[{"department":[{"_id":"JiFr"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","article_processing_charge":"No","issue":"4","doi":"10.1104/pp.15.00769","date_created":"2018-12-11T11:52:38Z","oa_version":"None","volume":169,"title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","external_id":{"isi":["000368472700025"]},"abstract":[{"lang":"eng","text":"A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta."}],"type":"journal_article","month":"12","year":"2015","author":[{"last_name":"Olvera Carrillo","first_name":"Yadira","full_name":"Olvera Carrillo, Yadira"},{"full_name":"Van Bel, Michiel","first_name":"Michiel","last_name":"Van Bel"},{"last_name":"Van Hautegem","first_name":"Tom","full_name":"Van Hautegem, Tom"},{"first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"last_name":"Huysmans","first_name":"Marlies","full_name":"Huysmans, Marlies"},{"last_name":"Šimášková","first_name":"Mária","full_name":"Šimášková, Mária"},{"last_name":"Van Durme","first_name":"Matthias","full_name":"Van Durme, Matthias"},{"full_name":"Buscaill, Pierre","first_name":"Pierre","last_name":"Buscaill"},{"first_name":"Susana","last_name":"Rivas","full_name":"Rivas, Susana"},{"first_name":"Núria","last_name":"Coll","full_name":"Coll, Núria"},{"full_name":"Coppens, Frederik","last_name":"Coppens","first_name":"Frederik"},{"first_name":"Steven","last_name":"Maere","full_name":"Maere, Steven"},{"first_name":"Moritz","last_name":"Nowack","full_name":"Nowack, Moritz"}],"_id":"1543","isi":1,"date_published":"2015-12-01T00:00:00Z","date_updated":"2025-09-22T14:28:43Z","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"American Society of Plant Biologists","citation":{"apa":"Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.15.00769\">https://doi.org/10.1104/pp.15.00769</a>","ama":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. <i>Plant Physiology</i>. 2015;169(4):2684-2699. doi:<a href=\"https://doi.org/10.1104/pp.15.00769\">10.1104/pp.15.00769</a>","mla":"Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” <i>Plant Physiology</i>, vol. 169, no. 4, American Society of Plant Biologists, 2015, pp. 2684–99, doi:<a href=\"https://doi.org/10.1104/pp.15.00769\">10.1104/pp.15.00769</a>.","ieee":"Y. Olvera Carrillo <i>et al.</i>, “A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants,” <i>Plant Physiology</i>, vol. 169, no. 4. American Society of Plant Biologists, pp. 2684–2699, 2015.","chicago":"Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2015. <a href=\"https://doi.org/10.1104/pp.15.00769\">https://doi.org/10.1104/pp.15.00769</a>.","short":"Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans, M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere, M. Nowack, Plant Physiology 169 (2015) 2684–2699.","ista":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 169(4), 2684–2699."},"publist_id":"5628","page":"2684 - 2699","publication_status":"published","intvolume":"       169","status":"public","publication":"Plant Physiology"},{"corr_author":"1","abstract":[{"lang":"eng","text":"Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility."}],"month":"04","type":"book_chapter","external_id":{"pmid":["25997350"],"isi":["000370490800013"]},"title":"Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/"}],"article_processing_charge":"No","date_created":"2018-12-11T11:52:38Z","oa_version":"Submitted Version","doi":"10.1016/bs.mcb.2015.01.007","department":[{"_id":"MaLo"}],"publication_status":"published","intvolume":"       128","pmid":1,"publist_id":"5627","language":[{"iso":"eng"}],"date_published":"2015-04-08T00:00:00Z","isi":1,"_id":"1544","quality_controlled":"1","oa":1,"volume":128,"day":"08","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Building a Cell from its Components Parts","status":"public","citation":{"ista":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from its Components Parts. vol. 128, 223–241.","chicago":"Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” In <i>Building a Cell from Its Components Parts</i>, 128:223–41. Academic Press, 2015. <a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">https://doi.org/10.1016/bs.mcb.2015.01.007</a>.","short":"P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell from Its Components Parts, Academic Press, 2015, pp. 223–241.","apa":"Nguyen, P., Field, C., Groen, A., Mitchison, T., &#38; Loose, M. (2015). Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In <i>Building a Cell from its Components Parts</i> (Vol. 128, pp. 223–241). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">https://doi.org/10.1016/bs.mcb.2015.01.007</a>","mla":"Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” <i>Building a Cell from Its Components Parts</i>, vol. 128, Academic Press, 2015, pp. 223–41, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">10.1016/bs.mcb.2015.01.007</a>.","ieee":"P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins,” in <i>Building a Cell from its Components Parts</i>, vol. 128, Academic Press, 2015, pp. 223–241.","ama":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: <i>Building a Cell from Its Components Parts</i>. Vol 128. Academic Press; 2015:223-241. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">10.1016/bs.mcb.2015.01.007</a>"},"page":"223 - 241","scopus_import":"1","publisher":"Academic Press","date_updated":"2025-09-29T11:03:06Z","year":"2015","author":[{"full_name":"Nguyen, Phuong","last_name":"Nguyen","first_name":"Phuong"},{"full_name":"Field, Christine","first_name":"Christine","last_name":"Field"},{"full_name":"Groen, Aaron","first_name":"Aaron","last_name":"Groen"},{"full_name":"Mitchison, Timothy","first_name":"Timothy","last_name":"Mitchison"},{"first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}]},{"language":[{"iso":"eng"}],"publication_status":"published","intvolume":"         3","keyword":["General Environmental Science"],"_id":"10794","date_published":"2015-06-10T00:00:00Z","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation.","lang":"eng"}],"file_date_updated":"2022-02-25T11:55:26Z","type":"journal_article","month":"06","corr_author":"1","acknowledgement":"The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX.","publication_identifier":{"issn":["2296-665X"]},"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"article_processing_charge":"No","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","doi":"10.3389/fenvs.2015.00042","date_created":"2022-02-25T11:42:25Z","title":"Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study","ec_funded":1,"scopus_import":"1","has_accepted_license":"1","publisher":"Frontiers","file":[{"content_type":"application/pdf","checksum":"26c222487564e1be02a11d688d6f769d","file_size":1371201,"success":1,"date_created":"2022-02-25T11:55:26Z","date_updated":"2022-02-25T11:55:26Z","access_level":"open_access","relation":"main_file","file_id":"10795","creator":"dernst","file_name":"2015_FrontiersEnvironmScience_Parise.pdf"}],"ddc":["000","570"],"article_number":"42","citation":{"ista":"Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.","short":"F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).","chicago":"Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>. Frontiers, 2015. