[{"publication_status":"published","doi":"10.1371/journal.pbio.1002169","oa_version":"Published Version","date_published":"2015-06-04T00:00:00Z","scopus_import":1,"file_date_updated":"2020-07-14T12:45:02Z","ddc":["570"],"citation":{"apa":"El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther, P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002169\">https://doi.org/10.1371/journal.pbio.1002169</a>","ista":"El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30.","mla":"El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” <i>PLoS Biology</i>, vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002169\">10.1371/journal.pbio.1002169</a>.","chicago":"El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann, Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” <i>PLoS Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002169\">https://doi.org/10.1371/journal.pbio.1002169</a>.","ama":"El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. <i>PLoS Biology</i>. 2015;13(6):1-30. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002169\">10.1371/journal.pbio.1002169</a>","ieee":"L. El Masri <i>et al.</i>, “Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes,” <i>PLoS Biology</i>, vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.","short":"L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther, S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R. Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30."},"intvolume":"        13","date_updated":"2021-01-12T06:51:33Z","abstract":[{"lang":"eng","text":"Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins.We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen's genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system."}],"issue":"6","year":"2015","_id":"1551","status":"public","oa":1,"month":"06","ec_funded":1,"has_accepted_license":"1","date_created":"2018-12-11T11:52:40Z","page":"1 - 30","publication":"PLoS Biology","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"publist_id":"5620","pubrep_id":"481","quality_controlled":"1","volume":13,"acknowledgement":"We are very grateful for funding from the German Science Foundation (DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI 1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission) to LM.","day":"04","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"author":[{"full_name":"El Masri, Leila","first_name":"Leila","last_name":"El Masri","id":"349A6E66-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Antoine","last_name":"Branca","full_name":"Branca, Antoine"},{"full_name":"Sheppard, Anna","last_name":"Sheppard","first_name":"Anna"},{"full_name":"Papkou, Andrei","last_name":"Papkou","first_name":"Andrei"},{"full_name":"Laehnemann, David","first_name":"David","last_name":"Laehnemann"},{"full_name":"Guenther, Patrick","last_name":"Guenther","first_name":"Patrick"},{"first_name":"Swantje","last_name":"Prahl","full_name":"Prahl, Swantje"},{"first_name":"Manja","last_name":"Saebelfeld","full_name":"Saebelfeld, Manja"},{"first_name":"Jacqueline","last_name":"Hollensteiner","full_name":"Hollensteiner, Jacqueline"},{"full_name":"Liesegang, Heiko","last_name":"Liesegang","first_name":"Heiko"},{"full_name":"Brzuszkiewicz, Elzbieta","last_name":"Brzuszkiewicz","first_name":"Elzbieta"},{"first_name":"Rolf","last_name":"Daniel","full_name":"Daniel, Rolf"},{"full_name":"Michiels, Nico","first_name":"Nico","last_name":"Michiels"},{"full_name":"Schulte, Rebecca","last_name":"Schulte","first_name":"Rebecca"},{"last_name":"Kurtz","first_name":"Joachim","full_name":"Kurtz, Joachim"},{"last_name":"Rosenstiel","first_name":"Philip","full_name":"Rosenstiel, Philip"},{"full_name":"Telschow, Arndt","last_name":"Telschow","first_name":"Arndt"},{"last_name":"Bornberg Bauer","first_name":"Erich","full_name":"Bornberg Bauer, Erich"},{"full_name":"Schulenburg, Hinrich","last_name":"Schulenburg","first_name":"Hinrich"}],"file":[{"file_size":3468956,"relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:14:13Z","file_name":"IST-2016-481-v1+1_journal.pbio.1002169.pdf","date_updated":"2020-07-14T12:45:02Z","access_level":"open_access","file_id":"5063","creator":"system","checksum":"30dee7a2c11ed09f2f5634655c0146f8"}],"publisher":"Public Library of Science","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes","license":"https://creativecommons.org/licenses/by/4.0/"},{"publist_id":"5618","scopus_import":1,"intvolume":"       161","citation":{"ieee":"P. Maiuri <i>et al.</i>, “Actin flows mediate a universal coupling between cell speed and cell persistence,” <i>Cell</i>, vol. 161, no. 2. Cell Press, pp. 374–386, 2015.","ama":"Maiuri P, Rupprecht J, Wieser S, et al. Actin flows mediate a universal coupling between cell speed and cell persistence. <i>Cell</i>. 2015;161(2):374-386. doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">10.1016/j.cell.2015.01.056</a>","short":"P. Maiuri, J. Rupprecht, S. Wieser, V. Ruprecht, O. Bénichou, N. Carpi, M. Coppey, S. De Beco, N. Gov, C.-P.J. Heisenberg, C. Lage Crespo, F. Lautenschlaeger, M. Le Berre, A. Lennon Duménil, M. Raab, H. Thiam, M. Piel, M.K. Sixt, R. Voituriez, Cell 161 (2015) 374–386.","apa":"Maiuri, P., Rupprecht, J., Wieser, S., Ruprecht, V., Bénichou, O., Carpi, N., … Voituriez, R. (2015). Actin flows mediate a universal coupling between cell speed and cell persistence. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">https://doi.org/10.1016/j.cell.2015.01.056</a>","ista":"Maiuri P, Rupprecht J, Wieser S, Ruprecht V, Bénichou O, Carpi N, Coppey M, De Beco S, Gov N, Heisenberg C-PJ, Lage Crespo C, Lautenschlaeger F, Le Berre M, Lennon Duménil A, Raab M, Thiam H, Piel M, Sixt MK, Voituriez R. 2015. Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. 161(2), 374–386.","mla":"Maiuri, Paolo, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” <i>Cell</i>, vol. 161, no. 2, Cell Press, 2015, pp. 374–86, doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">10.1016/j.cell.2015.01.056</a>.","chicago":"Maiuri, Paolo, Jean Rupprecht, Stefan Wieser, Verena Ruprecht, Olivier Bénichou, Nicolas Carpi, Mathieu Coppey, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” <i>Cell</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">https://doi.org/10.1016/j.cell.2015.01.056</a>."},"quality_controlled":"1","volume":161,"publication_status":"published","doi":"10.1016/j.cell.2015.01.056","page":"374 - 386","date_created":"2018-12-11T11:52:41Z","publication":"Cell","type":"journal_article","oa_version":"None","language":[{"iso":"eng"}],"date_published":"2015-04-09T00:00:00Z","department":[{"_id":"MiSi"},{"_id":"CaHe"}],"publisher":"Cell Press","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Actin flows mediate a universal coupling between cell speed and cell persistence","month":"04","ec_funded":1,"date_updated":"2021-01-12T06:51:33Z","abstract":[{"text":"Cell movement has essential functions in development, immunity, and cancer. Various cell migration patterns have been reported, but no general rule has emerged so far. Here, we show on the basis of experimental data in vitro and in vivo that cell persistence, which quantifies the straightness of trajectories, is robustly coupled to cell migration speed. We suggest that this universal coupling constitutes a generic law of cell migration, which originates in the advection of polarity cues by an actin cytoskeleton undergoing flows at the cellular scale. Our analysis relies on a theoretical model that we validate by measuring the persistence of cells upon modulation of actin flow speeds and upon optogenetic manipulation of the binding of an actin regulator to actin filaments. Beyond the quantitative prediction of the coupling, the model yields a generic phase diagram of cellular trajectories, which recapitulates the full range of observed migration patterns.","lang":"eng"}],"issue":"2","day":"09","year":"2015","project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","call_identifier":"FWF","_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17"},{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"grant_number":"RGP0058/2011","_id":"25ABD200-B435-11E9-9278-68D0E5697425","name":"Cell migration in complex environments: from in vivo experiments to theoretical