andrés G, Soriano Ortega E, Gao C, et al. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 2016;171(3):1965-1982. doi:10.1104/pp.16.00373","mla":"Sancho Andrés, Gloria, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology, vol. 171, no. 3, American Society of Plant Biologists, 2016, pp. 1965–82, doi:10.1104/pp.16.00373.","apa":"Sancho Andrés, G., Soriano Ortega, E., Gao, C., Bernabé Orts, J., Narasimhan, M., Müller, A., … Marcote, M. (2016). Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00373","short":"G. Sancho Andrés, E. Soriano Ortega, C. Gao, J. Bernabé Orts, M. Narasimhan, A. Müller, R. Tejos, L. Jiang, J. Friml, F. Aniento, M. Marcote, Plant Physiology 171 (2016) 1965–1982.","ieee":"G. Sancho Andrés et al., “Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier,” Plant Physiology, vol. 171, no. 3. American Society of Plant Biologists, pp. 1965–1982, 2016."},"day":"01","month":"07","date_created":"2018-12-11T11:51:01Z","date_published":"2016-07-01T00:00:00Z","volume":171,"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"language":[{"iso":"eng"}],"_id":"1264","publication_status":"published","acknowledgement":"We thank Dr. R. Offringa (Leiden University) for providing the GST-\r\nPIN-CL construct; Sandra Richter and Gerd Jurgens (University of Tübin-\r\ngen) for providing the estradiol-inducible PIN1-RFP construct and the\r\ngnl1 mutant expressing BFA-sensitive GNL1; F.J. Santonja (University of Valencia)\r\nfor help with the statistical analysis; Jurgen Kleine-Vehn, Elke Barbez, and\r\nEva Benkova for helpful discussions; the Salk Institute Genomic Analysis\r\nLaboratory for providing the sequence-indexed Arabidopsis T-DNA in-\r\nsertion mutants; and the greenhouse section and the microscopy section\r\nof SCSIE (University of Valencia) and Pilar Selvi for excellent technical\r\nassistance.","ec_funded":1,"abstract":[{"text":"n contrast with the wealth of recent reports about the function of μ-adaptins and clathrin adaptor protein (AP) complexes, there is very little information about the motifs that determine the sorting of membrane proteins within clathrin-coated vesicles in plants. Here, we investigated putative sorting signals in the large cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are involved in the binding of different μ-adaptins in vitro. However, only Phe-165, which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis but also localized to intracellular structures containing several layers of membranes and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin mutant, it accumulated in big intracellular structures containing LysoTracker in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants of other subunits of the AP-3 complex. Our data suggest that Phe-165, through the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis and for PIN1 trafficking along the secretory pathway, respectively.","lang":"eng"}],"type":"journal_article","year":"2016","scopus_import":1,"oa_version":"Submitted Version","doi":"10.1104/pp.16.00373","publist_id":"6059"},{"author":[{"full_name":"Elsayad, Kareem","last_name":"Elsayad","first_name":"Kareem"},{"full_name":"Werner, Stephanie","first_name":"Stephanie","last_name":"Werner"},{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi Rovira, Marcal","first_name":"Marcal","last_name":"Gallemi Rovira"},{"full_name":"Kong, Jixiang","last_name":"Kong","first_name":"Jixiang"},{"full_name":"Guajardo, Edmundo","last_name":"Guajardo","first_name":"Edmundo"},{"last_name":"Zhang","first_name":"Lijuan","full_name":"Zhang, Lijuan"},{"first_name":"Yvon","last_name":"Jaillais","full_name":"Jaillais, Yvon"},{"full_name":"Greb, Thomas","last_name":"Greb","first_name":"Thomas"},{"full_name":"Belkhadir, Youssef","last_name":"Belkhadir","first_name":"Youssef"}],"article_number":"rs5","title":"Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging","abstract":[{"lang":"eng","text":"Extracellular matrices (ECMs) are central to the advent of multicellular life, and their mechanical propertiesare modulated by and impinge on intracellular signaling pathways that regulate vital cellular functions. High spatial-resolution mapping of mechanical properties in live cells is, however, extremely challenging. Thus, our understanding of how signaling pathways process physiological signals to generate appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin scattering imaging (FBi), a method for the parallel and all-optical measurements of mechanical properties and fluorescence at the submicrometer scale in living organisms. Using FBi, we showed thatchanges in cellular hydrostatic pressure and cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We further established that the measured "stiffness" of plant ECMs is symmetrically patternedin hypocotyl cells undergoing directional growth. Finally, application of this method to Arabidopsis thaliana with photoreceptor mutants revealed that red and far-red light signals are essential modulators of ECM viscoelasticity. By mapping the viscoelastic signatures of a complex ECM, we provide proof of principlefor the organism-wide applicability of FBi for measuring the mechanical outputs of intracellular signaling pathways. As such, our work has implications for investigations of mechanosignaling pathways and developmental biology."}],"status":"public","publisher":"American Association for the Advancement of Science","quality_controlled":"1","department":[{"_id":"EvBe"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 9","publication":"Science Signaling","issue":"435","publication_status":"published","_id":"1265","language":[{"iso":"eng"}],"oa_version":"None","date_created":"2018-12-11T11:51:02Z","date_published":"2016-07-05T00:00:00Z","month":"07","volume":9,"doi":"10.1126/scisignal.aaf6326","publist_id":"6057","citation":{"short":"K. Elsayad, S. Werner, M. Gallemi, J. Kong, E. Guajardo, L. Zhang, Y. Jaillais, T. Greb, Y. Belkhadir, Science Signaling 9 (2016).","apa":"Elsayad, K., Werner, S., Gallemi, M., Kong, J., Guajardo, E., Zhang, L., … Belkhadir, Y. (2016). Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. American Association for the Advancement of Science. https://doi.org/10.1126/scisignal.aaf6326","ieee":"K. Elsayad et al., “Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging,” Science Signaling, vol. 9, no. 435. American Association for the Advancement of Science, 2016.","chicago":"Elsayad, Kareem, Stephanie Werner, Marçal Gallemi, Jixiang Kong, Edmundo Guajardo, Lijuan Zhang, Yvon Jaillais, Thomas Greb, and Youssef Belkhadir. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/scisignal.aaf6326.","ista":"Elsayad K, Werner S, Gallemi M, Kong J, Guajardo E, Zhang L, Jaillais Y, Greb T, Belkhadir Y. 2016. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 9(435), rs5.","ama":"Elsayad K, Werner S, Gallemi M, et al. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 2016;9(435). doi:10.1126/scisignal.aaf6326","mla":"Elsayad, Kareem, et al. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling, vol. 9, no. 435, rs5, American Association for the Advancement of Science, 2016, doi:10.1126/scisignal.aaf6326."},"day":"05","date_updated":"2021-01-12T06:49:29Z","scopus_import":1,"year":"2016","type":"journal_article"}]