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>.","apa":"Parise, F., Lygeros, J., &#38; Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>","mla":"Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>, vol. 3, 42, Frontiers, 2015, doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>.","ieee":"F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” <i>Frontiers in Environmental Science</i>, vol. 3. Frontiers, 2015.","ama":"Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. 2015;3. doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>"},"publication":"Frontiers in Environmental Science","status":"public","year":"2015","author":[{"full_name":"Parise, Francesca","last_name":"Parise","first_name":"Francesca"},{"full_name":"Lygeros, John","last_name":"Lygeros","first_name":"John"},{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","last_name":"Ruess","first_name":"Jakob","full_name":"Ruess, Jakob"}],"date_updated":"2025-04-15T06:50:01Z","oa":1,"quality_controlled":"1","article_type":"original","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","day":"10","volume":3},{"publisher":"SIAM","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2015-01-04","end_date":"2015-01-06","location":"San Diego, CA, United States"},"ec_funded":1,"scopus_import":"1","citation":{"ama":"Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In: <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2015. SIAM; 2015:1018-1029. doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2015, pp. 1018–1029). San Diego, CA, United States: SIAM. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2015, no. 1, SIAM, 2015, pp. 1018–29, doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>.","ieee":"K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory strategies for concurrent mean-payoff games,” in <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, San Diego, CA, United States, 2015, vol. 2015, no. 1, pp. 1018–1029.","ista":"Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2015, 1018–1029.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2015:1018–29. SIAM, 2015. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029."},"OA_type":"green","page":"1018-1029","status":"public","publication":"Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"}],"year":"2015","date_updated":"2025-06-26T06:54:08Z","oa":1,"quality_controlled":"1","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","issue":"1","volume":2015,"language":[{"iso":"eng"}],"intvolume":"      2015","publication_status":"published","_id":"10796","date_published":"2015-01-01T00:00:00Z","external_id":{"arxiv":["1409.6690"]},"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"type":"conference","arxiv":1,"month":"01","abstract":[{"lang":"eng","text":"We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy)."}],"acknowledgement":"The research was partly supported by FWF Grant No P 23499-N23, FWF NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","corr_author":"1","publication_identifier":{"isbn":["978-161197374-7"]},"department":[{"_id":"KrCh"}],"doi":"10.1137/1.9781611973730.69","oa_version":"Preprint","date_created":"2022-02-25T12:18:43Z","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1409.6690","open_access":"1"}],"title":"The value 1 problem under finite-memory strategies for concurrent mean-payoff games"},{"publisher":"Springer","scopus_import":"1","citation":{"ieee":"P. Nam and R. Seiringer, “Collective excitations of Bose gases in the mean-field regime,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 215, no. 2. Springer, pp. 381–417, 2015.","mla":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 215, no. 2, Springer, 2015, pp. 381–417, doi:<a href=\"https://doi.org/10.1007/s00205-014-0781-6\">10.1007/s00205-014-0781-6</a>.","ama":"Nam P, Seiringer R. Collective excitations of Bose gases in the mean-field regime. <i>Archive for Rational Mechanics and Analysis</i>. 2015;215(2):381-417. doi:<a href=\"https://doi.org/10.1007/s00205-014-0781-6\">10.1007/s00205-014-0781-6</a>","apa":"Nam, P., &#38; Seiringer, R. (2015). Collective excitations of Bose gases in the mean-field regime. <i>Archive for Rational Mechanics and Analysis</i>. Springer. <a href=\"https://doi.org/10.1007/s00205-014-0781-6\">https://doi.org/10.1007/s00205-014-0781-6</a>","short":"P. Nam, R. Seiringer, Archive for Rational Mechanics and Analysis 215 (2015) 381–417.","chicago":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” <i>Archive for Rational Mechanics and Analysis</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00205-014-0781-6\">https://doi.org/10.1007/s00205-014-0781-6</a>.","ista":"Nam P, Seiringer R. 2015. Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. 215(2), 381–417."},"page":"381 - 417","status":"public","publication":"Archive for Rational Mechanics and Analysis","author":[{"full_name":"Nam, Phan","last_name":"Nam","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"year":"2015","date_updated":"2025-09-23T08:17:14Z","oa":1,"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","issue":"2","volume":215,"language":[{"iso":"eng"}],"publist_id":"4951","intvolume":"       215","publication_status":"published","isi":1,"_id":"2085","date_published":"2015-02-01T00:00:00Z","external_id":{"isi":["000347150400002"],"arxiv":["1402.1153"]},"arxiv":1,"month":"02","type":"journal_article","abstract":[{"lang":"eng","text":"We study the spectrum of a large system of N identical bosons interacting via a two-body potential with strength 1/N. In this mean-field regime, Bogoliubov's theory predicts that the spectrum of the N-particle Hamiltonian can be approximated by that of an effective quadratic Hamiltonian acting on Fock space, which describes the fluctuations around a condensed state. Recently, Bogoliubov's theory has been justified rigorously in the case that the low-energy eigenvectors of the N-particle Hamiltonian display complete condensation in the unique minimizer of the corresponding Hartree functional. In this paper, we shall justify Bogoliubov's theory for the high-energy part of the spectrum of the N-particle Hamiltonian corresponding to (non-linear) excited states of the Hartree functional. Moreover, we shall extend the existing results on the excitation spectrum to the case of non-uniqueness and/or degeneracy of the Hartree minimizer. In particular, the latter covers the case of rotating Bose gases, when the rotation speed is large enough to break the symmetry and to produce multiple quantized vortices in the Hartree minimizer. "}],"corr_author":"1","department":[{"_id":"RoSe"}],"date_created":"2018-12-11T11:55:37Z","doi":"10.1007/s00205-014-0781-6","oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1402.1153","open_access":"1"}],"article_processing_charge":"No","title":"Collective excitations of Bose gases in the mean-field regime"},{"date_updated":"2025-09-23T13:39:37Z","author":[{"first_name":"László","last_name":"Erdös","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"full_name":"Knowles, Antti","last_name":"Knowles","first_name":"Antti"}],"year":"2015","publication":"Communications in Mathematical Physics","status":"public","citation":{"ieee":"L. Erdös and A. Knowles, “The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case,” <i>Communications in Mathematical Physics</i>, vol. 333, no. 3. Springer, pp. 1365–1416, 2015.","mla":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” <i>Communications in Mathematical Physics</i>, vol. 333, no. 3, Springer, 2015, pp. 1365–416, doi:<a href=\"https://doi.org/10.1007/s00220-014-2119-5\">10.1007/s00220-014-2119-5</a>.","apa":"Erdös, L., &#38; Knowles, A. (2015). The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-014-2119-5\">https://doi.org/10.1007/s00220-014-2119-5</a>","ama":"Erdös L, Knowles A. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. <i>Communications in Mathematical Physics</i>. 2015;333(3):1365-1416. doi:<a href=\"https://doi.org/10.1007/s00220-014-2119-5\">10.1007/s00220-014-2119-5</a>","chicago":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” <i>Communications in Mathematical Physics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00220-014-2119-5\">https://doi.org/10.1007/s00220-014-2119-5</a>.","ista":"Erdös L, Knowles A. 2015. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. 333(3), 1365–1416.","short":"L. Erdös, A. Knowles, Communications in Mathematical Physics 333 (2015) 1365–1416."},"page":"1365 - 1416","publisher":"Springer","scopus_import":"1","volume":333,"issue":"3","day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","oa":1,"date_published":"2015-02-01T00:00:00Z","isi":1,"_id":"2166","intvolume":"       333","publication_status":"published","publist_id":"4818","language":[{"iso":"eng"}],"title":"The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case","oa_version":"Preprint","doi":"10.1007/s00220-014-2119-5","date_created":"2018-12-11T11:56:05Z","article_processing_charge":"No","main_file_link":[{"url":"http://arxiv.org/abs/1309.5106","open_access":"1"}],"department":[{"_id":"LaEr"}],"arxiv":1,"month":"02","type":"journal_article","abstract":[{"text":"We consider the spectral statistics of large random band matrices on mesoscopic energy scales. We show that the correlation function of the local eigenvalue density exhibits a universal power law behaviour that differs from the Wigner-Dyson- Mehta statistics. This law had been predicted in the physics literature by Altshuler and Shklovskii in (Zh Eksp Teor Fiz (Sov Phys JETP) 91(64):220(127), 1986); it describes the correlations of the eigenvalue density in general metallic sampleswith weak disorder. Our result rigorously establishes the Altshuler-Shklovskii formulas for band matrices. In two dimensions, where the leading term vanishes owing to an algebraic cancellation, we identify the first non-vanishing term and show that it differs substantially from the prediction of Kravtsov and Lerner in (Phys Rev Lett 74:2563-2566, 1995). The proof is given in the current paper and its companion (Ann. H. Poincaré. arXiv:1309.5107, 2014). ","lang":"eng"}],"external_id":{"arxiv":["1309.5106"],"isi":["000348303100008"]}},{"year":"2015","author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johan","last_name":"Thapper","full_name":"Thapper, Johan"},{"full_name":"Živný, Stanislav","first_name":"Stanislav","last_name":"Živný"}],"date_updated":"2025-09-23T14:14:57Z","scopus_import":"1","publisher":"SIAM","page":"1 - 36","citation":{"mla":"Kolmogorov, Vladimir, et al. “The Power of Linear Programming for General-Valued CSPs.” <i>SIAM Journal on Computing</i>, vol. 44, no. 1, SIAM, 2015, pp. 1–36, doi:<a href=\"https://doi.org/10.1137/130945648\">10.1137/130945648</a>.","ieee":"V. Kolmogorov, J. Thapper, and S. Živný, “The power of linear programming for general-valued CSPs,” <i>SIAM Journal on Computing</i>, vol. 44, no. 1. SIAM, pp. 1–36, 2015.","apa":"Kolmogorov, V., Thapper, J., &#38; Živný, S. (2015). The power of linear programming for general-valued CSPs. <i>SIAM Journal on Computing</i>. SIAM. <a href=\"https://doi.org/10.1137/130945648\">https://doi.org/10.1137/130945648</a>","ama":"Kolmogorov V, Thapper J, Živný S. The power of linear programming for general-valued CSPs. <i>SIAM Journal on Computing</i>. 2015;44(1):1-36. doi:<a href=\"https://doi.org/10.1137/130945648\">10.1137/130945648</a>","ista":"Kolmogorov V, Thapper J, Živný S. 2015. The power of linear programming for general-valued CSPs. SIAM Journal on Computing. 44(1), 1–36.","short":"V. Kolmogorov, J. Thapper, S. Živný, SIAM Journal on Computing 44 (2015) 1–36.","chicago":"Kolmogorov, Vladimir, Johan Thapper, and Stanislav Živný. “The Power of Linear Programming for General-Valued CSPs.” <i>SIAM Journal on Computing</i>. SIAM, 2015. <a href=\"https://doi.org/10.1137/130945648\">https://doi.org/10.1137/130945648</a>."},"publication":"SIAM Journal on Computing","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","issue":"1","volume":44,"oa":1,"quality_controlled":"1","_id":"2271","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2518"}]},"isi":1,"date_published":"2015-02-01T00:00:00Z","language":[{"iso":"eng"}],"publist_id":"4673","publication_status":"published","intvolume":"        44","department":[{"_id":"VlKo"}],"article_processing_charge":"No","main_file_link":[{"url":"http://arxiv.org/abs/1311.4219","open_access":"1"}],"oa_version":"Preprint","date_created":"2018-12-11T11:56:41Z","doi":"10.1137/130945648","title":"The power of linear programming for general-valued CSPs","external_id":{"isi":["000353967100001"],"arxiv":["1311.4219"]},"abstract":[{"text":"A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. Finite-valued constraint languages contain functions that take on rational costs and general-valued constraint languages contain functions that take on rational or infinite costs. An instance of the problem is specified by a sum of functions from the language with the goal to minimise the sum. This framework includes and generalises well-studied constraint satisfaction problems (CSPs) and maximum constraint satisfaction problems (Max-CSPs).\r\nOur main result is a precise algebraic characterisation of valued constraint languages whose instances can be solved exactly by the basic linear programming relaxation (BLP). For a general-valued constraint language Γ, BLP is a decision procedure for Γ if and only if Γ admits a symmetric fractional polymorphism of every arity. For a finite-valued constraint language Γ, BLP is a decision procedure if and only if Γ admits a symmetric fractional polymorphism of some arity, or equivalently, if Γ admits a symmetric fractional polymorphism of arity 2.