[{"volume":58,"has_accepted_license":"1","year":"2013","issue":"SI-1-Track-G","language":[{"iso":"eng"}],"pmid":1,"publication_identifier":{"eissn":["1862-278X"],"issn":["0013-5585"]},"conference":{"end_date":"2013-09-21","start_date":"2013-09-19","name":"BMT: Biomedizinische Technik ","location":"Graz, Austria"},"author":[{"first_name":"Alois","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","orcid":"0000-0002-5621-8100"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804"},{"full_name":"Schmidt-Hieber, C.","last_name":"Schmidt-Hieber","first_name":"C."},{"full_name":"Guzman, S. J.","last_name":"Guzman","first_name":"S. J."}],"date_updated":"2021-12-02T12:51:12Z","file":[{"date_created":"2021-12-01T14:38:08Z","file_size":149825,"creator":"schloegl","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"10397","date_updated":"2021-12-01T14:38:08Z","file_name":"Schloegl_Abstract-BMT2013.pdf","checksum":"cdfc5339b530a25d6079f7223f0b1f16","success":1}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable.","lang":"eng"}],"article_type":"original","publisher":"De Gruyter","_id":"10396","file_date_updated":"2021-12-01T14:38:08Z","ddc":["005","610"],"publication_status":"published","title":"Stimfit: A fast visualization and analysis environment for cellular neurophysiology","department":[{"_id":"PeJo"}],"type":"journal_article","publication":"Biomedical Engineering / Biomedizinische Technik","date_created":"2021-12-01T14:35:35Z","oa_version":"Submitted Version","citation":{"ieee":"A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A fast visualization and analysis environment for cellular neurophysiology,” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G. De Gruyter, 2013.","short":"A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013).","chicago":"Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>. De Gruyter, 2013. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>.","ista":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.","ama":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. 2013;58(SI-1-Track-G). doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>","mla":"Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>.","apa":"Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., &#38; Guzman, S. J. (2013). Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. Graz, Austria: De Gruyter. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>"},"month":"08","quality_controlled":"1","intvolume":"        58","date_published":"2013-08-01T00:00:00Z","doi":"10.1515/bmt-2013-4181","article_number":"000010151520134181","status":"public","day":"01","external_id":{"pmid":["24042795"]},"oa":1,"keyword":["biomedical engineering","data analysis","free software"]},{"month":"03","quality_controlled":"1","type":"journal_article","publication":"Cell","date_created":"2021-06-04T12:23:28Z","citation":{"chicago":"Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>.","ista":"Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205.","ieee":"A. Zemach <i>et al.</i>, “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” <i>Cell</i>, vol. 153, no. 1. Elsevier, pp. 193–205, 2013.","short":"A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.","mla":"Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>.","apa":"Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>","ama":"Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. 2013;153(1):193-205. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>"},"oa_version":"Published Version","day":"28","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2013.02.033"}],"extern":"1","external_id":{"pmid":["23540698"]},"oa":1,"intvolume":"       153","date_published":"2013-03-28T00:00:00Z","doi":"10.1016/j.cell.2013.02.033","status":"public","language":[{"iso":"eng"}],"pmid":1,"author":[{"last_name":"Zemach","full_name":"Zemach, Assaf","first_name":"Assaf"},{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"last_name":"Hsieh","full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung"},{"first_name":"Devin","last_name":"Coleman-Derr","full_name":"Coleman-Derr, Devin"},{"first_name":"Leor","full_name":"Eshed-Williams, Leor","last_name":"Eshed-Williams"},{"full_name":"Thao, Ka","last_name":"Thao","first_name":"Ka"},{"first_name":"Stacey L.","full_name":"Harmer, Stacey L.","last_name":"Harmer"},{"orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"date_updated":"2021-12-14T08:25:35Z","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway.","lang":"eng"}],"volume":153,"year":"2013","issue":"1","scopus_import":"1","title":"The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin","page":"193-205","department":[{"_id":"DaZi"}],"article_type":"original","publisher":"Elsevier","_id":"9459","publication_status":"published"},{"language":[{"iso":"eng"}],"pmid":1,"author":[{"last_name":"Rodrigues","full_name":"Rodrigues, Jessica A.","first_name":"Jessica A."},{"first_name":"Randy","last_name":"Ruan","full_name":"Ruan, Randy"},{"first_name":"Toshiro","full_name":"Nishimura, Toshiro","last_name":"Nishimura"},{"last_name":"Sharma","full_name":"Sharma, Manoj K.","first_name":"Manoj K."