models"}],"author":[{"full_name":"Maiuri, Paolo","last_name":"Maiuri","first_name":"Paolo"},{"first_name":"Jean","last_name":"Rupprecht","full_name":"Rupprecht, Jean"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","last_name":"Wieser","first_name":"Stefan","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan"},{"full_name":"Ruprecht, Verena","first_name":"Verena","orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht"},{"full_name":"Bénichou, Olivier","first_name":"Olivier","last_name":"Bénichou"},{"last_name":"Carpi","first_name":"Nicolas","full_name":"Carpi, Nicolas"},{"full_name":"Coppey, Mathieu","last_name":"Coppey","first_name":"Mathieu"},{"last_name":"De Beco","first_name":"Simon","full_name":"De Beco, Simon"},{"last_name":"Gov","first_name":"Nir","full_name":"Gov, Nir"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"full_name":"Lage Crespo, Carolina","last_name":"Lage Crespo","first_name":"Carolina"},{"last_name":"Lautenschlaeger","first_name":"Franziska","full_name":"Lautenschlaeger, Franziska"},{"full_name":"Le Berre, Maël","last_name":"Le Berre","first_name":"Maël"},{"full_name":"Lennon Duménil, Ana","first_name":"Ana","last_name":"Lennon Duménil"},{"first_name":"Matthew","last_name":"Raab","full_name":"Raab, Matthew"},{"last_name":"Thiam","first_name":"Hawa","full_name":"Thiam, Hawa"},{"last_name":"Piel","first_name":"Matthieu","full_name":"Piel, Matthieu"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"}],"_id":"1553"},{"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"page":"207 - 210","date_created":"2018-12-11T11:52:41Z","publication":"Nature Methods","external_id":{"pmid":["25643149"]},"quality_controlled":"1","volume":12,"publist_id":"5617","author":[{"full_name":"Liao, Cheyang","first_name":"Cheyang","last_name":"Liao"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"full_name":"Brunoud, Géraldine","first_name":"Géraldine","last_name":"Brunoud"},{"full_name":"Yoshida, Saiko","first_name":"Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vernoux","first_name":"Teva","full_name":"Vernoux, Teva"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"}],"pmid":1,"day":"26","publisher":"Nature Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Reporters for sensitive and quantitative measurement of auxin response","oa_version":"Submitted Version","date_published":"2015-02-26T00:00:00Z","publication_status":"published","doi":"10.1038/nmeth.3279","citation":{"ieee":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” <i>Nature Methods</i>, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.","ama":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. <i>Nature Methods</i>. 2015;12(3):207-210. doi:<a href=\"https://doi.org/10.1038/nmeth.3279\">10.1038/nmeth.3279</a>","short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210.","ista":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210.","mla":"Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” <i>Nature Methods</i>, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:<a href=\"https://doi.org/10.1038/nmeth.3279\">10.1038/nmeth.3279</a>.","apa":"Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., &#38; Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. <i>Nature Methods</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nmeth.3279\">https://doi.org/10.1038/nmeth.3279</a>","chicago":"Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” <i>Nature Methods</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nmeth.3279\">https://doi.org/10.1038/nmeth.3279</a>."},"intvolume":"        12","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/","open_access":"1"}],"_id":"1554","date_updated":"2021-01-12T06:51:34Z","abstract":[{"text":"The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species.","lang":"eng"}],"issue":"3","year":"2015","month":"02","status":"public","oa":1},{"publist_id":"5616","article_type":"original","article_processing_charge":"No","volume":14,"quality_controlled":"1","page":"980 - 1017","date_created":"2018-12-11T11:52:42Z","publication":"SIAM Journal on Applied Dynamical Systems","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publisher":"Society for Industrial and Applied Mathematics ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Rich bifurcation structure in a two patch vaccination model","acknowledgement":"Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559 in the framework of the EPIDELAY project.","day":"01","project":[{"_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033","name":"Persistent Homology - Images, Data and Maps","call_identifier":"FP7"}],"author":[{"first_name":"Diána","last_name":"Knipl","full_name":"Knipl, Diána"},{"full_name":"Pilarczyk, Pawel","first_name":"Pawel","last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gergely","last_name":"Röst","full_name":"Röst, Gergely"}],"scopus_import":1,"main_file_link":[{"url":"http://discovery.ucl.ac.uk/1473750/1/99393.pdf","open_access":"1"}],"ddc":["510"],"citation":{"ama":"Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination model. <i>SIAM Journal on Applied Dynamical Systems</i>. 2015;14(2):980-1017. doi:<a href=\"https://doi.org/10.1137/140993934\">10.1137/140993934</a>","ieee":"D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two patch vaccination model,” <i>SIAM Journal on Applied Dynamical Systems</i>, vol. 14, no. 2. Society for Industrial and Applied Mathematics , pp. 980–1017, 2015.","short":"D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems 14 (2015) 980–1017.","chicago":"Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” <i>SIAM Journal on Applied Dynamical Systems</i>. Society for Industrial and Applied Mathematics , 2015. <a href=\"https://doi.org/10.1137/140993934\">https://doi.org/10.1137/140993934</a>.","mla":"Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” <i>SIAM Journal on Applied Dynamical Systems</i>, vol. 14, no. 2, Society for Industrial and Applied Mathematics , 2015, pp. 980–1017, doi:<a href=\"https://doi.org/10.1137/140993934\">10.1137/140993934</a>.","apa":"Knipl, D., Pilarczyk, P., &#38; Röst, G. (2015). Rich bifurcation structure in a two patch vaccination model. <i>SIAM Journal on Applied Dynamical Systems</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/140993934\">https://doi.org/10.1137/140993934</a>","ista":"Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017."},"intvolume":"        14","publication_status":"published","doi":"10.1137/140993934","oa_version":"Published Version","date_published":"2015-01-01T00:00:00Z","status":"public","publication_identifier":{"eissn":["1536-0040"]},"oa":1,"month":"01","ec_funded":1,"date_updated":"2021-01-12T06:51:34Z","issue":"2","abstract":[{"text":"We show that incorporating spatial dispersal of individuals into a simple vaccination epidemic model may give rise to a model that exhibits rich dynamical behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as a basis, we describe the spread of an infectious disease in a population split into two regions. In each subpopulation, both forward and backward bifurcations can occur. This implies that for disconnected regions the two-patch system may admit several steady states. We consider traveling between the regions and investigate the impact of spatial dispersal of individuals on the model dynamics. We establish conditions for the existence of multiple nontrivial steady states in the system, and we study the structure of the equilibria. The mathematical analysis reveals an unusually rich dynamical behavior, not normally found in the simple epidemic models. In addition to the disease-free equilibrium, eight endemic equilibria emerge from backward transcritical and saddle-node bifurcation points, forming an interesting bifurcation diagram. Stability of steady states, their bifurcations, and the global dynamics are investigated with analytical tools, numerical simulations, and rigorous set-oriented numerical computations.","lang":"eng"}],"year":"2015","_id":"1555"},{"year":"2015","issue":"15","abstract":[{"text":"The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators.","lang":"eng"}],"date_updated":"2021-01-12T06:51:35Z","_id":"1556","oa":1,"status":"public","month":"08","doi":"10.1093/jxb/erv230","publication_status":"published","date_published":"2015-08-01T00:00:00Z","oa_version":"Published Version","ddc":["570"],"scopus_import":1,"file_date_updated":"2020-07-14T12:45:02Z","citation":{"chicago":"Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml, and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/jxb/erv230\">https://doi.org/10.1093/jxb/erv230</a>.","apa":"Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., &#38; Ding, Z. (2015). The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erv230\">https://doi.org/10.1093/jxb/erv230</a>","ista":"Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 66(15), 4631–4642.","mla":"Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” <i>Journal of Experimental Botany</i>, vol. 66, no. 15, Oxford University Press, 2015, pp. 4631–42, doi:<a href=\"https://doi.org/10.1093/jxb/erv230\">10.1093/jxb/erv230</a>.","short":"Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642.","ieee":"Y. Jia <i>et al.