[{"status":"public","publication_identifier":{"eissn":["2234-3016"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0901.3015"}],"date_created":"2018-12-11T11:52:39Z","type":"journal_article","_id":"1547","language":[{"iso":"eng"}],"volume":52,"month":"05","issue":"3","author":[{"id":"2C29581E-F248-11E8-B48F-1D18A9856A87","full_name":"Mohammadi, Fatemeh","first_name":"Fatemeh","last_name":"Mohammadi"},{"last_name":"Moradi","first_name":"Somayeh","full_name":"Moradi, Somayeh"}],"quality_controlled":"1","oa_version":"Preprint","intvolume":"        52","publist_id":"5624","publication":"Bulletin of the Korean Mathematical Society","scopus_import":1,"year":"2015","page":"977 - 986","doi":"10.4134/BKMS.2015.52.3.977","day":"31","oa":1,"date_published":"2015-05-31T00:00:00Z","publisher":"Korean Mathematical Society","title":"Resolution of unmixed bipartite graphs","abstract":[{"lang":"eng","text":"Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G), and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals are associated to G, the edge ideal I(G) generated by all monomials xixj with {xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂ V(G) such that each edge has at least one vertex in C and no proper subset of C has the same property. Indeed, the vertex cover ideal of G is the Alexander dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we consider the lattice of vertex covers LG and we explicitly describe the minimal free resolution of the ideal associated to LG which is exactly the vertex cover ideal of G. Then we compute depth, projective dimension, regularity and extremal Betti numbers of R/I(G) in terms of the associated lattice."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:31Z","department":[{"_id":"CaUh"}],"citation":{"apa":"Mohammadi, F., &#38; Moradi, S. (2015). Resolution of unmixed bipartite graphs. <i>Bulletin of the Korean Mathematical Society</i>. Korean Mathematical Society. <a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">https://doi.org/10.4134/BKMS.2015.52.3.977</a>","ama":"Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. <i>Bulletin of the Korean Mathematical Society</i>. 2015;52(3):977-986. doi:<a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">10.4134/BKMS.2015.52.3.977</a>","ista":"Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 52(3), 977–986.","chicago":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” <i>Bulletin of the Korean Mathematical Society</i>. Korean Mathematical Society, 2015. <a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">https://doi.org/10.4134/BKMS.2015.52.3.977</a>.","ieee":"F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” <i>Bulletin of the Korean Mathematical Society</i>, vol. 52, no. 3. Korean Mathematical Society, pp. 977–986, 2015.","short":"F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986.","mla":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” <i>Bulletin of the Korean Mathematical Society</i>, vol. 52, no. 3, Korean Mathematical Society, 2015, pp. 977–86, doi:<a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">10.4134/BKMS.2015.52.3.977</a>."}},{"scopus_import":1,"publication":"Applied and Environmental Microbiology","publist_id":"5623","intvolume":"        81","oa":1,"year":"2015","day":"01","doi":"10.1128/AEM.02051-15","page":"8135 - 8144","publication_status":"published","abstract":[{"text":"Reproduction within a host and transmission to the next host are crucial for the virulence and fitness of pathogens. Nevertheless, basic knowledge about such parameters is often missing from the literature, even for well-studied bacteria, such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects its hosts via the oral route. To characterize bacterial replication success, we made use of an experimental oral infection system for the red flour beetle Tribolium castaneum and developed a flow cytometric assay for the quantification of both spore ingestion by the individual beetle larvae and the resulting spore load after bacterial replication and resporulation within cadavers. On average, spore numbers increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial stock cultures into nutrient medium, we next investigated outgrowth characteristics of vegetative cells and found that cadaver- derived bacteria showed reduced growth compared to bacteria from the stock cultures. Interestingly, this reduced growth was a consequence of inhibited spore germination, probably originating from the host and resulting in reduced host mortality in subsequent infections by cadaver-derived spores. Nevertheless, we further showed that Bacillus thuringiensis transmission was possible via larval cannibalism when no other food was offered. These results contribute to our understanding of the ecology of Bacillus thuringiensis as an insect pathogen.","lang":"eng"}],"title":"Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination","pmid":1,"publisher":"American Society for Microbiology","date_published":"2015-12-01T00:00:00Z","citation":{"apa":"Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., &#38; Kurtz, J. (2015). Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. <i>Applied and Environmental Microbiology</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/AEM.02051-15\">https://doi.org/10.1128/AEM.02051-15</a>","chicago":"Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” <i>Applied and Environmental Microbiology</i>. American Society for Microbiology, 2015. <a href=\"https://doi.org/10.1128/AEM.02051-15\">https://doi.org/10.1128/AEM.02051-15</a>.","ista":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 81(23), 8135–8144.","ama":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. <i>Applied and Environmental Microbiology</i>. 2015;81(23):8135-8144. doi:<a href=\"https://doi.org/10.1128/AEM.02051-15\">10.1128/AEM.02051-15</a>","ieee":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination,” <i>Applied and Environmental Microbiology</i>, vol. 81, no. 23. American Society for Microbiology, pp. 8135–8144, 2015.","mla":"Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” <i>Applied and Environmental Microbiology</i>, vol. 81, no. 23, American Society for Microbiology, 2015, pp. 8135–44, doi:<a href=\"https://doi.org/10.1128/AEM.02051-15\">10.1128/AEM.02051-15</a>.","short":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and Environmental Microbiology 81 (2015) 8135–8144."