},{"full_name":"Sharma, Rita","last_name":"Sharma","first_name":"Rita"},{"first_name":"Pamela C","last_name":"Ronald","full_name":"Ronald, Pamela C"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"date_updated":"2021-12-14T08:26:44Z","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants.","lang":"eng"}],"volume":110,"year":"2013","scopus_import":"1","issue":"19","page":"7934-7939","title":"Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm","department":[{"_id":"DaZi"}],"article_type":"original","publisher":"National Academy of Sciences","_id":"9481","publication_status":"published","month":"05","quality_controlled":"1","type":"journal_article","publication":"Proceedings of the National Academy of Sciences","date_created":"2021-06-07T07:31:02Z","citation":{"ista":"Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 110(19), 7934–7939.","chicago":"Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>.","ieee":"J. A. Rodrigues <i>et al.</i>, “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013.","short":"J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939.","mla":"Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7934–39, doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>.","apa":"Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>","ama":"Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2013;110(19):7934-7939. doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>"},"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1306164110"}],"day":"07","extern":"1","external_id":{"pmid":["23613580"]},"oa":1,"keyword":["Multidisciplinary"],"intvolume":"       110","doi":"10.1073/pnas.1306164110","date_published":"2013-05-07T00:00:00Z","status":"public"},{"oa":1,"external_id":{"pmid":["23410937"]},"extern":"1","day":"11","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2013.01.014","open_access":"1"}],"status":"public","doi":"10.1016/j.devcel.2013.01.014","date_published":"2013-02-11T00:00:00Z","intvolume":"        24","quality_controlled":"1","month":"02","oa_version":"Published Version","citation":{"apa":"Feng, X., Zilberman, D., &#38; Dickinson, H. (2013). A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>","mla":"Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>, vol. 24, no. 3, Elsevier, 2013, pp. 215–25, doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>.","ama":"Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. 2013;24(3):215-225. doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>","ista":"Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.","chicago":"Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>.","ieee":"X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” <i>Developmental Cell</i>, vol. 24, no. 3. Elsevier, pp. 215–225, 2013.","short":"X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225."},"date_created":"2021-06-08T06:14:50Z","publication":"Developmental Cell","type":"journal_article","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"title":"A conversation across generations: Soma-germ cell crosstalk in plants","page":"215-225","publication_status":"published","_id":"9520","publisher":"Elsevier","article_type":"review","abstract":[{"text":"Plants undergo alternation of generation in which reproductive cells develop in the plant body (\"sporophytic generation\") and then differentiate into a multicellular gamete-forming \"gametophytic generation.\" Different populations of helper cells assist in this transgenerational journey, with somatic tissues supporting early development and single nurse cells supporting gametogenesis. New data reveal a two-way relationship between early reproductive cells and their helpers involving complex epigenetic and signaling networks determining cell number and fate. Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2023-05-08T11:00:59Z","author":[{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Dickinson, Hugh","last_name":"Dickinson","first_name":"Hugh"}],"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"pmid":1,"language":[{"iso":"eng"}],"issue":"3","scopus_import":"1","year":"2013","volume":24},{"article_processing_charge":"No","date_updated":"2023-02-23T10:34:39Z","abstract":[{"lang":"eng","text":"Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"12","author":[{"last_name":"Zagorsky","full_name":"Zagorsky, Benjamin","first_name":"Benjamin"},{"orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","full_name":"Reiter, Johannes","first_name":"Johannes"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"year":"2013","citation":{"short":"B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013).","ieee":"B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma .” Public Library of Science, 2013.","ista":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma , Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>.","chicago":"Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">https://doi.org/10.1371/journal.pone.0080814.s001</a>.","ama":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . 2013. doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>","apa":"Zagorsky, B., Reiter, J., Chatterjee, K., &#38; Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">https://doi.org/10.1371/journal.pone.0080814.s001</a>","mla":"Zagorsky, Benjamin, et al. <i>Forgiver Triumphs in Alternating Prisoner’s Dilemma </i>. Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>."},"oa_version":"Published Version","date_created":"2021-07-28T15:45:07Z","type":"research_data_reference","department":[{"_id":"KrCh"}],"day":"12","title":"Forgiver triumphs in alternating prisoner's dilemma ","status":"public","related_material":{"record":[{"id":"2247","relation":"used_in_publication","status":"public"}]},"publisher":"Public Library of Science","date_published":"2013-12-12T00:00:00Z","doi":"10.1371/journal.pone.0080814.s001","_id":"9749"},{"_id":"9751","date_published":"2013-03-21T00:00:00Z","doi":"10.5061/dryad.b1q2n","publisher":"Dryad","related_material":{"record":[{"id":"2853","relation":"used_in_publication","status":"public"}]},"status":"public","title":"Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection","oa":1,"day":"21","main_file_link":[{"url":"https://doi.org/10.5061/dryad.b1q2n","open_access":"1"}],"department":[{"_id":"CaGu"}],"type":"research_data_reference","oa_version":"Published Version","citation":{"apa":"Refardt, D., Bergmiller, T., &#38; Kümmerli, R. (2013). Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. Dryad. <a href=\"https://doi.org/10.5061/dryad.b1q2n\">https://doi.org/10.5061/dryad.b1q2n</a>","mla":"Refardt, Dominik, et al. <i>Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection</i>. Dryad, 2013, doi:<a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>.","ama":"Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. 2013. doi:<a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>","ista":"Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection, Dryad, <a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>.","chicago":"Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” Dryad, 2013. <a href=\"https://doi.org/10.5061/dryad.b1q2n\">https://doi.org/10.5061/dryad.b1q2n</a>.","short":"D. Refardt, T. Bergmiller, R. Kümmerli, (2013).","ieee":"D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection.” Dryad, 2013."},"date_created":"2021-07-30T08:08:09Z","year":"2013","author":[{"full_name":"Refardt, Dominik","last_name":"Refardt","first_name":"Dominik"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias"},{"full_name":"Kümmerli, Rolf","last_name":"Kümmerli","first_name":"Rolf"}],"month":"03","abstract":[{"lang":"eng","text":"High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","date_updated":"2023-10-18T06:43:22Z"},{"oa":1,"title":"Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r3r60"}],"day":"01","department":[{"_id":"NiBa"}],"_id":"9754","doi":"10.5061/dryad.r3r60","date_published":"2013-10-01T00:00:00Z","publisher":"Dryad","related_material":{"record":[{"relation":"used_in_publication","id":"2170","status":"public"}]},"status":"public","author":[{"last_name":"Hearn","full_name":"Hearn, Jack","first_name":"Jack"},{"last_name":"Stone","full_name":"Stone, Graham","first_name":"Graham"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"last_name":"Bunnefeld","full_name":"Bunnefeld, Lynsey","first_name":"Lynsey"}],"month":"10","abstract":[{"lang":"eng","text":"Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","date_updated":"2023-02-23T10:31:17Z","type":"research_data_reference","oa_version":"Published Version","citation":{"ieee":"J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013.","short":"J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).","chicago":"Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies.” Dryad, 2013. <a href=\"https://doi.org/10.5061/dryad.r3r60\">https://doi.org/10.5061/dryad.r3r60</a>.","ista":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies, Dryad, <a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>.","ama":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. 2013. doi:<a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>","apa":"Hearn, J., Stone, G., Barton, N. H., Lohse, K., &#38; Bunnefeld, L. (2013). Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. Dryad. <a href=\"https://doi.org/10.5061/dryad.r3r60\">https://doi.org/10.5061/dryad.r3r60</a>","mla":"Hearn, Jack, et al. <i>Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies</i>. Dryad, 2013, doi:<a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>."