</i>, “The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development,” <i>Journal of Experimental Botany</i>, vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015.","ama":"Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. <i>Journal of Experimental Botany</i>. 2015;66(15):4631-4642. doi:<a href=\"https://doi.org/10.1093/jxb/erv230\">10.1093/jxb/erv230</a>"},"intvolume":"        66","day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","file_id":"5051","creator":"system","checksum":"257919be0ce3d306185d3891ad7acf39","date_created":"2018-12-12T10:14:02Z","date_updated":"2020-07-14T12:45:02Z","file_name":"IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf","file_size":7753043,"content_type":"application/pdf","relation":"main_file"}],"author":[{"full_name":"Jia, Yuebin","first_name":"Yuebin","last_name":"Jia"},{"full_name":"Tian, Huiyu","first_name":"Huiyu","last_name":"Tian"},{"full_name":"Li, Hongjiang","last_name":"Li","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660","first_name":"Hongjiang"},{"full_name":"Yu, Qianqian","first_name":"Qianqian","last_name":"Yu"},{"full_name":"Wang, Lei","first_name":"Lei","last_name":"Wang"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"}],"title":"The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","publication":"Journal of Experimental Botany","page":"4631 - 4642","date_created":"2018-12-11T11:52:42Z","has_accepted_license":"1","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"type":"journal_article","pubrep_id":"480","publist_id":"5615","volume":66,"quality_controlled":"1"},{"volume":523,"quality_controlled":"1","citation":{"ama":"Javdani F, Holló K, Hegedűs K, et al. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. <i>Journal of Comparative Neurology</i>. 2015;523(13):1967-1983. doi:<a href=\"https://doi.org/10.1002/cne.23774\">10.1002/cne.23774</a>","ieee":"F. Javdani <i>et al.</i>, “Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats,” <i>Journal of Comparative Neurology</i>, vol. 523, no. 13. Wiley-Blackwell, pp. 1967–1983, 2015.","short":"F. Javdani, K. Holló, K. Hegedűs, G. Kis, Z. Hegyi, K. Dócs, Y. Kasugai, Y. Fukazawa, R. Shigemoto, M. Antal, Journal of Comparative Neurology 523 (2015) 1967–1983.","chicago":"Javdani, Fariba, Krisztina Holló, Krisztina Hegedűs, Gréta Kis, Zoltán Hegyi, Klaudia Dócs, Yu Kasugai, Yugo Fukazawa, Ryuichi Shigemoto, and Miklós Antal. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” <i>Journal of Comparative Neurology</i>. Wiley-Blackwell, 2015. <a href=\"https://doi.org/10.1002/cne.23774\">https://doi.org/10.1002/cne.23774</a>.","ista":"Javdani F, Holló K, Hegedűs K, Kis G, Hegyi Z, Dócs K, Kasugai Y, Fukazawa Y, Shigemoto R, Antal M. 2015. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 523(13), 1967–1983.","apa":"Javdani, F., Holló, K., Hegedűs, K., Kis, G., Hegyi, Z., Dócs, K., … Antal, M. (2015). Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. <i>Journal of Comparative Neurology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cne.23774\">https://doi.org/10.1002/cne.23774</a>","mla":"Javdani, Fariba, et al. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” <i>Journal of Comparative Neurology</i>, vol. 523, no. 13, Wiley-Blackwell, 2015, pp. 1967–83, doi:<a href=\"https://doi.org/10.1002/cne.23774\">10.1002/cne.23774</a>."},"intvolume":"       523","publist_id":"5614","scopus_import":1,"department":[{"_id":"RySh"}],"date_published":"2015-09-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","publication":"Journal of Comparative Neurology","page":"1967 - 1983","date_created":"2018-12-11T11:52:42Z","doi":"10.1002/cne.23774","publication_status":"published","month":"09","title":"Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley-Blackwell","status":"public","_id":"1557","author":[{"full_name":"Javdani, Fariba","first_name":"Fariba","last_name":"Javdani"},{"full_name":"Holló, Krisztina","last_name":"Holló","first_name":"Krisztina"},{"full_name":"Hegedűs, Krisztina","first_name":"Krisztina","last_name":"Hegedűs"},{"full_name":"Kis, Gréta","last_name":"Kis","first_name":"Gréta"},{"full_name":"Hegyi, Zoltán","last_name":"Hegyi","first_name":"Zoltán"},{"last_name":"Dócs","first_name":"Klaudia","full_name":"Dócs, Klaudia"},{"full_name":"Kasugai, Yu","last_name":"Kasugai","first_name":"Yu"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Antal","first_name":"Miklós","full_name":"Antal, Miklós"}],"year":"2015","day":"01","issue":"13","abstract":[{"lang":"eng","text":"γ-Aminobutyric acid (GABA)- and glycine-mediated hyperpolarizing inhibition is associated with a chloride influx that depends on the inwardly directed chloride electrochemical gradient. In neurons, the extrusion of chloride from the cytosol primarily depends on the expression of an isoform of potassium-chloride cotransporters (KCC2s). KCC2 is crucial in the regulation of the inhibitory tone of neural circuits, including pain processing neural assemblies. Thus we investigated the cellular distribution of KCC2 in neurons underlying pain processing in the superficial spinal dorsal horn of rats by using high-resolution immunocytochemical methods. We demonstrated that perikarya and dendrites widely expressed KCC2, but axon terminals proved to be negative for KCC2. In single ultrathin sections, silver deposits labeling KCC2 molecules showed different densities on the surface of dendritic profiles, some of which were negative for KCC2. In freeze fracture replicas and tissue sections double stained for the β3-subunit of GABAA receptors and KCC2, GABAA receptors were revealed on dendritic segments with high and also with low KCC2 densities. By measuring the distances between spots immunoreactive for gephyrin (a scaffolding protein of GABAA and glycine receptors) and KCC2 on the surface of neurokinin 1 (NK1) receptor-immunoreactive dendrites, we found that gephyrin-immunoreactive spots were located at various distances from KCC2 cotransporters; 5.7 % of them were recovered in the middle of 4-10-μm-long dendritic segments that were free of KCC2 immunostaining. The variable local densities of KCC2 may result in variable postsynaptic potentials evoked by the activation of GABAA and glycine receptors along the dendrites of spinal neurons."}],"acknowledgement":"Funded by:\r\nHungarian Academy of Sciences. Grant Number: MTA-TKI 242\r\nHungarian Brain Research Program. Grant Number: KTIA_NAP_13-1-2013-0001\r\nSolution Oriented Research for Science and Technology from the Japan Science and Technology Agency Japanese Ministry of Education, Culture, Sports, Science and Technology","date_updated":"2021-01-12T06:51:35Z"},{"quality_controlled":"1","citation":{"mla":"Ivanchenko, Maria, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” <i>Development</i>, vol. 142, no. 4, Company of Biologists, 2015, pp. 712–21, doi:<a href=\"https://doi.org/10.1242/dev.113225\">10.1242/dev.113225</a>.","ista":"Ivanchenko M, Zhu J, Wang B, Medvecka E, Du Y, Azzarello E, Mancuso S, Megraw M, Filichkin S, Dubrovsky J, Friml J, Geisler M. 2015. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 142(4), 712–721.","apa":"Ivanchenko, M., Zhu, J., Wang, B., Medvecka, E., Du, Y., Azzarello, E., … Geisler, M. (2015). The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.113225\">https://doi.org/10.1242/dev.113225</a>","chicago":"Ivanchenko, Maria, Jinsheng Zhu, Bangjun Wang, Eva Medvecka, Yunlong Du, Elisa Azzarello, Stefano Mancuso, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” <i>Development</i>. Company of Biologists, 2015. <a href=\"https://doi.org/10.1242/dev.113225\">https://doi.org/10.1242/dev.113225</a>.","short":"M. Ivanchenko, J. Zhu, B. Wang, E. Medvecka, Y. Du, E. Azzarello, S. Mancuso, M. Megraw, S. Filichkin, J. Dubrovsky, J. Friml, M. Geisler, Development 142 (2015) 712–721.","ieee":"M. Ivanchenko <i>et al.