\r\nUsing these results, we obtain tractability of several novel and previously widely-open classes of VCSPs, including problems over valued constraint languages that are: (1) submodular on arbitrary lattices; (2) bisubmodular (also known as k-submodular) on arbitrary finite domains; (3) weakly (and hence strongly) tree-submodular on arbitrary trees. ","lang":"eng"}],"arxiv":1,"type":"journal_article","month":"02"},{"date_published":"2015-01-07T00:00:00Z","isi":1,"_id":"1546","pmid":1,"publist_id":"5625","publication_status":"published","intvolume":"        85","language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","license":"https://creativecommons.org/licenses/by/3.0/","doi":"10.1016/j.neuron.2014.11.019","oa_version":"Published Version","date_created":"2018-12-11T11:52:39Z","title":"Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development","department":[{"_id":"RySh"}],"pubrep_id":"482","acknowledgement":"This work was supported by the Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.; by the funding provided by Okinawa Institute of Science and Technology (OIST) to T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture, Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la Recherche Scientifique through the Actions Thematiques et Initatives sur Programme, Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01) to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063) to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413) and Principal (095667) Research Fellowship and an ERC advance grant (294667) to RAS.","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"external_id":{"isi":["000348295100015"],"pmid":["25533484"]},"abstract":[{"text":"Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (&lt;30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This &quot;perimeter release model&quot; provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:01Z","type":"journal_article","month":"01","date_updated":"2025-09-23T09:38:39Z","year":"2015","author":[{"full_name":"Nakamura, Yukihiro","last_name":"Nakamura","first_name":"Yukihiro"},{"full_name":"Harada, Harumi","first_name":"Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896"},{"full_name":"Kamasawa, Naomi","first_name":"Naomi","last_name":"Kamasawa"},{"full_name":"Matsui, Ko","first_name":"Ko","last_name":"Matsui"},{"last_name":"Rothman","first_name":"Jason","full_name":"Rothman, Jason"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"full_name":"Silver, R Angus","first_name":"R Angus","last_name":"Silver"},{"last_name":"Digregorio","first_name":"David","full_name":"Digregorio, David"},{"full_name":"Takahashi, Tomoyuki","last_name":"Takahashi","first_name":"Tomoyuki"}],"OA_type":"hybrid","ddc":["570"],"page":"145 - 158","citation":{"mla":"Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” <i>Neuron</i>, vol. 85, no. 1, Elsevier, 2015, pp. 145–58, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">10.1016/j.neuron.2014.11.019</a>.","ieee":"Y. Nakamura <i>et al.</i>, “Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development,” <i>Neuron</i>, vol. 85, no. 1. Elsevier, pp. 145–158, 2015.","apa":"Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto, R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">https://doi.org/10.1016/j.neuron.2014.11.019</a>","ama":"Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. <i>Neuron</i>. 2015;85(1):145-158. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">10.1016/j.neuron.2014.11.019</a>","short":"Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto, R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158.","chicago":"Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman, Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” <i>Neuron</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">https://doi.org/10.1016/j.neuron.2014.11.019</a>.","ista":"Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 85(1), 145–158."},"status":"public","publication":"Neuron","scopus_import":"1","has_accepted_license":"1","file":[{"file_size":3080111,"content_type":"application/pdf","checksum":"725f4d5be2dbb44b283ce722645ef37d","access_level":"open_access","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:15:47Z","file_name":"IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf","creator":"system","file_id":"5170","relation":"main_file"}],"publisher":"Elsevier","issue":"1","volume":85,"OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"07","tmp":{"image":"/images/cc_by.png","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"oa":1,"quality_controlled":"1","article_type":"original"},{"publist_id":"5624","intvolume":"        52","publication_status":"published","language":[{"iso":"eng"}],"date_published":"2015-05-31T00:00:00Z","isi":1,"_id":"1547","publication_identifier":{"eissn":["2234-3016"]},"external_id":{"arxiv":["0901.3015"],"isi":["000355776600024"]},"type":"journal_article","arxiv":1,"month":"05","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","doi":"10.4134/BKMS.2015.52.3.977","date_created":"2018-12-11T11:52:39Z","main_file_link":[{"url":"http://arxiv.org/abs/0901.3015","open_access":"1"}],"article_processing_charge":"No","title":"Resolution of unmixed bipartite graphs","department":[{"_id":"CaUh"}],"page":"977 - 986","citation":{"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>.","short":"F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986.","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>","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>","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>.","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."},"status":"public","publication":"Bulletin of the Korean Mathematical Society","publisher":"Korean Mathematical Society","scopus_import":"1","date_updated":"2025-09-23T10:36:36Z","author":[{"id":"2C29581E-F248-11E8-B48F-1D18A9856A87","full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi","first_name":"Fatemeh"},{"last_name":"Moradi","first_name":"Somayeh","full_name":"Moradi, Somayeh"}],"year":"2015","oa":1,"quality_controlled":"1","issue":"3","volume":52,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"31"},{"date_published":"2015-12-01T00:00:00Z","isi":1,"_id":"1548","pmid":1,"publist_id":"5623","intvolume":"        81","publication_status":"published","language":[{"iso":"eng"}],"doi":"10.1128/AEM.02051-15","date_created":"2018-12-11T11:52:39Z","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/"}],"article_processing_charge":"No","title":"Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination","department":[{"_id":"SyCr"}],"external_id":{"isi":["000364775700018"],"pmid":["26386058"]},"type":"journal_article","month":"12","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"}],"date_updated":"2025-09-23T09:22:27Z","author":[{"orcid":"0000-0002-8214-4758","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","full_name":"Milutinovic, Barbara","last_name":"Milutinovic","first_name":"Barbara"},{"last_name":"Höfling","first_name":"Christina","full_name":"Höfling, Christina"},{"first_name":"Momir","last_name":"Futo","full_name":"Futo, Momir"},{"full_name":"Scharsack, Jörn","last_name":"Scharsack","first_name":"Jörn"},{"full_name":"Kurtz, Joachim","first_name":"Joachim","last_name":"Kurtz"}],"year":"2015","citation":{"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.","short":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and Environmental Microbiology 81 (2015) 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>","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>.","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.","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>"},"page":"8135 - 8144","publication":"Applied and Environmental Microbiology","status":"public","publisher":"American Society for Microbiology","scopus_import":"1","issue":"23","volume":81,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","oa":1,"quality_controlled":"1"},{"oa":1,"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","series_title":"Advances in Experimental Medicine and Biology","day":"18","volume":869,"scopus_import":"1","has_accepted_license":"1","publisher":"Springer","file":[{"file_id":"4854","relation":"main_file","file_name":"IST-2017-839-v1+1_mckenzie.pdf","creator":"system","file_size":1919655,"content_type":"application/pdf","checksum":"bd1bfdf2423a0c3b6e7cabfa8b44bc0f","date_created":"2018-12-12T10:11:02Z","date_updated":"2020-07-14T12:45:01Z","access_level":"open_access"}],"citation":{"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.","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>.","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>","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>","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.","short":"C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools to Study Ion Channel Biology, Springer, 2015, pp. 101–117.","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>."