},"department":[{"_id":"SyCr"}],"date_updated":"2021-01-12T06:51:31Z","external_id":{"pmid":["26386058"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"1548","date_created":"2018-12-11T11:52:39Z","status":"public","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/"}],"issue":"23","month":"12","volume":81,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","quality_controlled":"1","author":[{"last_name":"Milutinovic","first_name":"Barbara","orcid":"0000-0002-8214-4758","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","full_name":"Milutinovic, Barbara"},{"full_name":"Höfling, Christina","last_name":"Höfling","first_name":"Christina"},{"full_name":"Futo, Momir","last_name":"Futo","first_name":"Momir"},{"first_name":"Jörn","last_name":"Scharsack","full_name":"Scharsack, Jörn"},{"full_name":"Kurtz, Joachim","first_name":"Joachim","last_name":"Kurtz"}]},{"page":"101 - 117","doi":"10.1007/978-1-4939-2845-3_6","year":"2015","day":"18","oa":1,"publication":"Novel chemical tools to study ion channel biology","intvolume":"       869","publist_id":"5622","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under Light Control.” <i>Novel Chemical Tools to Study Ion Channel Biology</i>, vol. 869, Springer, 2015, pp. 101–17, doi:<a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">10.1007/978-1-4939-2845-3_6</a>.","short":"C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools to Study Ion Channel Biology, Springer, 2015, pp. 101–117.","apa":"Mckenzie, C., Sanchez-Romero, I., &#38; Janovjak, H. L. (2015). Flipping the photoswitch: Ion channels under light control. In <i>Novel chemical tools to study ion channel biology</i> (Vol. 869, pp. 101–117). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">https://doi.org/10.1007/978-1-4939-2845-3_6</a>","chicago":"Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak. “Flipping the Photoswitch: Ion Channels under Light Control.” In <i>Novel Chemical Tools to Study Ion Channel Biology</i>, 869:101–17. Advances in Experimental Medicine and Biology. Springer, 2015. <a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">https://doi.org/10.1007/978-1-4939-2845-3_6</a>.","ama":"Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels under light control. In: <i>Novel Chemical Tools to Study Ion Channel Biology</i>. Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117. doi:<a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">10.1007/978-1-4939-2845-3_6</a>","ista":"Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch: Ion channels under light control. In: Novel chemical tools to study ion channel biology. vol. 869, 101–117.","ieee":"C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch: Ion channels under light control,” in <i>Novel chemical tools to study ion channel biology</i>, vol. 869, Springer, 2015, pp. 101–117."},"date_updated":"2021-01-12T06:51:32Z","department":[{"_id":"HaJa"}],"title":"Flipping the photoswitch: Ion channels under light control","file_date_updated":"2020-07-14T12:45:01Z","publisher":"Springer","date_published":"2015-09-18T00:00:00Z","ddc":["571","576"],"series_title":"Advances in Experimental Medicine and Biology","abstract":[{"lang":"eng","text":"Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology."}],"publication_status":"published","status":"public","publication_identifier":{"isbn":["978-1-4939-2844-6"]},"type":"book_chapter","_id":"1549","date_created":"2018-12-11T11:52:39Z","pubrep_id":"839","author":[{"first_name":"Catherine","last_name":"Mckenzie","full_name":"Mckenzie, Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada","first_name":"Inmaculada","last_name":"Sanchez Romero"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"}],"oa_version":"Submitted Version","quality_controlled":"1","volume":869,"language":[{"iso":"eng"}],"file":[{"creator":"system","checksum":"bd1bfdf2423a0c3b6e7cabfa8b44bc0f","file_id":"4854","file_size":1919655,"access_level":"open_access","relation":"main_file","file_name":"IST-2017-839-v1+1_mckenzie.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:11:02Z"}],"has_accepted_license":"1","month":"09"},{"doi":"10.1016/j.neuron.2015.07.011","year":"2015","page":"989 - 998","day":"02","acknowledgement":"Research in the G.F. laboratory is supported by NIH (NS 081297, MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF (1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n","oa":1,"publication":"Neuron","intvolume":"        87","publist_id":"5621","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["26299473"]},"citation":{"short":"C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer, G. Fishell, Neuron 87 (2015) 989–998.","mla":"Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” <i>Neuron</i>, vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:<a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">10.1016/j.neuron.2015.07.011</a>.","apa":"Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., … Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">https://doi.org/10.1016/j.neuron.2015.07.011</a>","chicago":"Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher, Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” <i>Neuron</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">https://doi.org/10.1016/j.neuron.2015.07.011</a>.","ista":"Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S, Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 87(5), 989–998.","ama":"Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. <i>Neuron</i>. 2015;87(5):989-998. doi:<a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">10.1016/j.neuron.2015.07.011</a>","ieee":"C. Mayer <i>et al.</i>, “Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries,” <i>Neuron</i>, vol. 87, no. 5. Elsevier, pp. 989–998, 2015."