</i>, “The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation,” <i>Development</i>, vol. 142, no. 4. Company of Biologists, pp. 712–721, 2015.","ama":"Ivanchenko M, Zhu J, Wang B, et al. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. <i>Development</i>. 2015;142(4):712-721. doi:<a href=\"https://doi.org/10.1242/dev.113225\">10.1242/dev.113225</a>"},"volume":142,"intvolume":"       142","scopus_import":1,"publist_id":"5613","department":[{"_id":"JiFr"}],"date_published":"2015-02-15T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","publication":"Development","date_created":"2018-12-11T11:52:42Z","page":"712 - 721","doi":"10.1242/dev.113225","publication_status":"published","month":"02","title":"The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Company of Biologists","status":"public","_id":"1558","author":[{"full_name":"Ivanchenko, Maria","last_name":"Ivanchenko","first_name":"Maria"},{"full_name":"Zhu, Jinsheng","first_name":"Jinsheng","last_name":"Zhu"},{"first_name":"Bangjun","last_name":"Wang","full_name":"Wang, Bangjun"},{"first_name":"Eva","last_name":"Medvecka","id":"298814E2-F248-11E8-B48F-1D18A9856A87","full_name":"Medvecka, Eva"},{"first_name":"Yunlong","last_name":"Du","full_name":"Du, Yunlong"},{"last_name":"Azzarello","first_name":"Elisa","full_name":"Azzarello, Elisa"},{"last_name":"Mancuso","first_name":"Stefano","full_name":"Mancuso, Stefano"},{"last_name":"Megraw","first_name":"Molly","full_name":"Megraw, Molly"},{"full_name":"Filichkin, Sergei","first_name":"Sergei","last_name":"Filichkin"},{"full_name":"Dubrovsky, Joseph","first_name":"Joseph","last_name":"Dubrovsky"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"}],"year":"2015","day":"15","abstract":[{"text":"CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation.","lang":"eng"}],"issue":"4","date_updated":"2021-01-12T06:51:35Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","title":"Computational complexity of ecological and evolutionary spatial dynamics","pmid":1,"day":"22","author":[{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"publist_id":"5612","volume":112,"quality_controlled":"1","external_id":{"pmid":["26644569"]},"publication":"PNAS","date_created":"2018-12-11T11:52:43Z","page":"15636 - 15641","type":"journal_article","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"status":"public","oa":1,"month":"12","abstract":[{"text":"There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant)will take over a resident population?We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP).","lang":"eng"}],"issue":"51","date_updated":"2021-01-12T06:51:36Z","year":"2015","_id":"1559","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/","open_access":"1"}],"scopus_import":1,"citation":{"ieee":"R. Ibsen-Jensen, K. Chatterjee, and M. Nowak, “Computational complexity of ecological and evolutionary spatial dynamics,” <i>PNAS</i>, vol. 112, no. 51. National Academy of Sciences, pp. 15636–15641, 2015.","ama":"Ibsen-Jensen R, Chatterjee K, Nowak M. Computational complexity of ecological and evolutionary spatial dynamics. <i>PNAS</i>. 2015;112(51):15636-15641. doi:<a href=\"https://doi.org/10.1073/pnas.1511366112\">10.1073/pnas.1511366112</a>","short":"R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641.","chicago":"Ibsen-Jensen, Rasmus, Krishnendu Chatterjee, and Martin Nowak. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1511366112\">https://doi.org/10.1073/pnas.1511366112</a>.","apa":"Ibsen-Jensen, R., Chatterjee, K., &#38; Nowak, M. (2015). Computational complexity of ecological and evolutionary spatial dynamics. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1511366112\">https://doi.org/10.1073/pnas.1511366112</a>","mla":"Ibsen-Jensen, Rasmus, et al. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” <i>PNAS</i>, vol. 112, no. 51, National Academy of Sciences, 2015, pp. 15636–41, doi:<a href=\"https://doi.org/10.1073/pnas.1511366112\">10.1073/pnas.1511366112</a>.","ista":"Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641."},"intvolume":"       112","doi":"10.1073/pnas.1511366112","publication_status":"published","oa_version":"Submitted Version","date_published":"2015-12-22T00:00:00Z"},{"_id":"1560","author":[{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","first_name":"Miroslav","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"day":"19","year":"2015","date_updated":"2021-01-12T06:51:36Z","abstract":[{"lang":"eng","text":"Stromal cells in the subcapsular sinus of the lymph node 'decide' which cells and molecules are allowed access to the deeper parenchyma. The glycoprotein PLVAP is a crucial component of this selector function."}],"issue":"4","month":"03","title":"The lymph node filter revealed","status":"public","publisher":"Nature Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"}],"date_published":"2015-03-19T00:00:00Z","oa_version":"None","type":"journal_article","page":"338 - 340","date_created":"2018-12-11T11:52:43Z","publication":"Nature Immunology","publication_status":"published","doi":"10.1038/ni.3126","intvolume":"        16","quality_controlled":"1","volume":16,"citation":{"short":"M. Hons, M.K. Sixt, Nature Immunology 16 (2015) 338–340.","ama":"Hons M, Sixt MK. The lymph node filter revealed. <i>Nature Immunology</i>. 2015;16(4):338-340. doi:<a href=\"https://doi.org/10.1038/ni.3126\">10.1038/ni.3126</a>","ieee":"M. Hons and M. K. Sixt, “The lymph node filter revealed,” <i>Nature Immunology</i>, vol. 16, no. 4. Nature Publishing Group, pp. 338–340, 2015.","chicago":"Hons, Miroslav, and Michael K Sixt. “The Lymph Node Filter Revealed.” <i>Nature Immunology</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ni.3126\">https://doi.org/10.1038/ni.3126</a>.","ista":"Hons M, Sixt MK. 2015. The lymph node filter revealed. Nature Immunology. 16(4), 338–340.","apa":"Hons, M., &#38; Sixt, M. K. (2015). The lymph node filter revealed. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3126\">https://doi.org/10.1038/ni.3126</a>","mla":"Hons, Miroslav, and Michael K. Sixt. “The Lymph Node Filter Revealed.” <i>Nature Immunology</i>, vol. 16, no. 4, Nature Publishing Group, 2015, pp. 338–40, doi:<a href=\"https://doi.org/10.1038/ni.3126\">10.1038/ni.3126</a>."},"scopus_import":1,"publist_id":"5611"},{"year":"2015","day":"01","abstract":[{"text":"Replication-deficient recombinant adenoviruses are potent vectors for the efficient transient expression of exogenous genes in resting immune cells. However, most leukocytes are refractory to efficient adenoviral transduction as they lack expression of the coxsackie/adenovirus receptor (CAR). To circumvent this obstacle, we generated the R26/CAG-CARΔ1StopF (where R26 is ROSA26 and CAG is CMV early enhancer/chicken β actin promoter) knock-in mouse line. This strain allows monitoring of in situ Cre recombinase activity through expression of CARΔ1. Simultaneously, CARΔ1 expression permits selective and highly efficient adenoviral transduction of immune cell populations, such as mast cells or T cells, directly ex vivo in bulk cultures without prior cell purification or activation. Furthermore, we show that CARΔ1 expression dramatically improves adenoviral infection of in vitro differentiated conventional and plasmacytoid dendritic cells (DCs), basophils, mast cells, as well as Hoxb8-immortalized hematopoietic progenitor cells. This novel dual function mouse strain will hence be a valuable tool to rapidly dissect the function of specific genes in leukocyte physiology.","lang":"eng"}],"issue":"6","date_updated":"2021-01-12T06:51:36Z","_id":"1561","author":[{"full_name":"Heger, Klaus","last_name":"Heger","first_name":"Klaus"},{"first_name":"Maike","last_name":"Kober","full_name":"Kober, Maike"},{"full_name":"Rieß, David","last_name":"Rieß","first_name":"David"},{"first_name":"Christoph","last_name":"Drees","full_name":"Drees, Christoph"},{"full_name":"De Vries, Ingrid","first_name":"Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bertossi, Arianna","first_name":"Arianna","last_name":"Bertossi"},{"last_name":"Roers","first_name":"Axel","full_name":"Roers, Axel"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"first_name":"Marc","last_name":"Schmidt Supprian","full_name":"Schmidt Supprian, Marc"}],"title":"A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","status":"public","month":"06","publication":"European Journal of Immunology","page":"1614 - 1620","date_created":"2018-12-11T11:52:44Z","doi":"10.1002/eji.201545457","publication_status":"published","department":[{"_id":"MiSi"}],"date_published":"2015-06-01T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","scopus_import":1,"publist_id":"5610","citation":{"chicago":"Heger, Klaus, Maike Kober, David Rieß, Christoph Drees, Ingrid de Vries, Arianna Bertossi, Axel Roers, Michael K Sixt, and Marc Schmidt Supprian. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” <i>European Journal of Immunology</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/eji.201545457\">https://doi.org/10.1002/eji.201545457</a>.","ista":"Heger K, Kober M, Rieß D, Drees C, de Vries I, Bertossi A, Roers A, Sixt MK, Schmidt Supprian M. 2015. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 45(6), 1614–1620.","apa":"Heger, K., Kober, M., Rieß, D., Drees, C., de Vries, I., Bertossi, A., … Schmidt Supprian, M. (2015). A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. <i>European Journal of Immunology</i>. Wiley. <a href=\"https://doi.org/10.1002/eji.201545457\">https://doi.org/10.1002/eji.201545457</a>","mla":"Heger, Klaus, et al. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” <i>European Journal of Immunology</i>, vol. 45, no. 6, Wiley, 2015, pp. 1614–20, doi:<a href=\"https://doi.org/10.1002/eji.201545457\">10.1002/eji.201545457</a>.","ieee":"K. Heger <i>et al.</i>, “A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors,” <i>European Journal of Immunology</i>, vol. 45, no. 6. Wiley, pp. 1614–1620, 2015.","ama":"Heger K, Kober M, Rieß D, et al. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. <i>European Journal of Immunology</i>. 2015;45(6):1614-1620. doi:<a href=\"https://doi.org/10.1002/eji.201545457\">10.1002/eji.201545457</a>","short":"K. Heger, M. Kober, D. Rieß, C. Drees, I. de Vries, A. Bertossi, A. Roers, M.K. Sixt, M. Schmidt Supprian, European Journal of Immunology 45 (2015) 1614–1620."},"quality_controlled":"1","intvolume":"        45","volume":45},{"year":"2015","abstract":[{"lang":"eng","text":"The plant hormone auxin is a key regulator of plant growth and development. Auxin levels are sensed and interpreted by distinct receptor systems that activate a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has been identified based on its ability to bind auxin with high affinity is a prime candidate for the extracellular receptor responsible for mediating a range of auxin effects, in particular, the fast non-transcriptional ones. Contradictory genetic studies suggested prominent or no importance of ABP1 in many developmental processes. However, how crucial the role of auxin binding to ABP1 is for its functions has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is essential for its gain-of-function cellular and developmental roles. In total, 16 different abp1 mutants were prepared that possessed substitutions in the metal core or in the hydrophobic amino acids of the auxin-binding pocket as well as neutral mutations. Their analysis revealed that an intact auxin-binding pocket is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association with membranes for endocytosis regulation. In planta analyses demonstrated the importance of the auxin binding pocket for all known ABP1-mediated postembryonic developmental processes, including morphology of leaf epidermal cells, root growth and root meristem activity, and vascular tissue differentiation. Taken together, these findings suggest that auxin binding to ABP1 is central to its function, supporting the role of ABP1 as auxin receptor."}],"issue":"16","date_updated":"2023-02-23T10:04:26Z","_id":"1562","status":"public","ec_funded":1,"month":"08","doi":"10.1093/jxb/erv177","publication_status":"published","date_published":"2015-08-01T00:00:00Z","oa_version":"None","scopus_import":1,"intvolume":"        66","citation":{"ista":"Grones P, Chen X, Simon S, Kaufmann W, De Rycke R, Nodzyński T, Zažímalová E, Friml J. 2015. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 66(16), 5055–5065.","apa":"Grones, P., Chen, X., Simon, S., Kaufmann, W., De Rycke, R., Nodzyński, T., … Friml, J. (2015). Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erv177\">https://doi.org/10.1093/jxb/erv177</a>","mla":"Grones, Peter, et al. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” <i>Journal of Experimental Botany</i>, vol. 66, no. 16, Oxford University Press, 2015, pp. 5055–65, doi:<a href=\"https://doi.org/10.1093/jxb/erv177\">10.1093/jxb/erv177</a>.","chicago":"Grones, Peter, Xu Chen, Sibu Simon, Walter Kaufmann, Riet De Rycke, Tomasz Nodzyński, Eva Zažímalová, and Jiří Friml. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/jxb/erv177\">https://doi.org/10.1093/jxb/erv177</a>.","ieee":"P. Grones <i>et al.</i>, “Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles,” <i>Journal of Experimental Botany</i>, vol. 66, no. 16. Oxford University Press, pp. 5055–5065, 2015.","ama":"Grones P, Chen X, Simon S, et al. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. <i>Journal of Experimental Botany</i>. 2015;66(16):5055-5065. doi:<a href=\"https://doi.org/10.1093/jxb/erv177\">10.1093/jxb/erv177</a>","short":"P. Grones, X. Chen, S. Simon, W. Kaufmann, R. De Rycke, T. Nodzyński, E. Zažímalová, J. Friml, Journal of Experimental Botany 66 (2015) 5055–5065."},"day":"01","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG- 20101109-PSDP to JF); the European Social Fund and the state budget of the Czech Republic [the project ‘Employment of Newly Graduated Doctors of Science for Scientific Excellence’ (CZ.1.07/2.3.00/30.0009) to TN]; the Czech Science Foundation (GACR) [project 13-40637S to JF].","author":[{"last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Grones, Peter"},{"full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Xu"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","first_name":"Sibu","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"title":"Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","publication":"Journal of Experimental Botany","date_created":"2018-12-11T11:52:44Z","page":"5055 - 5065","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","publist_id":"5609","volume":66,"quality_controlled":"1"},{"month":"03","title":"An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds","status":"public","publisher":"Juliusz Schauder Center for Nonlinear Studies","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1563","author":[{"first_name":"Grzegorz","last_name":"Graff","full_name":"Graff, Grzegorz"},{"full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","last_name":"Pilarczyk","first_name":"Pawel"}],"day":"01","year":"2015","date_updated":"2021-01-12T06:51:37Z","issue":"1","abstract":[{"lang":"eng","text":"For a given self-map $f$ of $M$, a closed smooth connected and simply-connected manifold of dimension $m\\geq 4$, we provide an algorithm for estimating the values of the topological invariant $D^m_r[f]$, which equals the minimal number of $r$-periodic points in the smooth homotopy class of $f$. Our results are based on the combinatorial scheme for computing $D^m_r[f]$ introduced by G. Graff and J. Jezierski [J. Fixed Point Theory Appl. 13 (2013), 63-84]. An open-source implementation of the algorithm programmed in C++ is publicly available at {\\tt http://www.pawelpilarczyk.com/combtop/}."}],"volume":45,"citation":{"short":"G. Graff, P. Pilarczyk, Topological Methods in Nonlinear Analysis 45 (2015) 273–286.","ama":"Graff G, Pilarczyk P. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. <i>Topological Methods in Nonlinear Analysis</i>. 2015;45(1):273-286. doi:<a href=\"https://doi.org/10.12775/TMNA.2015.014\">10.12775/TMNA.2015.014</a>","ieee":"G. Graff and P. Pilarczyk, “An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds,” <i>Topological Methods in Nonlinear Analysis</i>, vol. 45, no. 1. Juliusz Schauder Center for Nonlinear Studies, pp. 273–286, 2015.","mla":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” <i>Topological Methods in Nonlinear Analysis</i>, vol. 45, no. 1, Juliusz Schauder Center for Nonlinear Studies, 2015, pp. 273–86, doi:<a href=\"https://doi.org/10.12775/TMNA.2015.014\">10.12775/TMNA.2015.014</a>.","apa":"Graff, G., &#38; Pilarczyk, P. (2015). An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. <i>Topological Methods in Nonlinear Analysis</i>. Juliusz Schauder Center for Nonlinear Studies. <a href=\"https://doi.org/10.12775/TMNA.2015.014\">https://doi.org/10.12775/TMNA.2015.014</a>","ista":"Graff G, Pilarczyk P. 2015. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 45(1), 273–286.","chicago":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” <i>Topological Methods in Nonlinear Analysis</i>. Juliusz Schauder Center for Nonlinear Studies, 2015. <a href=\"https://doi.org/10.12775/TMNA.2015.014\">https://doi.org/10.12775/TMNA.2015.014</a>."},"quality_controlled":"1","intvolume":"        45","scopus_import":1,"publist_id":"5608","language":[{"iso":"eng"}],"date_published":"2015-03-01T00:00:00Z","department":[{"_id":"HeEd"}],"oa_version":"None","type":"journal_article","page":"273 - 286","date_created":"2018-12-11T11:52:44Z","publication":"Topological Methods in Nonlinear Analysis","publication_status":"published","doi":"10.12775/TMNA.2015.014"},{"date_updated":"2021-01-12T06:51:37Z","issue":"11","year":"2015","article_number":"145","_id":"1564","status":"public","oa":1,"month":"11","ec_funded":1,"publication_status":"published","doi":"10.3389/fncom.2015.00145","oa_version":"Published Version","date_published":"2015-11-30T00:00:00Z","scopus_import":1,"file_date_updated":"2020-07-14T12:45:02Z","ddc":["570"],"intvolume":"         9","citation":{"short":"M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015).","ieee":"M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” <i>Frontiers in Computational Neuroscience</i>, vol. 9, no. 11. Frontiers Research Foundation, 2015.","ama":"Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the interaction of different forms of plasticity. <i>Frontiers in Computational Neuroscience</i>. 2015;9(11). doi:<a href=\"https://doi.org/10.3389/fncom.2015.00145\">10.3389/fncom.2015.00145</a>","apa":"Gilson, M., Savin, C., &#38; Zenke, F. (2015). Editorial: Emergent neural computation from the interaction of different forms of plasticity. <i>Frontiers in Computational Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fncom.2015.00145\">https://doi.org/10.3389/fncom.2015.00145</a>","ista":"Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145.","mla":"Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” <i>Frontiers in Computational Neuroscience</i>, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:<a href=\"https://doi.org/10.3389/fncom.2015.00145\">10.3389/fncom.2015.00145</a>.","chicago":"Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” <i>Frontiers in Computational Neuroscience</i>. Frontiers Research Foundation, 2015. <a href=\"https://doi.org/10.3389/fncom.2015.00145\">https://doi.org/10.3389/fncom.2015.00145</a>."},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"30","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Gilson, Matthieu","first_name":"Matthieu","last_name":"Gilson"},{"full_name":"Savin, Cristina","last_name":"Savin","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina"},{"last_name":"Zenke","first_name":"Friedemann","full_name":"Zenke, Friedemann"}],"file":[{"date_updated":"2020-07-14T12:45:02Z","file_name":"IST-2016-479-v1+1_fncom-09-00145.pdf","date_created":"2018-12-12T10:12:09Z","creator":"system","file_id":"4927","checksum":"cea73b6d3ef1579f32da10b82f4de4fd","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":187038}],"publisher":"Frontiers Research Foundation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Editorial: Emergent neural computation from the interaction of different forms of plasticity","has_accepted_license":"1","date_created":"2018-12-11T11:52:45Z","publication":"Frontiers in Computational Neuroscience","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"publist_id":"5607","pubrep_id":"479","volume":9,"quality_controlled":"1"},{"oa":1,"status":"public","month":"11","year":"2015","date_updated":"2021-01-12T06:51:38Z","abstract":[{"text":"Leptin is an adipokine produced by the adipose tissue regulating body weight through its appetite-suppressing effect. Besides being expressed in the hypothalamus and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells of the adrenal medulla. In the present study, we report the effect of leptin on mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused a slowly developing membrane hyperpolarization followed by complete blockade of action potential (AP) firing. This inhibitory effect at rest was abolished by the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium channels. Single-channel recordings in 'perforated microvesicles' confirmed that leptin increased BK channel open probability without altering its unitary conductance. BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K) signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully prevented BK current increase. We also tested the effect of leptin on evoked AP firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains of lower frequency, APs are broader and depolarization-evoked exocytosis is increased as a result of the larger size of the ready-releasable pool and higher frequency of vesicle release. The kinetics and quantal size of single secretory events remained unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual action on MCC activity. It dampens AP firing at rest but preserves AP firing and increases catecholamine secretion during sustained stimulation, highlighting the importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic tone and catecholamine release.","lang":"eng"}],"issue":"22","_id":"1565","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/","open_access":"1"}],"scopus_import":1,"citation":{"apa":"Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., &#38; Carabelli, V. (2015). Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. <i>Journal of Physiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1113/JP271078\">https://doi.org/10.1113/JP271078</a>","mla":"Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” <i>Journal of Physiology</i>, vol. 593, no. 22, Wiley-Blackwell, 2015, pp. 4835–53, doi:<a href=\"https://doi.org/10.1113/JP271078\">10.1113/JP271078</a>.","ista":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 593(22), 4835–4853.","chicago":"Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” <i>Journal of Physiology</i>. Wiley-Blackwell, 2015. <a href=\"https://doi.org/10.1113/JP271078\">https://doi.org/10.1113/JP271078</a>.","ieee":"D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” <i>Journal of Physiology</i>, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015.","ama":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. <i>Journal of Physiology</i>. 2015;593(22):4835-4853. doi:<a href=\"https://doi.org/10.1113/JP271078\">10.1113/JP271078</a>","short":"D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of Physiology 593 (2015) 4835–4853."},"intvolume":"       593","publication_status":"published","doi":"10.1113/JP271078","date_published":"2015-11-15T00:00:00Z","oa_version":"Submitted Version","title":"Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells","publisher":"Wiley-Blackwell","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","pmid":1,"acknowledgement":"This work was supported by the Compagnia di San Paolo Foundation ‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank Dr Claudio Franchino for cell preparation and for providing excellent technical support.","author":[{"full_name":"Gavello, Daniela","last_name":"Gavello","first_name":"Daniela"},{"full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","orcid":"0000-0001-7577-1676","first_name":"David H"},{"full_name":"Gosso, Sara","first_name":"Sara","last_name":"Gosso"},{"first_name":"Emilio","last_name":"Carbone","full_name":"Carbone, Emilio"},{"full_name":"Carabelli, Valentina","last_name":"Carabelli","first_name":"Valentina"}],"publist_id":"5606","external_id":{"pmid":["26282459"]},"quality_controlled":"1","volume":593,"page":"4835 - 4853","date_created":"2018-12-11T11:52:45Z","publication":"Journal of Physiology","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"type":"journal_article"},{"doi":"10.1371/journal.pcbi.1004541","publication_status":"published","oa_version":"Published Version","date_published":"2015-10-23T00:00:00Z","scopus_import":1,"file_date_updated":"2020-07-14T12:45:02Z","ddc":["570"],"intvolume":"        11","citation":{"ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures. <i>PLoS Computational Biology</i>. 2015;11(10). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">10.1371/journal.pcbi.1004541</a>","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures,” <i>PLoS Computational Biology</i>, vol. 11, no. 10. Public Library of Science, 2015.","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational Biology 11 (2015).","mla":"Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine Structures.” <i>PLoS Computational Biology</i>, vol. 11, no. 10, e1004541, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">10.1371/journal.pcbi.1004541</a>.","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., &#38; Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">https://doi.org/10.1371/journal.pcbi.1004541</a>","ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 11(10), e1004541.","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” <i>PLoS Computational Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">https://doi.org/10.1371/journal.pcbi.1004541</a>."},"issue":"10","abstract":[{"lang":"eng","text":"Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease."}],"date_updated":"2023-02-23T14:05:55Z","year":"2015","article_number":"e1004541","_id":"1566","status":"public","oa":1,"month":"10","has_accepted_license":"1","publication":"PLoS Computational Biology","date_created":"2018-12-11T11:52:45Z","type":"journal_article","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"pubrep_id":"478","publist_id":"5605","volume":11,"quality_controlled":"1","related_material":{"record":[{"id":"9714","status":"public","relation":"research_data"}]},"acknowledgement":"We acknowledge the support by the EU Joint Programme in Neurodegenerative Diseases (JPND AC14/00037) project. The project is supported through the following funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland, National Science Centre; and Spain, ISCIII. ","day":"23","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Gómez Sicilia, Àngel","first_name":"Àngel","last_name":"Gómez Sicilia"},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K"},{"full_name":"Cieplak, Marek","last_name":"Cieplak","first_name":"Marek"},{"full_name":"Carrión Vázquez, Mariano","last_name":"Carrión Vázquez","first_name":"Mariano"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":1412511,"date_updated":"2020-07-14T12:45:02Z","file_name":"IST-2016-478-v1+1_journal.pcbi.1004541.pdf","date_created":"2018-12-12T10:16:21Z","checksum":"8b67d729be663bfc9af04bfd94459655","file_id":"5207","creator":"system","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","title":"An exploration of the universe of polyglutamine structures"},{"publist_id":"5604","scopus_import":"1","article_processing_charge":"No","volume":9411,"citation":{"chicago":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” In <i>23rd International Symposium</i>, Vol. 9411. Springer Nature, 2015.","mla":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” <i>23rd International Symposium</i>, vol. 9411, Springer Nature, 2015.","apa":"Edelsbrunner, H. (2015). Shape, homology, persistence, and stability. In <i>23rd International Symposium</i> (Vol. 9411). Los Angeles, CA, United States: Springer Nature.","ista":"Edelsbrunner H. 2015. Shape, homology, persistence, and stability. 23rd International Symposium. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411.","ieee":"H. Edelsbrunner, “Shape, homology, persistence, and stability,” in <i>23rd International Symposium</i>, Los Angeles, CA, United States, 2015, vol. 9411.","ama":"Edelsbrunner H. Shape, homology, persistence, and stability. In: <i>23rd International Symposium</i>. Vol 9411. Springer Nature; 2015.","short":"H. Edelsbrunner, in:, 23rd International Symposium, Springer Nature, 2015."},"intvolume":"      9411","quality_controlled":"1","date_created":"2018-12-11T11:52:46Z","publication":"23rd International Symposium","publication_status":"published","conference":{"start_date":"2015-09-24","name":"GD: Graph Drawing and Network Visualization","end_date":"2015-09-26","location":"Los Angeles, CA, United States"},"language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"date_published":"2015-01-01T00:00:00Z","oa_version":"None","type":"conference","title":"Shape, homology, persistence, and stability","publisher":"Springer Nature","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"01","alternative_title":["LNCS"],"day":"01","year":"2015","date_updated":"2022-01-28T08:25:00Z","abstract":[{"text":"My personal journey to the fascinating world of geometric forms started more than 30 years ago with the invention of alpha shapes in the plane. It took about 10 years before we generalized the concept to higher dimensions, we produced working software with a graphics interface for the three-dimensional case. At the same time, we added homology to the computations. Needless to say that this foreshadowed the inception of persistent homology, because it suggested the study of filtrations to capture the scale of a shape or data set. Importantly, this method has fast algorithms. The arguably most useful result on persistent homology is the stability of its diagrams under perturbations.","lang":"eng"}],"_id":"1567","author":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}]},{"year":"2015","day":"05","acknowledgement":"This research is supported by the project No. 477 of P.G. Demidov Yaroslavl State University within State Assignment for Research.","abstract":[{"lang":"eng","text":"Aiming at the automatic diagnosis of tumors from narrow band imaging (NBI) magnifying endoscopy (ME) images of the stomach, we combine methods from image processing, computational topology, and machine learning to classify patterns into normal, tubular, vessel. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions."}],"date_updated":"2023-02-21T16:57:29Z","_id":"1568","author":[{"full_name":"Dunaeva, Olga","last_name":"Dunaeva","first_name":"Olga"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"last_name":"Lukyanov","first_name":"Anton","full_name":"Lukyanov, Anton"},{"first_name":"Michael","last_name":"Machin","full_name":"Machin, Michael"},{"full_name":"Malkova, Daria","first_name":"Daria","last_name":"Malkova"}],"title":"The classification of endoscopy images with persistent homology","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"IEEE","month":"02","publication":"Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing","page":"7034731","date_created":"2018-12-11T11:52:46Z","doi":"10.1109/SYNASC.2014.81","publication_status":"published","conference":{"location":"Timisoara, Romania","end_date":"2014-09-25","name":"SYNASC: Symbolic and Numeric Algorithms for Scientific Computing","start_date":"2014-09-22"},"date_published":"2015-02-05T00:00:00Z","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"type":"conference","oa_version":"None","scopus_import":1,"publist_id":"5603","related_material":{"record":[{"status":"public","relation":"later_version","id":"1289"}]},"citation":{"apa":"Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., &#38; Malkova, D. (2015). The classification of endoscopy images with persistent homology. In <i>Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i> (p. 7034731). Timisoara, Romania: IEEE. <a href=\"https://doi.org/10.1109/SYNASC.2014.81\">https://doi.org/10.1109/SYNASC.2014.81</a>","ista":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. 2015. The classification of endoscopy images with persistent homology. Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. SYNASC: Symbolic and Numeric Algorithms for Scientific Computing, 7034731.","mla":"Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” <i>Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>, IEEE, 2015, p. 7034731, doi:<a href=\"https://doi.org/10.1109/SYNASC.2014.81\">10.1109/SYNASC.2014.81</a>.","chicago":"Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, and Daria Malkova. “The Classification of Endoscopy Images with Persistent Homology.” In <i>Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>, 7034731. IEEE, 2015. <a href=\"https://doi.org/10.1109/SYNASC.2014.81\">https://doi.org/10.1109/SYNASC.2014.81</a>.","ieee":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, and D. Malkova, “The classification of endoscopy images with persistent homology,” in <i>Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>, Timisoara, Romania, 2015, p. 7034731.","ama":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. The classification of endoscopy images with persistent homology. In: <i>Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>. IEEE; 2015:7034731. doi:<a href=\"https://doi.org/10.1109/SYNASC.2014.81\">10.1109/SYNASC.2014.81</a>","short":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, in:, Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731."