},"page":"101 - 117","ddc":["571","576"],"publication":"Novel chemical tools to study ion channel biology","status":"public","year":"2015","author":[{"full_name":"Mckenzie, Catherine","first_name":"Catherine","last_name":"Mckenzie","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez Romero","first_name":"Inmaculada","full_name":"Sanchez Romero, Inmaculada"},{"last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-09-23T08:52:05Z","external_id":{"isi":["000361794300006"]},"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."}],"type":"book_chapter","month":"09","file_date_updated":"2020-07-14T12:45:01Z","corr_author":"1","pubrep_id":"839","publication_identifier":{"isbn":["978-1-4939-2844-6"]},"department":[{"_id":"HaJa"}],"article_processing_charge":"No","doi":"10.1007/978-1-4939-2845-3_6","oa_version":"Submitted Version","date_created":"2018-12-11T11:52:39Z","title":"Flipping the photoswitch: Ion channels under light control","language":[{"iso":"eng"}],"publist_id":"5622","publication_status":"published","intvolume":"       869","_id":"1549","isi":1,"date_published":"2015-09-18T00:00:00Z"},{"_id":"1550","isi":1,"date_published":"2015-09-02T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published","intvolume":"        87","publist_id":"5621","pmid":1,"department":[{"_id":"SiHi"}],"title":"Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/"}],"article_processing_charge":"No","date_created":"2018-12-11T11:52:40Z","doi":"10.1016/j.neuron.2015.07.011","oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"type":"journal_article","month":"09","external_id":{"isi":["000361146300009"],"pmid":["26299473"]},"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","year":"2015","author":[{"full_name":"Mayer, Christian","first_name":"Christian","last_name":"Mayer"},{"last_name":"Jaglin","first_name":"Xavier","full_name":"Jaglin, Xavier"},{"full_name":"Cobbs, Lucy","first_name":"Lucy","last_name":"Cobbs"},{"full_name":"Bandler, Rachel","last_name":"Bandler","first_name":"Rachel"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"first_name":"Constance","last_name":"Cepko","full_name":"Cepko, Constance"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"full_name":"Fishell, Gord","last_name":"Fishell","first_name":"Gord"}],"date_updated":"2025-09-23T08:16:35Z","scopus_import":"1","publisher":"Elsevier","publication":"Neuron","status":"public","page":"989 - 998","citation":{"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>.","short":"C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer, G. Fishell, Neuron 87 (2015) 989–998.","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.","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>.","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>","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>","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."},"day":"02","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":87,"issue":"5","quality_controlled":"1","oa":1},{"oa":1,"quality_controlled":"1","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":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"04","issue":"6","volume":13,"has_accepted_license":"1","ec_funded":1,"scopus_import":"1","file":[{"creator":"system","file_name":"IST-2016-481-v1+1_journal.pbio.1002169.pdf","relation":"main_file","file_id":"5063","date_updated":"2020-07-14T12:45:02Z","access_level":"open_access","date_created":"2018-12-12T10:14:13Z","file_size":3468956,"checksum":"30dee7a2c11ed09f2f5634655c0146f8","content_type":"application/pdf"}],"publisher":"Public Library of Science","ddc":["570"],"page":"1 - 30","citation":{"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.","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.","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>.","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>.","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>","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>","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."},"status":"public","publication":"PLoS Biology","year":"2015","author":[{"full_name":"El Masri, Leila","last_name":"El Masri","first_name":"Leila","id":"349A6E66-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Branca, Antoine","first_name":"Antoine","last_name":"Branca"},{"full_name":"Sheppard, Anna","first_name":"Anna","last_name":"Sheppard"},{"first_name":"Andrei","last_name":"Papkou","full_name":"Papkou, Andrei"},{"last_name":"Laehnemann","first_name":"David","full_name":"Laehnemann, David"},{"full_name":"Guenther, Patrick","first_name":"Patrick","last_name":"Guenther"},{"full_name":"Prahl, Swantje","first_name":"Swantje","last_name":"Prahl"},{"full_name":"Saebelfeld, Manja","first_name":"Manja","last_name":"Saebelfeld"},{"last_name":"Hollensteiner","first_name":"Jacqueline","full_name":"Hollensteiner, Jacqueline"},{"full_name":"Liesegang, Heiko","last_name":"Liesegang","first_name":"Heiko"},{"full_name":"Brzuszkiewicz, Elzbieta","first_name":"Elzbieta","last_name":"Brzuszkiewicz"},{"last_name":"Daniel","first_name":"Rolf","full_name":"Daniel, Rolf"},{"first_name":"Nico","last_name":"Michiels","full_name":"Michiels, Nico"},{"first_name":"Rebecca","last_name":"Schulte","full_name":"Schulte, Rebecca"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"last_name":"Rosenstiel","first_name":"Philip","full_name":"Rosenstiel, Philip"},{"full_name":"Telschow, Arndt","first_name":"Arndt","last_name":"Telschow"},{"first_name":"Erich","last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich"},{"last_name":"Schulenburg","first_name":"Hinrich","full_name":"Schulenburg, Hinrich"}],"date_updated":"2025-09-23T09:19:00Z","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"external_id":{"isi":["000357339600009"]},"abstract":[{"lang":"eng","text":"Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins.We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen's genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system."