},"date_updated":"2021-01-12T06:51:32Z","department":[{"_id":"SiHi"}],"title":"Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries","publisher":"Elsevier","date_published":"2015-09-02T00:00:00Z","pmid":1,"abstract":[{"text":"The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain interneurons. Here, we examine the lineage relationship among MGE-derived interneurons using a replication-defective retroviral library containing a highly diverse set of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor cells enabled us to unambiguously determine their respective lineal relationship. We found that clonal dispersion occurs across large areas of the brain and is not restricted by anatomical divisions. As such, sibling interneurons can populate the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons appeared to be generated from asymmetric divisions of MGE progenitor cells, followed by symmetric divisions within the subventricular zone. Altogether, our findings uncover that lineage relationships do not appear to determine interneuron allocation to particular regions. As such, it is likely that clonally related interneurons have considerable flexibility as to the particular forebrain circuits to which they can contribute.","lang":"eng"}],"publication_status":"published","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/","open_access":"1"}],"status":"public","type":"journal_article","_id":"1550","date_created":"2018-12-11T11:52:40Z","author":[{"first_name":"Christian","last_name":"Mayer","full_name":"Mayer, Christian"},{"full_name":"Jaglin, Xavier","last_name":"Jaglin","first_name":"Xavier"},{"first_name":"Lucy","last_name":"Cobbs","full_name":"Cobbs, Lucy"},{"first_name":"Rachel","last_name":"Bandler","full_name":"Bandler, Rachel"},{"first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"full_name":"Cepko, Constance","last_name":"Cepko","first_name":"Constance"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"full_name":"Fishell, Gord","last_name":"Fishell","first_name":"Gord"}],"oa_version":"Submitted Version","quality_controlled":"1","volume":87,"language":[{"iso":"eng"}],"issue":"5","month":"09"},{"date_published":"2015-06-04T00:00:00Z","publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:45:02Z","title":"Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes","abstract":[{"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.","lang":"eng"}],"publication_status":"published","ddc":["570"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2021-01-12T06:51:33Z","department":[{"_id":"SyCr"}],"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.","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>","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>.","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.","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>.","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","publist_id":"5620","publication":"PLoS Biology","scopus_import":1,"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","page":"1 - 30","doi":"10.1371/journal.pbio.1002169","year":"2015","oa":1,"language":[{"iso":"eng"}],"volume":13,"month":"06","has_accepted_license":"1","issue":"6","file":[{"file_size":3468956,"access_level":"open_access","creator":"system","file_id":"5063","checksum":"30dee7a2c11ed09f2f5634655c0146f8","relation":"main_file","file_name":"IST-2016-481-v1+1_journal.pbio.1002169.pdf","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:14:13Z","content_type":"application/pdf"}],"author":[{"first_name":"Leila","last_name":"El Masri","id":"349A6E66-F248-11E8-B48F-1D18A9856A87","full_name":"El Masri, Leila"},{"first_name":"Antoine","last_name":"Branca","full_name":"Branca, Antoine"},{"first_name":"Anna","last_name":"Sheppard","full_name":"Sheppard, Anna"},{"full_name":"Papkou, Andrei","last_name":"Papkou","first_name":"Andrei"},{"full_name":"Laehnemann, David","last_name":"Laehnemann","first_name":"David"},{"first_name":"Patrick","last_name":"Guenther","full_name":"Guenther, Patrick"},{"last_name":"Prahl","first_name":"Swantje","full_name":"Prahl, Swantje"},{"first_name":"Manja","last_name":"Saebelfeld","full_name":"Saebelfeld, Manja"},{"full_name":"Hollensteiner, Jacqueline","first_name":"Jacqueline","last_name":"Hollensteiner"},{"last_name":"Liesegang","first_name":"Heiko","full_name":"Liesegang, Heiko"},{"full_name":"Brzuszkiewicz, Elzbieta","first_name":"Elzbieta","last_name":"Brzuszkiewicz"},{"first_name":"Rolf","last_name":"Daniel","full_name":"Daniel, Rolf"},{"full_name":"Michiels, Nico","first_name":"Nico","last_name":"Michiels"},{"last_name":"Schulte","first_name":"Rebecca","full_name":"Schulte, Rebecca"},{"last_name":"Kurtz","first_name":"Joachim","full_name":"Kurtz, Joachim"},{"first_name":"Philip","last_name":"Rosenstiel","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"}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","oa_version":"Published Version","ec_funded":1,"pubrep_id":"481","status":"public","date_created":"2018-12-11T11:52:40Z","_id":"1551","type":"journal_article"},{"publication_status":"published","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"}],"pmid":1,"date_published":"2015-02-26T00:00:00Z","publisher":"Nature Publishing Group","title":"Reporters for sensitive and quantitative measurement of auxin response","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:51:34Z","citation":{"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.","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>.","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>","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>","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.","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>.","short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210."},"external_id":{"pmid":["25643149"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publist_id":"5617","intvolume":"        12","publication":"Nature Methods","oa":1,"day":"26","doi":"10.1038/nmeth.3279","page":"207 - 210","year":"2015","month":"02","issue":"3","language":[{"iso":"eng"}],"volume":12,"quality_controlled":"1","oa_version":"Submitted Version","author":[{"full_name":"Liao, Cheyang","last_name":"Liao","first_name":"Cheyang"},{"last_name":"Smet","first_name":"Wouter","full_name":"Smet, Wouter"},{"last_name":"Brunoud","first_name":"Géraldine","full_name":"Brunoud, Géraldine"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko","first_name":"Saiko","last_name":"Yoshida"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"}],"date_created":"2018-12-11T11:52:41Z","type":"journal_article","_id":"1554","status":"public","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/"}]},{"year":"2015","page":"980 - 1017","doi":"10.1137/140993934","day":"01","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.","oa":1,"publication":"SIAM Journal on Applied Dynamical Systems","intvolume":"        14","publist_id":"5616","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems 14 (2015) 980–1017.","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>.","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>.","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>","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.","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>","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."