},"date_created":"2021-07-30T08:31:22Z","year":"2013"},{"department":[{"_id":"JiFr"}],"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"page":"1034 - 1048","title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","das_tickbox":"1","ddc":["580"],"publication_status":"published","publisher":"Wiley","publist_id":"4460","article_type":"original","ec_funded":1,"_id":"2443","article_processing_charge":"No","date_updated":"2026-06-18T07:49:41Z","abstract":[{"lang":"eng","text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741"},{"full_name":"Kubeš, Martin","last_name":"Kubeš","first_name":"Martin"},{"first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","full_name":"Baster, Pawel"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"full_name":"Dobrev, Petre","last_name":"Dobrev","first_name":"Petre"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"first_name":"Eva","full_name":"Zažímalová, Eva","last_name":"Zažímalová"}],"scopus_import":"1","issue":"4","year":"2013","volume":200,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/nph.12437"}],"day":"01","oa":1,"status":"public","date_published":"2013-12-01T00:00:00Z","doi":"10.1111/nph.12437","intvolume":"       200","quality_controlled":"1","acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","month":"12","publication":"New Phytologist","oa_version":"Published Version","citation":{"chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>.","ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.","ieee":"S. Simon <i>et al.</i>, “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” <i>New Phytologist</i>, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048.","apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>","mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>.","ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. 2013;200(4):1034-1048. doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>"},"date_created":"2018-12-11T11:57:41Z","type":"journal_article"},{"volume":8044,"scopus_import":"1","year":"2013","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Jakub","full_name":"Ła̧Cki, Jakub","last_name":"Ła̧Cki"}],"conference":{"end_date":"2013-07-19","name":"CAV: Computer Aided Verification","start_date":"2013-07-13","location":"St. Petersburg, Russia"},"language":[{"iso":"eng"}],"abstract":[{"text":"We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2026-06-18T07:50:03Z","ec_funded":1,"_id":"2444","publisher":"Springer","publist_id":"4459","series_title":"Lecture Notes in Computer Science","publication_status":"published","ddc":["000"],"das_tickbox":"1","title":"Faster algorithms for Markov decision processes with low treewidth","page":"543 - 558","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"alternative_title":["LNCS"],"department":[{"_id":"KrCh"}],"type":"conference","citation":{"chicago":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>.","ista":"Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558.","ieee":"K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.","short":"K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.","mla":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. <i>Faster Algorithms for Markov Decision Processes with Low Treewidth</i>. Vol. 8044, Springer, 2013, pp. 543–58, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>.","apa":"Chatterjee, K., &#38; Ła̧Cki, J. (2013). Faster algorithms for Markov decision processes with low treewidth. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>","ama":"Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with low treewidth. 2013;8044:543-558. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>"},"oa_version":"Preprint","date_created":"2018-12-11T11:57:42Z","month":"07","arxiv":1,"quality_controlled":"1","doi":"10.1007/978-3-642-39799-8_36","date_published":"2013-07-01T00:00:00Z","intvolume":"      8044","status":"public","oa":1,"external_id":{"arxiv":["1304.0084"]},"day":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.0084"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","date_updated":"2021-01-12T07:42:38Z","month":"01","author":[{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T12:02:39Z","citation":{"chicago":"Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” In <i>Encyclopedia of Systems Biology</i>, edited by Werner Dubitzky, Olaf Wolkenhauer, Kwang Cho, and Hiroki Yokota, 3:1069–1069. Springer, 2013. <a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">https://doi.org/10.1007/978-1-4419-9863-7_604</a>.","ista":"Quadrianto N, Lampert C. 2013.Kernel based learning. In: Encyclopedia of Systems Biology. vol. 3, 1069–1069.","short":"N. Quadrianto, C. Lampert, in:, W. Dubitzky, O. Wolkenhauer, K. Cho, H. Yokota (Eds.), Encyclopedia of Systems Biology, Springer, 2013, pp. 1069–1069.","ieee":"N. Quadrianto and C. Lampert, “Kernel based learning,” in <i>Encyclopedia of Systems Biology</i>, vol. 3, W. Dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota, Eds. Springer, 2013, pp. 1069–1069.","apa":"Quadrianto, N., &#38; Lampert, C. (2013). Kernel based learning. In W. Dubitzky, O. Wolkenhauer, K. Cho, &#38; H. Yokota (Eds.), <i>Encyclopedia of Systems Biology</i> (Vol. 3, pp. 1069–1069). Springer. <a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">https://doi.org/10.1007/978-1-4419-9863-7_604</a>","mla":"Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” <i>Encyclopedia of Systems Biology</i>, edited by Werner Dubitzky et al., vol. 3, Springer, 2013, pp. 1069–1069, doi:<a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">10.1007/978-1-4419-9863-7_604</a>.","ama":"Quadrianto N, Lampert C. Kernel based learning. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H, eds. <i>Encyclopedia of Systems Biology</i>. Vol 3. Springer; 2013:1069-1069. doi:<a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">10.1007/978-1-4419-9863-7_604</a>"},"oa_version":"None","publication":"Encyclopedia of Systems Biology","year":"2013","volume":3,"type":"encyclopedia_article","department":[{"_id":"ChLa"}],"title":"Kernel based learning","page":"1069 - 1069","editor":[{"first_name":"Werner","full_name":"Dubitzky, Werner","last_name":"Dubitzky"},{"full_name":"Wolkenhauer, Olaf","last_name":"Wolkenhauer","first_name":"Olaf"},{"first_name":"Kwang","last_name":"Cho","full_name":"Cho, Kwang"},{"full_name":"Yokota, Hiroki","last_name":"Yokota","first_name":"Hiroki"}],"day":"01","publication_status":"published","status":"public","_id":"3321","intvolume":"         3","publist_id":"3314","publisher":"Springer","date_published":"2013-01-01T00:00:00Z","doi":"10.1007/978-1-4419-9863-7_604"},{"department":[{"_id":"NiBa"}],"title":"Source population characteristics affect heterosis following genetic rescue of fragmented plant populations","publication_status":"published","publist_id":"7372","publisher":"Royal Society, The","_id":"450","date_updated":"2021-01-12T07:57:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations.","lang":"eng"}],"language":[{"iso":"eng"}],"pmid":1,"author":[{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541"},{"first_name":"David","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","orcid":"0000-0002-4014-8478"},{"last_name":"Rowell","full_name":"Rowell, David","first_name":"David"},{"first_name":"Andrew","full_name":"Young, Andrew","last_name":"Young"}],"year":"2013","issue":"1750","volume":280,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/"}],"day":"07","external_id":{"pmid":["23173202"]},"oa":1,"status":"public","intvolume":"       280","doi":"10.1098/rspb.2012.2058","date_published":"2013-01-07T00:00:00Z","article_number":"2058","quality_controlled":"1","month":"01","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","date_created":"2018-12-11T11:46:32Z","citation":{"apa":"Pickup, M., Field, D., Rowell, D., &#38; Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>","mla":"Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750, 2058, Royal Society, The, 2013, doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>.","ama":"Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2013;280(1750). doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>","ista":"Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1750), 2058.","chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The, 2013. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750. Royal Society, The, 2013."},"oa_version":"Submitted Version","type":"journal_article"},{"month":"12","pubrep_id":"953","license":"https://creativecommons.org/licenses/by/4.0/","quality_controlled":"1","type":"journal_article","date_created":"2018-12-11T11:46:41Z","oa_version":"Published Version","citation":{"ista":"Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. 7(DEC).","chicago":"Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” <i>Frontiers in Behavioral Neuroscience</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">https://doi.org/10.3389/fnbeh.2013.00217</a>.","ieee":"D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions,” <i>Frontiers in Behavioral Neuroscience</i>, vol. 7, no. DEC. Frontiers Research Foundation, 2013.","short":"D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013).","mla":"Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” <i>Frontiers in Behavioral Neuroscience</i>, vol. 7, no. DEC, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">10.3389/fnbeh.2013.00217</a>.","apa":"Dickerson, D., &#38; Bilkey, D. (2013). Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. <i>Frontiers in Behavioral Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">https://doi.org/10.3389/fnbeh.2013.00217</a>","ama":"Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. <i>Frontiers in Behavioral Neuroscience</i>. 2013;7(DEC). doi:<a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">10.3389/fnbeh.2013.00217</a>"},"publication":"Frontiers in Behavioral Neuroscience","oa":1,"day":"27","intvolume":"         7","date_published":"2013-12-27T00:00:00Z","doi":"10.3389/fnbeh.2013.00217","status":"public","author":[{"last_name":"Dickerson","id":"444EB89E-F248-11E8-B48F-1D18A9856A87","full_name":"Dickerson, Desiree","first_name":"Desiree"},{"full_name":"Bilkey, David","last_name":"Bilkey","first_name":"David"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Maternal exposure to infection occurring mid-gestation produces a three-fold increase in the risk of schizophrenia in the offspring. The critical initiating factor appears to be the maternal immune activation (MIA) that follows infection. This process can be induced in rodents by exposure of pregnant dams to the viral mimic Poly I:C, which triggers an immune response that results in structural, functional, behavioral, and electrophysiological phenotypes in the adult offspring