}],"file_date_updated":"2020-07-14T12:45:02Z","type":"journal_article","month":"06","pubrep_id":"481","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.","department":[{"_id":"SyCr"}],"article_processing_charge":"No","oa_version":"Published Version","doi":"10.1371/journal.pbio.1002169","date_created":"2018-12-11T11:52:40Z","title":"Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes","language":[{"iso":"eng"}],"publist_id":"5620","publication_status":"published","intvolume":"        13","isi":1,"_id":"1551","date_published":"2015-06-04T00:00:00Z"},{"corr_author":"1","project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","grant_number":"T 560-B17","_id":"2529486C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"name":"Cell migration in complex environments: from in vivo experiments to theoretical models","grant_number":"RGP0058/2011","_id":"25ABD200-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000352708300028"]},"abstract":[{"text":"Cell movement has essential functions in development, immunity, and cancer. Various cell migration patterns have been reported, but no general rule has emerged so far. Here, we show on the basis of experimental data in vitro and in vivo that cell persistence, which quantifies the straightness of trajectories, is robustly coupled to cell migration speed. We suggest that this universal coupling constitutes a generic law of cell migration, which originates in the advection of polarity cues by an actin cytoskeleton undergoing flows at the cellular scale. Our analysis relies on a theoretical model that we validate by measuring the persistence of cells upon modulation of actin flow speeds and upon optogenetic manipulation of the binding of an actin regulator to actin filaments. Beyond the quantitative prediction of the coupling, the model yields a generic phase diagram of cellular trajectories, which recapitulates the full range of observed migration patterns.","lang":"eng"}],"month":"04","type":"journal_article","article_processing_charge":"No","doi":"10.1016/j.cell.2015.01.056","date_created":"2018-12-11T11:52:41Z","oa_version":"None","title":"Actin flows mediate a universal coupling between cell speed and cell persistence","department":[{"_id":"MiSi"},{"_id":"CaHe"}],"publist_id":"5618","publication_status":"published","intvolume":"       161","language":[{"iso":"eng"}],"date_published":"2015-04-09T00:00:00Z","_id":"1553","isi":1,"quality_controlled":"1","issue":"2","volume":161,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"09","page":"374 - 386","citation":{"chicago":"Maiuri, Paolo, Jean Rupprecht, Stefan Wieser, Verena Ruprecht, Olivier Bénichou, Nicolas Carpi, Mathieu Coppey, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” <i>Cell</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">https://doi.org/10.1016/j.cell.2015.01.056</a>.","short":"P. Maiuri, J. Rupprecht, S. Wieser, V. Ruprecht, O. Bénichou, N. Carpi, M. Coppey, S. De Beco, N. Gov, C.-P.J. Heisenberg, C. Lage Crespo, F. Lautenschlaeger, M. Le Berre, A. Lennon Duménil, M. Raab, H. Thiam, M. Piel, M.K. Sixt, R. Voituriez, Cell 161 (2015) 374–386.","ista":"Maiuri P, Rupprecht J, Wieser S, Ruprecht V, Bénichou O, Carpi N, Coppey M, De Beco S, Gov N, Heisenberg C-PJ, Lage Crespo C, Lautenschlaeger F, Le Berre M, Lennon Duménil A, Raab M, Thiam H, Piel M, Sixt MK, Voituriez R. 2015. Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. 161(2), 374–386.","ieee":"P. Maiuri <i>et al.</i>, “Actin flows mediate a universal coupling between cell speed and cell persistence,” <i>Cell</i>, vol. 161, no. 2. Cell Press, pp. 374–386, 2015.","mla":"Maiuri, Paolo, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” <i>Cell</i>, vol. 161, no. 2, Cell Press, 2015, pp. 374–86, doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">10.1016/j.cell.2015.01.056</a>.","apa":"Maiuri, P., Rupprecht, J., Wieser, S., Ruprecht, V., Bénichou, O., Carpi, N., … Voituriez, R. (2015). Actin flows mediate a universal coupling between cell speed and cell persistence. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">https://doi.org/10.1016/j.cell.2015.01.056</a>","ama":"Maiuri P, Rupprecht J, Wieser S, et al. Actin flows mediate a universal coupling between cell speed and cell persistence. <i>Cell</i>. 2015;161(2):374-386. doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">10.1016/j.cell.2015.01.056</a>"},"publication":"Cell","status":"public","ec_funded":1,"scopus_import":"1","publisher":"Cell Press","date_updated":"2025-09-23T07:31:01Z","year":"2015","author":[{"full_name":"Maiuri, Paolo","first_name":"Paolo","last_name":"Maiuri"},{"full_name":"Rupprecht, Jean","first_name":"Jean","last_name":"Rupprecht"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2670-2217","last_name":"Wieser","first_name":"Stefan","full_name":"Wieser, Stefan"},{"id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","first_name":"Verena","last_name":"Ruprecht"},{"first_name":"Olivier","last_name":"Bénichou","full_name":"Bénichou, Olivier"},{"last_name":"Carpi","first_name":"Nicolas","full_name":"Carpi, Nicolas"},{"full_name":"Coppey, Mathieu","first_name":"Mathieu","last_name":"Coppey"},{"full_name":"De Beco, Simon","first_name":"Simon","last_name":"De Beco"},{"first_name":"Nir","last_name":"Gov","full_name":"Gov, Nir"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"full_name":"Lage Crespo, Carolina","last_name":"Lage Crespo","first_name":"Carolina"},{"first_name":"Franziska","last_name":"Lautenschlaeger","full_name":"Lautenschlaeger, Franziska"},{"full_name":"Le Berre, Maël","last_name":"Le Berre","first_name":"Maël"},{"first_name":"Ana","last_name":"Lennon Duménil","full_name":"Lennon Duménil, Ana"},{"full_name":"Raab, Matthew","first_name":"Matthew","last_name":"Raab"},{"last_name":"Thiam","first_name":"Hawa","full_name":"Thiam, Hawa"},{"first_name":"Matthieu","last_name":"Piel","full_name":"Piel, Matthieu"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"}]},{"language":[{"iso":"eng"}],"intvolume":"        12","publication_status":"published","publist_id":"5617","pmid":1,"isi":1,"_id":"1554","date_published":"2015-02-26T00:00:00Z","month":"02","type":"journal_article","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"}],"external_id":{"isi":["000350670300017"],"pmid":["25643149"]},"department":[{"_id":"JiFr"}],"title":"Reporters for sensitive and quantitative measurement of auxin response","date_created":"2018-12-11T11:52:41Z","doi":"10.1038/nmeth.3279","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/"}],"article_processing_charge":"No","publisher":"Nature Publishing Group","scopus_import":"1","publication":"Nature Methods","status":"public","page":"207 - 210","citation":{"short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210.","ista":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210.","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>.","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.","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>","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>","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>."