},"date_updated":"2021-01-12T06:51:34Z","department":[{"_id":"HeEd"}],"title":"Rich bifurcation structure in a two patch vaccination model","publisher":"Society for Industrial and Applied Mathematics ","date_published":"2015-01-01T00:00:00Z","ddc":["510"],"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"}],"publication_status":"published","status":"public","main_file_link":[{"url":"http://discovery.ucl.ac.uk/1473750/1/99393.pdf","open_access":"1"}],"publication_identifier":{"eissn":["1536-0040"]},"_id":"1555","type":"journal_article","article_type":"original","date_created":"2018-12-11T11:52:42Z","ec_funded":1,"author":[{"first_name":"Diána","last_name":"Knipl","full_name":"Knipl, Diána"},{"full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","last_name":"Pilarczyk"},{"full_name":"Röst, Gergely","last_name":"Röst","first_name":"Gergely"}],"oa_version":"Published Version","project":[{"call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps","_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033"}],"quality_controlled":"1","article_processing_charge":"No","volume":14,"language":[{"iso":"eng"}],"issue":"2","month":"01"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:51:35Z","citation":{"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.","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.","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>.","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>","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>","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."},"file_date_updated":"2020-07-14T12:45:02Z","date_published":"2015-08-01T00:00:00Z","publisher":"Oxford University Press","title":"The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development","publication_status":"published","abstract":[{"lang":"eng","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."}],"ddc":["570"],"doi":"10.1093/jxb/erv230","year":"2015","page":"4631 - 4642","day":"01","oa":1,"publist_id":"5615","intvolume":"        66","publication":"Journal of Experimental Botany","scopus_import":1,"author":[{"last_name":"Jia","first_name":"Yuebin","full_name":"Jia, Yuebin"},{"full_name":"Tian, Huiyu","first_name":"Huiyu","last_name":"Tian"},{"orcid":"0000-0001-5039-9660","last_name":"Li","first_name":"Hongjiang","full_name":"Li, Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yu, Qianqian","first_name":"Qianqian","last_name":"Yu"},{"first_name":"Lei","last_name":"Wang","full_name":"Wang, Lei"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ding, Zhaojun","first_name":"Zhaojun","last_name":"Ding"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":66,"month":"08","has_accepted_license":"1","file":[{"file_name":"IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:14:02Z","date_updated":"2020-07-14T12:45:02Z","file_id":"5051","checksum":"257919be0ce3d306185d3891ad7acf39","creator":"system","access_level":"open_access","file_size":7753043,"relation":"main_file"}],"issue":"15","status":"public","date_created":"2018-12-11T11:52:42Z","type":"journal_article","_id":"1556","pubrep_id":"480"},{"language":[{"iso":"eng"}],"volume":112,"month":"12","issue":"51","author":[{"orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"quality_controlled":"1","oa_version":"Submitted Version","status":"public","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/"}],"date_created":"2018-12-11T11:52:43Z","_id":"1559","type":"journal_article","pmid":1,"date_published":"2015-12-22T00:00:00Z","publisher":"National Academy of Sciences","title":"Computational complexity of ecological and evolutionary spatial dynamics","publication_status":"published","abstract":[{"lang":"eng","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)."}],"external_id":{"pmid":["26644569"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T06:51:36Z","citation":{"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>.","short":"R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641.","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.","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>","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>","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>.","ista":"Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641."},"publist_id":"5612","intvolume":"       112","publication":"PNAS","scopus_import":1,"year":"2015","page":"15636 - 15641","doi":"10.1073/pnas.1511366112","day":"22","oa":1},{"oa":1,"doi":"10.3389/fncom.2015.00145","year":"2015","day":"30","scopus_import":1,"publist_id":"5607","intvolume":"         9","publication":"Frontiers in Computational Neuroscience","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:51:37Z","citation":{"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.","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>","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>.","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>","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>.","short":"M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015)."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","ddc":["570"],"publisher":"Frontiers Research Foundation","date_published":"2015-11-30T00:00:00Z","file_date_updated":"2020-07-14T12:45:02Z","title":"Editorial: Emergent neural computation from the interaction of different forms of plasticity","date_created":"2018-12-11T11:52:45Z","type":"journal_article","_id":"1564","status":"public","pubrep_id":"479","ec_funded":1,"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","oa_version":"Published Version","author":[{"last_name":"Gilson","first_name":"Matthieu","full_name":"Gilson, Matthieu"},{"last_name":"Savin","first_name":"Cristina","full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zenke, Friedemann","last_name":"Zenke","first_name":"Friedemann"}],"has_accepted_license":"1","month":"11","article_number":"145","file":[{"file_name":"IST-2016-479-v1+1_fncom-09-00145.