},"quality_controlled":"1"},{"author":[{"last_name":"Doyle","first_name":"Siamsa","full_name":"Doyle, Siamsa"},{"first_name":"Ash","last_name":"Haegera","full_name":"Haegera, Ash"},{"last_name":"Vain","first_name":"Thomas","full_name":"Vain, Thomas"},{"full_name":"Rigala, Adeline","last_name":"Rigala","first_name":"Adeline"},{"full_name":"Viotti, Corrado","first_name":"Corrado","last_name":"Viotti"},{"full_name":"Łangowskaa, Małgorzata","last_name":"Łangowskaa","first_name":"Małgorzata"},{"last_name":"Maa","first_name":"Qian","full_name":"Maa, Qian"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Raikhel, Natasha","last_name":"Raikhel","first_name":"Natasha"},{"full_name":"Hickse, Glenn","first_name":"Glenn","last_name":"Hickse"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"}],"project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"day":"17","acknowledgement":"This work was supported by Vetenskapsrådet and Vinnova (Verket för Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP (to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). ","title":"An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"PNAS","page":"E806 - E815","date_created":"2018-12-11T11:52:46Z","quality_controlled":"1","volume":112,"publist_id":"5602","_id":"1569","year":"2015","issue":"7","abstract":[{"lang":"eng","text":"Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development."}],"date_updated":"2021-01-12T06:51:39Z","ec_funded":1,"month":"02","oa":1,"status":"public","date_published":"2015-02-17T00:00:00Z","oa_version":"Published Version","doi":"10.1073/pnas.1424856112","publication_status":"published","intvolume":"       112","citation":{"chicago":"Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti, Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1424856112\">https://doi.org/10.1073/pnas.1424856112</a>.","mla":"Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” <i>PNAS</i>, vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:<a href=\"https://doi.org/10.1073/pnas.1424856112\">10.1073/pnas.1424856112</a>.","apa":"Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., … Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1424856112\">https://doi.org/10.1073/pnas.1424856112</a>","ista":"Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 112(7), E806–E815.","short":"S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa, J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815.","ama":"Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. <i>PNAS</i>. 2015;112(7):E806-E815. doi:<a href=\"https://doi.org/10.1073/pnas.1424856112\">10.1073/pnas.1424856112</a>","ieee":"S. Doyle <i>et al.</i>, “An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,” <i>PNAS</i>, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015."},"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/"}]},{"year":"2015","issue":"45","abstract":[{"text":"Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution.","lang":"eng"}],"date_updated":"2021-01-12T06:51:40Z","_id":"1570","oa":1,"status":"public","ec_funded":1,"month":"11","doi":"10.1073/pnas.1508400112","publication_status":"published","date_published":"2015-11-10T00:00:00Z","oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/"}],"citation":{"short":"R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.","ama":"Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor intelligence. <i>PNAS</i>. 2015;112(45):E6224-E6232. doi:<a href=\"https://doi.org/10.1073/pnas.1508400112\">10.1073/pnas.1508400112</a>","ieee":"R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” <i>PNAS</i>, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015.","ista":"Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.","apa":"Der, R., &#38; Martius, G. S. (2015). Novel plasticity rule can explain the development of sensorimotor intelligence. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1508400112\">https://doi.org/10.1073/pnas.1508400112</a>","mla":"Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” <i>PNAS</i>, vol. 112, no. 45, National Academy of Sciences, 2015, pp. E6224–32, doi:<a href=\"https://doi.org/10.1073/pnas.1508400112\">10.1073/pnas.1508400112</a>.","chicago":"Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1508400112\">https://doi.org/10.1073/pnas.1508400112</a>."},"intvolume":"       112","day":"10","pmid":1,"author":[{"last_name":"Der","first_name":"Ralf","full_name":"Der, Ralf"},{"full_name":"Martius, Georg S","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius"}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"title":"Novel plasticity rule can explain the development of sensorimotor intelligence","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","publication":"PNAS","page":"E6224 - E6232","date_created":"2018-12-11T11:52:47Z","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"type":"journal_article","publist_id":"5601","quality_controlled":"1","volume":112,"external_id":{"pmid":["26504200"]}},{"publication":"PNAS","page":"14906 - 14911","date_created":"2018-12-11T11:52:47Z","doi":"10.1073/pnas.1510282112","publication_status":"published","date_published":"2015-12-01T00:00:00Z","department":[{"_id":"ToBo"}],"language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","publist_id":"5600","scopus_import":1,"quality_controlled":"1","intvolume":"       112","volume":112,"citation":{"ieee":"M. de Vos, A. Dawid, V. Šunderlíková, and S. Tans, “Breaking evolutionary constraint with a tradeoff ratchet,” <i>PNAS</i>, vol. 112, no. 48. National Academy of Sciences, pp. 14906–14911, 2015.","ama":"de Vos M, Dawid A, Šunderlíková V, Tans S. Breaking evolutionary constraint with a tradeoff ratchet. <i>PNAS</i>. 2015;112(48):14906-14911. doi:<a href=\"https://doi.org/10.1073/pnas.1510282112\">10.1073/pnas.1510282112</a>","short":"M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911.","apa":"de Vos, M., Dawid, A., Šunderlíková, V., &#38; Tans, S. (2015). Breaking evolutionary constraint with a tradeoff ratchet. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1510282112\">https://doi.org/10.1073/pnas.1510282112</a>","ista":"de Vos M, Dawid A, Šunderlíková V, Tans S. 2015. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 112(48), 14906–14911.","mla":"de Vos, Marjon, et al. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” <i>PNAS</i>, vol. 112, no. 48, National Academy of Sciences, 2015, pp. 14906–11, doi:<a href=\"https://doi.org/10.1073/pnas.1510282112\">10.1073/pnas.1510282112</a>.","chicago":"Vos, Marjon de, Alexandre Dawid, Vanda Šunderlíková, and Sander Tans. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1510282112\">https://doi.org/10.1073/pnas.1510282112</a>."},"year":"2015","day":"01","issue":"48","abstract":[{"lang":"eng","text":"Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype-environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor-operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that crossenvironmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance."}],"acknowledgement":"This work is part of the research program of the Foundation for Fundamental Research on Matter, which is part of the Netherlands Organization for Scientific Research (NWO). M.G.J.d.V. was (partially) funded by NWO Earth and Life Sciences (ALW), project 863.14.015. We thank D. M. Weinreich, J. A. G. M. de Visser, T. Paixão, J. Polechová, T. Friedlander, and A. E. Mayo for reading and commenting on earlier versions of the manuscript and B. Houchmandzadeh, O. Rivoire, and M. Hemery for discussions and suggestions on the Markov computation. Furthermore, we thank F. J. Poelwijk for sharing plasmid pCascade5 and pRD007 and Y. Yokobayashi for sharing plasmid pINV-110. We also thank the anonymous reviewers for remarks on the initial version of the manuscript.","date_updated":"2021-01-12T06:51:40Z","_id":"1571","author":[{"first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","last_name":"De Vos","full_name":"De Vos, Marjon"},{"last_name":"Dawid","first_name":"Alexandre","full_name":"Dawid, Alexandre"},{"last_name":"Šunderlíková","first_name":"Vanda","full_name":"Šunderlíková, Vanda"},{"first_name":"Sander","last_name":"Tans","full_name":"Tans, Sander"}],"title":"Breaking evolutionary constraint with a tradeoff ratchet","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"National Academy of Sciences","month":"12"}]