},"author":[{"full_name":"Liao, Cheyang","first_name":"Cheyang","last_name":"Liao"},{"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","first_name":"Teva","last_name":"Vernoux"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"}],"year":"2015","date_updated":"2025-09-23T10:34:32Z","quality_controlled":"1","oa":1,"day":"26","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":12,"issue":"3"},{"issue":"2","volume":14,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","oa":1,"quality_controlled":"1","article_type":"original","date_updated":"2025-09-23T10:37:17Z","year":"2015","author":[{"last_name":"Knipl","first_name":"Diána","full_name":"Knipl, Diána"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel","first_name":"Pawel","last_name":"Pilarczyk"},{"full_name":"Röst, Gergely","first_name":"Gergely","last_name":"Röst"}],"ddc":["510"],"page":"980 - 1017","citation":{"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>","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>","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>.","ieee":"D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two patch vaccination model,” <i>SIAM Journal on Applied Dynamical Systems</i>, vol. 14, no. 2. Society for Industrial and Applied Mathematics , pp. 980–1017, 2015.","short":"D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems 14 (2015) 980–1017.","chicago":"Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” <i>SIAM Journal on Applied Dynamical Systems</i>. Society for Industrial and Applied Mathematics , 2015. <a href=\"https://doi.org/10.1137/140993934\">https://doi.org/10.1137/140993934</a>.","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."},"publication":"SIAM Journal on Applied Dynamical Systems","status":"public","ec_funded":1,"scopus_import":"1","publisher":"Society for Industrial and Applied Mathematics ","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"http://discovery.ucl.ac.uk/1473750/1/99393.pdf"}],"oa_version":"Published Version","date_created":"2018-12-11T11:52:42Z","doi":"10.1137/140993934","title":"Rich bifurcation structure in a two patch vaccination model","department":[{"_id":"HeEd"}],"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.","publication_identifier":{"eissn":["1536-0040"]},"project":[{"call_identifier":"FP7","grant_number":"622033","name":"Persistent Homology - Images, Data and Maps","_id":"255F06BE-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000357310400015"]},"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"}],"type":"journal_article","month":"01","date_published":"2015-01-01T00:00:00Z","isi":1,"_id":"1555","publist_id":"5616","publication_status":"published","intvolume":"        14","language":[{"iso":"eng"}]},{"date_updated":"2025-09-23T13:42:27Z","year":"2015","author":[{"last_name":"Jia","first_name":"Yuebin","full_name":"Jia, Yuebin"},{"full_name":"Tian, Huiyu","first_name":"Huiyu","last_name":"Tian"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660","first_name":"Hongjiang","last_name":"Li","full_name":"Li, Hongjiang"},{"first_name":"Qianqian","last_name":"Yu","full_name":"Yu, Qianqian"},{"full_name":"Wang, Lei","last_name":"Wang","first_name":"Lei"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"}],"ddc":["570"],"page":"4631 - 4642","citation":{"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>","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.","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>.","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>.","short":"Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642.","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."},"publication":"Journal of Experimental Botany","status":"public","has_accepted_license":"1","scopus_import":"1","file":[{"creator":"system","file_name":"IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf","relation":"main_file","file_id":"5051","date_updated":"2020-07-14T12:45:02Z","access_level":"open_access","date_created":"2018-12-12T10:14:02Z","file_size":7753043,"checksum":"257919be0ce3d306185d3891ad7acf39","content_type":"application/pdf"}],"publisher":"Oxford University Press","issue":"15","volume":66,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","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)"},"oa":1,"quality_controlled":"1","date_published":"2015-08-01T00:00:00Z","_id":"1556","isi":1,"publist_id":"5615","publication_status":"published","intvolume":"        66","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Published Version","date_created":"2018-12-11T11:52:42Z","doi":"10.1093/jxb/erv230","title":"The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development","department":[{"_id":"JiFr"}],"pubrep_id":"480","external_id":{"isi":["000359687400017"]},"abstract":[{"text":"The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators.","lang":"eng"}],"month":"08","type":"journal_article","file_date_updated":"2020-07-14T12:45:02Z"},{"isi":1,"_id":"1557","date_published":"2015-09-01T00:00:00Z","language":[{"iso":"eng"}],"intvolume":"       523","publication_status":"published","publist_id":"5614","department":[{"_id":"RySh"}],"title":"Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats","doi":"10.1002/cne.23774","date_created":"2018-12-11T11:52:42Z","oa_version":"None","article_processing_charge":"No","type":"journal_article","month":"09","abstract":[{"lang":"eng","text":"γ-Aminobutyric acid (GABA)- and glycine-mediated hyperpolarizing inhibition is associated with a chloride influx that depends on the inwardly directed chloride electrochemical gradient. In neurons, the extrusion of chloride from the cytosol primarily depends on the expression of an isoform of potassium-chloride cotransporters (KCC2s). KCC2 is crucial in the regulation of the inhibitory tone of neural circuits, including pain processing neural assemblies. Thus we investigated the cellular distribution of KCC2 in neurons underlying pain processing in the superficial spinal dorsal horn of rats by using high-resolution immunocytochemical methods. We demonstrated that perikarya and dendrites widely expressed KCC2, but axon terminals proved to be negative for KCC2. In single ultrathin sections, silver deposits labeling KCC2 molecules showed different densities on the surface of dendritic profiles, some of which were negative for KCC2. In freeze fracture replicas and tissue sections double stained for the β3-subunit of GABAA receptors and KCC2, GABAA receptors were revealed on dendritic segments with high and also with low KCC2 densities. By measuring the distances between spots immunoreactive for gephyrin (a scaffolding protein of GABAA and glycine receptors) and KCC2 on the surface of neurokinin 1 (NK1) receptor-immunoreactive dendrites, we found that gephyrin-immunoreactive spots were located at various distances from KCC2 cotransporters; 5.7 % of them were recovered in the middle of 4-10-μm-long dendritic segments that were free of KCC2 immunostaining. The variable local densities of KCC2 may result in variable postsynaptic potentials evoked by the activation of GABAA and glycine receptors along the dendrites of spinal neurons."