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:12:09Z","creator":"system","checksum":"cea73b6d3ef1579f32da10b82f4de4fd","file_id":"4927","file_size":187038,"access_level":"open_access","relation":"main_file"}],"issue":"11","language":[{"iso":"eng"}],"volume":9},{"status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/","open_access":"1"}],"_id":"1565","type":"journal_article","date_created":"2018-12-11T11:52:45Z","volume":593,"language":[{"iso":"eng"}],"issue":"22","month":"11","author":[{"last_name":"Gavello","first_name":"Daniela","full_name":"Gavello, Daniela"},{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H","last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676"},{"full_name":"Gosso, Sara","last_name":"Gosso","first_name":"Sara"},{"last_name":"Carbone","first_name":"Emilio","full_name":"Carbone, Emilio"},{"full_name":"Carabelli, Valentina","first_name":"Valentina","last_name":"Carabelli"}],"oa_version":"Submitted Version","quality_controlled":"1","publication":"Journal of Physiology","publist_id":"5606","intvolume":"       593","scopus_import":1,"page":"4835 - 4853","doi":"10.1113/JP271078","year":"2015","day":"15","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.","oa":1,"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","pmid":1,"publisher":"Wiley-Blackwell","date_published":"2015-11-15T00:00:00Z","publication_status":"published","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"}],"external_id":{"pmid":["26282459"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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>","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>.","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>","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.","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.","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>.","short":"D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of Physiology 593 (2015) 4835–4853."},"department":[{"_id":"PeJo"}],"date_updated":"2021-01-12T06:51:38Z"},{"publication_status":"published","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."}],"ddc":["570"],"file_date_updated":"2020-07-14T12:45:02Z","date_published":"2015-10-23T00:00:00Z","publisher":"Public Library of Science","title":"An exploration of the universe of polyglutamine structures","department":[{"_id":"CaHe"}],"date_updated":"2023-02-23T14:05:55Z","citation":{"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>.","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.","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>","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>","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.","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>.","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational Biology 11 (2015)."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"related_material":{"record":[{"relation":"research_data","id":"9714","status":"public"}]},"publist_id":"5605","intvolume":"        11","publication":"PLoS Computational Biology","oa":1,"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. ","year":"2015","doi":"10.1371/journal.pcbi.1004541","day":"23","has_accepted_license":"1","month":"10","article_number":"e1004541","file":[{"file_name":"IST-2016-478-v1+1_journal.pcbi.1004541.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:16:21Z","creator":"system","file_id":"5207","checksum":"8b67d729be663bfc9af04bfd94459655","file_size":1412511,"access_level":"open_access","relation":"main_file"}],"issue":"10","language":[{"iso":"eng"}],"volume":11,"quality_controlled":"1","oa_version":"Published Version","author":[{"first_name":"Àngel","last_name":"Gómez Sicilia","full_name":"Gómez Sicilia, Àngel"},{"first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"first_name":"Marek","last_name":"Cieplak","full_name":"Cieplak, Marek"},{"full_name":"Carrión Vázquez, Mariano","first_name":"Mariano","last_name":"Carrión Vázquez"}],"pubrep_id":"478","date_created":"2018-12-11T11:52:45Z","_id":"1566","type":"journal_article","status":"public"},{"volume":112,"language":[{"iso":"eng"}],"issue":"7","month":"02","author":[{"last_name":"Doyle","first_name":"Siamsa","full_name":"Doyle, Siamsa"},{"first_name":"Ash","last_name":"Haegera","full_name":"Haegera, Ash"},{"first_name":"Thomas","last_name":"Vain","full_name":"Vain, Thomas"},{"full_name":"Rigala, Adeline","last_name":"Rigala","first_name":"Adeline"},{"full_name":"Viotti, Corrado","last_name":"Viotti","first_name":"Corrado"},{"first_name":"Małgorzata","last_name":"Łangowskaa","full_name":"Łangowskaa, Małgorzata"},{"first_name":"Qian","last_name":"Maa","full_name":"Maa, Qian"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Raikhel, Natasha","last_name":"Raikhel","first_name":"Natasha"},{"first_name":"Glenn","last_name":"Hickse","full_name":"Hickse, Glenn"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"}],"oa_version":"Published Version","project":[{"call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","ec_funded":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/"}],"status":"public","type":"journal_article","_id":"1569","date_created":"2018-12-11T11:52:46Z","title":"An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana","date_published":"2015-02-17T00:00:00Z","publisher":"National Academy of Sciences","abstract":[{"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.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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>.","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>.","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>","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.","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>","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."},"date_updated":"2021-01-12T06:51:39Z","department":[{"_id":"JiFr"}],"publication":"PNAS","intvolume":"       112","publist_id":"5602","scopus_import":1,"doi":"10.1073/pnas.1424856112","page":"E806 - E815","year":"2015","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.). ","oa":1},{"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"date_updated":"2021-01-12T06:51:40Z","citation":{"short":"R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.","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>.","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.","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>","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>.","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>"},"external_id":{"pmid":["26504200"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","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"}],"pmid":1,"publisher":"National Academy of Sciences","date_published":"2015-11-10T00:00:00Z","title":"Novel plasticity rule can explain the development of sensorimotor intelligence","oa":1,"page":"E6224 - E6232","doi":"10.1073/pnas.1508400112","year":"2015","day":"10","scopus_import":1,"publist_id":"5601","intvolume":"       