}],"external_id":{"isi":["000358228700006"]},"acknowledgement":"Funded by:\r\nHungarian Academy of Sciences. Grant Number: MTA-TKI 242\r\nHungarian Brain Research Program. Grant Number: KTIA_NAP_13-1-2013-0001\r\nSolution Oriented Research for Science and Technology from the Japan Science and Technology Agency Japanese Ministry of Education, Culture, Sports, Science and Technology","author":[{"last_name":"Javdani","first_name":"Fariba","full_name":"Javdani, Fariba"},{"full_name":"Holló, Krisztina","first_name":"Krisztina","last_name":"Holló"},{"full_name":"Hegedűs, Krisztina","last_name":"Hegedűs","first_name":"Krisztina"},{"full_name":"Kis, Gréta","first_name":"Gréta","last_name":"Kis"},{"last_name":"Hegyi","first_name":"Zoltán","full_name":"Hegyi, Zoltán"},{"first_name":"Klaudia","last_name":"Dócs","full_name":"Dócs, Klaudia"},{"full_name":"Kasugai, Yu","last_name":"Kasugai","first_name":"Yu"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto"},{"full_name":"Antal, Miklós","last_name":"Antal","first_name":"Miklós"}],"year":"2015","date_updated":"2025-09-23T08:26:48Z","publisher":"Wiley-Blackwell","scopus_import":"1","status":"public","publication":"Journal of Comparative Neurology","page":"1967 - 1983","citation":{"ista":"Javdani F, Holló K, Hegedűs K, Kis G, Hegyi Z, Dócs K, Kasugai Y, Fukazawa Y, Shigemoto R, Antal M. 2015. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 523(13), 1967–1983.","chicago":"Javdani, Fariba, Krisztina Holló, Krisztina Hegedűs, Gréta Kis, Zoltán Hegyi, Klaudia Dócs, Yu Kasugai, Yugo Fukazawa, Ryuichi Shigemoto, and Miklós Antal. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” <i>Journal of Comparative Neurology</i>. Wiley-Blackwell, 2015. <a href=\"https://doi.org/10.1002/cne.23774\">https://doi.org/10.1002/cne.23774</a>.","short":"F. Javdani, K. Holló, K. Hegedűs, G. Kis, Z. Hegyi, K. Dócs, Y. Kasugai, Y. Fukazawa, R. Shigemoto, M. Antal, Journal of Comparative Neurology 523 (2015) 1967–1983.","apa":"Javdani, F., Holló, K., Hegedűs, K., Kis, G., Hegyi, Z., Dócs, K., … Antal, M. (2015). Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. <i>Journal of Comparative Neurology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cne.23774\">https://doi.org/10.1002/cne.23774</a>","ieee":"F. Javdani <i>et al.</i>, “Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats,” <i>Journal of Comparative Neurology</i>, vol. 523, no. 13. Wiley-Blackwell, pp. 1967–1983, 2015.","ama":"Javdani F, Holló K, Hegedűs K, et al. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. <i>Journal of Comparative Neurology</i>. 2015;523(13):1967-1983. doi:<a href=\"https://doi.org/10.1002/cne.23774\">10.1002/cne.23774</a>","mla":"Javdani, Fariba, et al. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” <i>Journal of Comparative Neurology</i>, vol. 523, no. 13, Wiley-Blackwell, 2015, pp. 1967–83, doi:<a href=\"https://doi.org/10.1002/cne.23774\">10.1002/cne.23774</a>."},"day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":523,"issue":"13","quality_controlled":"1"},{"title":"The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation","oa_version":"None","date_created":"2018-12-11T11:52:42Z","doi":"10.1242/dev.113225","article_processing_charge":"No","department":[{"_id":"JiFr"}],"month":"02","type":"journal_article","abstract":[{"lang":"eng","text":"CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation."}],"external_id":{"isi":["000351697100012"]},"date_published":"2015-02-15T00:00:00Z","isi":1,"_id":"1558","intvolume":"       142","publication_status":"published","publist_id":"5613","language":[{"iso":"eng"}],"volume":142,"issue":"4","day":"15","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","date_updated":"2025-09-23T13:49:06Z","author":[{"full_name":"Ivanchenko, Maria","last_name":"Ivanchenko","first_name":"Maria"},{"last_name":"Zhu","first_name":"Jinsheng","full_name":"Zhu, Jinsheng"},{"full_name":"Wang, Bangjun","first_name":"Bangjun","last_name":"Wang"},{"id":"298814E2-F248-11E8-B48F-1D18A9856A87","last_name":"Medvecka","first_name":"Eva","full_name":"Medvecka, Eva"},{"full_name":"Du, Yunlong","first_name":"Yunlong","last_name":"Du"},{"full_name":"Azzarello, Elisa","last_name":"Azzarello","first_name":"Elisa"},{"first_name":"Stefano","last_name":"Mancuso","full_name":"Mancuso, Stefano"},{"full_name":"Megraw, Molly","last_name":"Megraw","first_name":"Molly"},{"full_name":"Filichkin, Sergei","last_name":"Filichkin","first_name":"Sergei"},{"first_name":"Joseph","last_name":"Dubrovsky","full_name":"Dubrovsky, Joseph"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"}],"year":"2015","publication":"Development","status":"public","citation":{"chicago":"Ivanchenko, Maria, Jinsheng Zhu, Bangjun Wang, Eva Medvecka, Yunlong Du, Elisa Azzarello, Stefano Mancuso, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” <i>Development</i>. Company of Biologists, 2015. <a href=\"https://doi.org/10.1242/dev.113225\">https://doi.org/10.1242/dev.113225</a>.","short":"M. Ivanchenko, J. Zhu, B. Wang, E. Medvecka, Y. Du, E. Azzarello, S. Mancuso, M. Megraw, S. Filichkin, J. Dubrovsky, J. Friml, M. Geisler, Development 142 (2015) 712–721.","ista":"Ivanchenko M, Zhu J, Wang B, Medvecka E, Du Y, Azzarello E, Mancuso S, Megraw M, Filichkin S, Dubrovsky J, Friml J, Geisler M. 2015. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 142(4), 712–721.","apa":"Ivanchenko, M., Zhu, J., Wang, B., Medvecka, E., Du, Y., Azzarello, E., … Geisler, M. (2015). The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.113225\">https://doi.org/10.1242/dev.113225</a>","ama":"Ivanchenko M, Zhu J, Wang B, et al. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. <i>Development</i>. 2015;142(4):712-721. doi:<a href=\"https://doi.org/10.1242/dev.113225\">10.1242/dev.113225</a>","mla":"Ivanchenko, Maria, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” <i>Development</i>, vol. 142, no. 4, Company of Biologists, 2015, pp. 712–21, doi:<a href=\"https://doi.org/10.1242/dev.113225\">10.1242/dev.113225</a>.","ieee":"M. Ivanchenko <i>et al.</i>, “The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation,” <i>Development</i>, vol. 142, no. 4. Company of Biologists, pp. 712–721, 2015."},"page":"712 - 721","publisher":"Company of Biologists","scopus_import":"1"},{"doi":"10.1073/pnas.1511366112","date_created":"2018-12-11T11:52:43Z","oa_version":"Submitted Version","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/","open_access":"1"}],"article_processing_charge":"No","title":"Computational complexity of ecological and evolutionary spatial dynamics","department":[{"_id":"KrCh"}],"corr_author":"1","external_id":{"isi":["000366916000044"],"pmid":["26644569"]},"type":"journal_article","month":"12","abstract":[{"text":"There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant)will take over a resident population?We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP).","lang":"eng"}],"date_published":"2015-12-22T00:00:00Z","isi":1,"_id":"1559","pmid":1,"publist_id":"5612","intvolume":"       112","publication_status":"published","language":[{"iso":"eng"}],"issue":"51","volume":112,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"22","oa":1,"quality_controlled":"1","date_updated":"2025-09-23T08:20:08Z","author":[{"last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"year":"2015","page":"15636 - 15641","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>.","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>","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.","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.","short":"R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641."},"publication":"PNAS","status":"public","publisher":"National Academy of Sciences","scopus_import":"1"}]