112","publication":"PNAS","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","oa_version":"Submitted Version","author":[{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"},{"first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S"}],"month":"11","issue":"45","language":[{"iso":"eng"}],"volume":112,"date_created":"2018-12-11T11:52:47Z","_id":"1570","type":"journal_article","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/"}],"status":"public","ec_funded":1},{"issue":"1","abstract":[{"lang":"eng","text":"We consider the quantum ferromagnetic Heisenberg model in three dimensions, for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation for the excitation spectrum, at the level of the first non-trivial contribution to the free energy at low temperatures. Our proof comes with explicit, constructive upper and lower bounds on the error term. It uses in an essential way the bosonic formulation of the model in terms of the Holstein-Primakoff representation. In this language, the model describes interacting bosons with a hard-core on-site repulsion and a nearest-neighbor attraction. This attractive interaction makes the lower bound on the free energy particularly tricky: the key idea there is to prove a differential inequality for the two-particle density, which is thereby shown to be smaller than the probability density of a suitably weighted two-particle random process on the lattice.\r\n"}],"month":"06","publication_status":"published","volume":339,"title":"Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet","language":[{"iso":"eng"}],"publisher":"Springer","date_published":"2015-06-23T00:00:00Z","citation":{"ama":"Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. <i>Communications in Mathematical Physics</i>. 2015;339(1):279-307. doi:<a href=\"https://doi.org/10.1007/s00220-015-2402-0\">10.1007/s00220-015-2402-0</a>","ista":"Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 339(1), 279–307.","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” <i>Communications in Mathematical Physics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00220-015-2402-0\">https://doi.org/10.1007/s00220-015-2402-0</a>.","apa":"Correggi, M., Giuliani, A., &#38; Seiringer, R. (2015). Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-015-2402-0\">https://doi.org/10.1007/s00220-015-2402-0</a>","ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet,” <i>Communications in Mathematical Physics</i>, vol. 339, no. 1. Springer, pp. 279–307, 2015.","short":"M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics 339 (2015) 279–307.","mla":"Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” <i>Communications in Mathematical Physics</i>, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:<a href=\"https://doi.org/10.1007/s00220-015-2402-0\">10.1007/s00220-015-2402-0</a>."},"oa_version":"Preprint","date_updated":"2021-01-12T06:51:41Z","quality_controlled":"1","department":[{"_id":"RoSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Michele","last_name":"Correggi","full_name":"Correggi, Michele"},{"full_name":"Giuliani, Alessandro","first_name":"Alessandro","last_name":"Giuliani"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"scopus_import":1,"publication":"Communications in Mathematical Physics","intvolume":"       339","publist_id":"5599","_id":"1572","type":"journal_article","oa":1,"date_created":"2018-12-11T11:52:47Z","doi":"10.1007/s00220-015-2402-0","main_file_link":[{"url":"http://arxiv.org/abs/1312.7873","open_access":"1"}],"status":"public","page":"279 - 307","day":"23","year":"2015"},{"intvolume":"        68","publist_id":"5598","publication":"Communications on Pure and Applied Mathematics","scopus_import":1,"page":"1845 - 1884","year":"2015","doi":"10.1002/cpa.21552","day":"01","oa":1,"date_published":"2015-10-01T00:00:00Z","publisher":"Wiley","title":"Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti","abstract":[{"lang":"eng","text":"We present a new, simpler proof of the unconditional uniqueness of solutions to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis is the quantum de Finetti theorem. Our uniqueness result is equivalent to the one established in the celebrated works of Erdos, Schlein, and Yau."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:41Z","department":[{"_id":"RoSe"}],"citation":{"short":"T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and Applied Mathematics 68 (2015) 1845–1884.","mla":"Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” <i>Communications on Pure and Applied Mathematics</i>, vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:<a href=\"https://doi.org/10.1002/cpa.21552\">10.1002/cpa.21552</a>.","apa":"Chen, T., Hainzl, C., Pavlović, N., &#38; Seiringer, R. (2015). Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21552\">https://doi.org/10.1002/cpa.21552</a>","ama":"Chen T, Hainzl C, Pavlović N, Seiringer R. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. <i>Communications on Pure and Applied Mathematics</i>. 2015;68(10):1845-1884. doi:<a href=\"https://doi.org/10.1002/cpa.21552\">10.1002/cpa.21552</a>","ista":"Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 68(10), 1845–1884.","chicago":"Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/cpa.21552\">https://doi.org/10.1002/cpa.21552</a>.","ieee":"T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti,” <i>Communications on Pure and Applied Mathematics</i>, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015."},"status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3168"}],"date_created":"2018-12-11T11:52:48Z","type":"journal_article","_id":"1573","language":[{"iso":"eng"}],"volume":68,"month":"10","issue":"10","author":[{"first_name":"Thomas","last_name":"Chen","full_name":"Chen, Thomas"},{"full_name":"Hainzl, Christian","first_name":"Christian","last_name":"Hainzl"},{"first_name":"Nataša","last_name":"Pavlović","full_name":"Pavlović, Nataša"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"quality_controlled":"1","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"oa_version":"Preprint"},{"title":"A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development","file_date_updated":"2020-07-14T12:45:02Z","date_published":"2015-11-18T00:00:00Z","publisher":"Nature Publishing Group","ddc":["580"],"publication_status":"published","abstract":[{"lang":"eng","text":"Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"short":"Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015).","mla":"Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” <i>Nature Communications</i>, vol. 6, 8821, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms9821\">10.1038/ncomms9821</a>.","ieee":"Q. Chen <i>et al.</i>, “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015.","chicago":"Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms9821\">https://doi.org/10.1038/ncomms9821</a>.","ama":"Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms9821\">10.1038/ncomms9821</a>","ista":"Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821.","apa":"Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms9821\">https://doi.org/10.1038/ncomms9821</a>"},"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"date_updated":"2021-01-12T06:51:42Z","publication":"Nature Communications","publist_id":"5597","intvolume":"         6","scopus_import":1,"doi":"10.1038/ncomms9821","year":"2015","day":"18","acknowledgement":"of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ","oa":1,"volume":6,"language":[{"iso":"eng"}],"file":[{"checksum":"8ff5c108899b548806e1cb7a302fe76d","file_id":"5085","creator":"system","access_level":"open_access","file_size":1701815,"relation":"main_file","file_name":"IST-2016-477-v1+1_ncomms9821.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:14:32Z","date_updated":"2020-07-14T12:45:02Z"}],"article_number":"8821","has_accepted_license":"1","month":"11","author":[{"first_name":"Qian","last_name":"Chen","full_name":"Chen, Qian"},{"first_name":"Yang","last_name":"Liu","full_name":"Liu, Yang"},{"last_name":"Maere","first_name":"Steven","full_name":"Maere, Steven"},{"first_name":"Eunkyoung","last_name":"Lee","full_name":"Lee, Eunkyoung"},{"full_name":"Van Isterdael, Gert","last_name":"Van Isterdael","first_name":"Gert"},{"full_name":"Xie, Zidian","first_name":"Zidian","last_name":"Xie"},{"first_name":"Wei","last_name":"Xuan","full_name":"Xuan, Wei"},{"full_name":"Lucas, Jessica","first_name":"Jessica","last_name":"Lucas"},{"first_name":"Valya","last_name":"Vassileva","full_name":"Vassileva, Valya"},{"last_name":"Kitakura","first_name":"Saeko","full_name":"Kitakura, Saeko"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavy, Peter","last_name":"Marhavy","first_name":"Peter","orcid":"0000-0001-5227-5741"},{"first_name":"Krzysztof T","last_name":"Wabnik","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T"},{"full_name":"Geldner, Niko","first_name":"Niko","last_name":"Geldner"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jie","last_name":"Le","full_name":"Le, Jie"},{"full_name":"Fukaki, Hidehiro","last_name":"Fukaki","first_name":"Hidehiro"},{"first_name":"Erich","last_name":"Grotewold","full_name":"Grotewold, Erich"},{"full_name":"Li, Chuanyou","first_name":"Chuanyou","last_name":"Li"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"full_name":"Sack, Fred","first_name":"Fred","last_name":"Sack"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"}],"oa_version":"Published Version","quality_controlled":"1","pubrep_id":"477","status":"public","type":"journal_article","_id":"1574","date_created":"2018-12-11T11:52:48Z"},{"author":[{"full_name":"Chabaud, Mélanie","first_name":"Mélanie","last_name":"Chabaud"},{"full_name":"Heuzé, Mélina","last_name":"Heuzé","first_name":"Mélina"},{"full_name":"Bretou, Marine","first_name":"Marine","last_name":"Bretou"},{"last_name":"Vargas","first_name":"Pablo","full_name":"Vargas, Pablo"},{"first_name":"Paolo","last_name":"Maiuri","full_name":"Maiuri, Paolo"},{"first_name":"Paola","last_name":"Solanes","full_name":"Solanes, Paola"},{"full_name":"Maurin, Mathieu","last_name":"Maurin","first_name":"Mathieu"},{"full_name":"Terriac, Emmanuel","last_name":"Terriac","first_name":"Emmanuel"},{"full_name":"Le Berre, Maël","last_name":"Le Berre","first_name":"Maël"},{"first_name":"Danielle","last_name":"Lankar","full_name":"Lankar, Danielle"},{"first_name":"Tristan","last_name":"Piolot","full_name":"Piolot, Tristan"},{"first_name":"Robert","last_name":"Adelstein","full_name":"Adelstein, Robert"},{"full_name":"Zhang, Yingfan","last_name":"Zhang","first_name":"Yingfan"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Jacobelli, Jordan","first_name":"Jordan","last_name":"Jacobelli"},{"last_name":"Bénichou","first_name":"Olivier","full_name":"Bénichou, Olivier"},{"first_name":"Raphaël","last_name":"Voituriez","full_name":"Voituriez, Raphaël"},{"full_name":"Piel, Matthieu","first_name":"Matthieu","last_name":"Piel"},{"last_name":"Lennon Duménil","first_name":"Ana","full_name":"Lennon Duménil, Ana"}],"oa_version":"Published Version","quality_controlled":"1","volume":6,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","checksum":"bae12e86be2adb28253f890b8bba8315","file_id":"4915","creator":"system","access_level":"open_access","file_size":4530215,"content_type":"application/pdf","date_created":"2018-12-12T10:11:58Z","date_updated":"2020-07-14T12:45:02Z","file_name":"IST-2016-476-v1+1_ncomms8526.pdf"}],"article_number":"7526","month":"06","has_accepted_license":"1","status":"public","type":"journal_article","_id":"1575","date_created":"2018-12-11T11:52:48Z","pubrep_id":"476","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"ieee":"M. Chabaud <i>et al.</i>, “Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015.","apa":"Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., … Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms8526\">https://doi.org/10.1038/ncomms8526</a>","chicago":"Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri, Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms8526\">https://doi.org/10.1038/ncomms8526</a>.","ista":"Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J, Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 6, 7526.","ama":"Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms8526\">10.1038/ncomms8526</a>","short":"M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin, E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt, J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications 6 (2015).","mla":"Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” <i>Nature Communications</i>, vol. 6, 7526, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms8526\">10.1038/ncomms8526</a>."},"date_updated":"2021-01-12T06:51:42Z","department":[{"_id":"MiSi"}],"title":"Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells","date_published":"2015-06-25T00:00:00Z","file_date_updated":"2020-07-14T12:45:02Z","publisher":"Nature Publishing Group","ddc":["570"],"abstract":[{"text":"The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space.","lang":"eng"}],"publication_status":"published","doi":"10.1038/ncomms8526","year":"2015","day":"25","acknowledgement":"M.C. and M.L.H. were supported by fellowships from the Fondation pour la Recherche Médicale and the Association pour la Recherche contre le Cancer, respectively. This work was funded by grants from the City of Paris and the European Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico) to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL* and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934, Institut Curie).","oa":1,"publication":"Nature Communications","intvolume":"         6","publist_id":"5596","scopus_import":1},{"publisher":"American Physical Society","date_published":"2015-12-08T00:00:00Z","title":"Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation","publication_status":"published","abstract":[{"lang":"eng","text":"Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect regulatory crosstalk: the possibility that noncognate TFs could initiate transcription, with potentially disastrous effects for the cell. Here, we estimate the importance of crosstalk, suggest that its avoidance strongly constrains equilibrium models of TF binding, and propose an alternative nonequilibrium scheme that implements kinetic proofreading to suppress erroneous initiation. This proposal is consistent with the observed covalent modifications of the transcriptional apparatus and predicts increased noise in gene expression as a trade-off for improved specificity. Using information theory, we quantify this trade-off to find when optimal proofreading architectures are favored over their equilibrium counterparts. Such architectures exhibit significant super-Poisson noise at low expression in steady state."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"date_updated":"2023-09-07T12:55:21Z","citation":{"short":"S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).","mla":"Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” <i>Physical Review Letters</i>, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.115.248101\">10.1103/PhysRevLett.115.248101</a>.","ieee":"S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” <i>Physical Review Letters</i>, vol. 115, no. 24. American Physical Society, 2015.","chicago":"Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” <i>Physical Review Letters</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevLett.115.248101\">https://doi.org/10.1103/PhysRevLett.115.248101</a>.","ista":"Cepeda Humerez SA, Rieckh G, Tkačik G. 2015. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24), 248101.","ama":"Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. <i>Physical Review Letters</i>. 2015;115(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.115.248101\">10.1103/PhysRevLett.115.248101</a>","apa":"Cepeda Humerez, S. A., Rieckh, G., &#38; Tkačik, G. (2015). Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.115.248101\">https://doi.org/10.1103/PhysRevLett.115.248101</a>"},"publist_id":"5595","intvolume":"       115","publication":"Physical Review Letters","scopus_import":1,"related_material":{"record":[{"id":"6473","relation":"part_of_dissertation","status":"public"}]},"day":"08","year":"2015","doi":"10.1103/PhysRevLett.115.248101","oa":1,"language":[{"iso":"eng"}],"volume":115,"month":"12","article_number":"248101","issue":"24","author":[{"id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","full_name":"Cepeda Humerez, Sarah A","last_name":"Cepeda Humerez","first_name":"Sarah A"},{"last_name":"Rieckh","first_name":"Georg","full_name":"Rieckh, Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"oa_version":"Preprint","ec_funded":1,"status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.05716"}],"date_created":"2018-12-11T11:52:49Z","_id":"1576","type":"journal_article"},{"date_created":"2018-12-11T11:52:49Z","article_type":"original","_id":"1577","type":"journal_article","status":"public","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/","open_access":"1"}],"month":"10","issue":"40","language":[{"iso":"eng"}],"volume":112,"article_processing_charge":"No","quality_controlled":"1","oa_version":"Published Version","author":[{"last_name":"Carvalho","first_name":"Antonio","full_name":"Carvalho, Antonio"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"},{"last_name":"Russo","first_name":"Claudia","full_name":"Russo, Claudia"},{"first_name":"Bonnielin","last_name":"Swenor","full_name":"Swenor, Bonnielin"},{"full_name":"Clark, Andrew","first_name":"Andrew","last_name":"Clark"}],"scopus_import":1,"publist_id":"5594","intvolume":"       112","publication":"PNAS","oa":1,"acknowledgement":"This work was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski, C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski, B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments on the manuscript.","day":"06","page":"12450 - 12455","doi":"10.1073/pnas.1516543112","year":"2015","publication_status":"published","abstract":[{"text":"Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.","lang":"eng"}],"pmid":1,"date_published":"2015-10-06T00:00:00Z","publisher":"National Academy of Sciences","title":"Birth of a new gene on the Y chromosome of Drosophila melanogaster","department":[{"_id":"BeVi"}],"date_updated":"2021-01-12T06:51:43Z","citation":{"short":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455.","mla":"Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” <i>PNAS</i>, vol. 112, no. 40, National Academy of Sciences, 2015, pp. 12450–55, doi:<a href=\"https://doi.org/10.1073/pnas.1516543112\">10.1073/pnas.1516543112</a>.","apa":"Carvalho, A., Vicoso, B., Russo, C., Swenor, B., &#38; Clark, A. (2015). Birth of a new gene on the Y chromosome of Drosophila melanogaster. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1516543112\">https://doi.org/10.1073/pnas.1516543112</a>","ista":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455.","chicago":"Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1516543112\">https://doi.org/10.1073/pnas.1516543112</a>.","ama":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the Y chromosome of Drosophila melanogaster. <i>PNAS</i>. 2015;112(40):12450-12455. doi:<a href=\"https://doi.org/10.1073/pnas.1516543112\">10.1073/pnas.1516543112</a>","ieee":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” <i>PNAS</i>, vol. 112, no. 40. National Academy of Sciences, pp. 12450–12455, 2015."},"external_id":{"pmid":["26385968"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]