that model those seen in schizophrenia. We used this model to explore the role of synchronization in brain neural networks, a process thought to be dysfunctional in schizophrenia and previously associated with positive, negative, and cognitive symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced an impairment in long-range neural synchrony in adult offspring between two regions implicated in schizophrenia pathology; the hippocampus and the medial prefrontal cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the antipsychotic clozapine. MIA animals have previously been shown to have impaired pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits in animal models. Our data showed that deficits in synchrony were positively correlated with the impairments in PPI. Subsequent analysis of LFP activity during the PPI response also showed that reduced coupling between the mPFC and the hippocampus following processing of the pre-pulse was associated with reduced PPI. The ability of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology provides a useful platform from which to investigate the ontogeny of aberrant synchronous processes. Further, the way in which the model expresses translatable deficits such as aberrant synchrony and reduced PPI will allow researchers to explore novel intervention strategies targeted to these changes. "}],"date_updated":"2021-01-12T08:00:53Z","file":[{"access_level":"open_access","content_type":"application/pdf","creator":"system","file_id":"5128","relation":"main_file","file_size":530134,"date_created":"2018-12-12T10:15:10Z","file_name":"IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf","date_updated":"2020-07-14T12:46:35Z","checksum":"cd7183121e56251176100ccac165c95c"}],"has_accepted_license":"1","volume":7,"year":"2013","issue":"DEC","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions","department":[{"_id":"JoCs"}],"_id":"476","publist_id":"7346","publisher":"Frontiers Research Foundation","publication_status":"published","ddc":["571"],"file_date_updated":"2020-07-14T12:46:35Z"},{"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"day":"04","page":"91 - 95","title":"Dynamic persistence of antibiotic-stressed mycobacteria","status":"public","publication_status":"published","date_published":"2013-01-04T00:00:00Z","publisher":"American Association for the Advancement of Science","doi":"10.1126/science.1229858","publist_id":"7321","intvolume":"       339","_id":"499","quality_controlled":"1","date_updated":"2021-01-12T08:01:06Z","abstract":[{"lang":"eng","text":"Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to infrequently dividing or nondividing &quot;persisters.&quot; Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although persistence in these studies was characterized by stable numbers of cells, this apparent stability was actually a dynamic state of balanced division and death. Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic pulses that were negatively correlated with cell survival. These behaviors may reflect epigenetic effects, because KatG pulsing and death were correlated between sibling cells. Selection of lineages characterized by infrequent KatG pulsing could allow nonresponsive adaptation during prolonged drug exposure."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"last_name":"Wakamoto","full_name":"Wakamoto, Yurichi","first_name":"Yurichi"},{"full_name":"Dhar, Neraaj","last_name":"Dhar","first_name":"Neraaj"},{"last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","first_name":"Remy P","orcid":"0000-0003-0876-3187"},{"full_name":"Schneider, Katrin","last_name":"Schneider","first_name":"Katrin"},{"first_name":"François","full_name":"Signorino Gelo, François","last_name":"Signorino Gelo"},{"last_name":"Leibler","full_name":"Leibler, Stanislas","first_name":"Stanislas"},{"full_name":"Mckinney, John","last_name":"Mckinney","first_name":"John"}],"month":"01","issue":"6115","scopus_import":1,"year":"2013","publication":"Science","citation":{"apa":"Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler, S., &#38; Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1229858\">https://doi.org/10.1126/science.1229858</a>","mla":"Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” <i>Science</i>, vol. 339, no. 6115, American Association for the Advancement of Science, 2013, pp. 91–95, doi:<a href=\"https://doi.org/10.1126/science.1229858\">10.1126/science.1229858</a>.","ama":"Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed mycobacteria. <i>Science</i>. 2013;339(6115):91-95. doi:<a href=\"https://doi.org/10.1126/science.1229858\">10.1126/science.1229858</a>","chicago":"Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” <i>Science</i>. American Association for the Advancement of Science, 2013. <a href=\"https://doi.org/10.1126/science.1229858\">https://doi.org/10.1126/science.1229858</a>.","ista":"Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115), 91–95.","short":"Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.","ieee":"Y. Wakamoto <i>et al.</i>, “Dynamic persistence of antibiotic-stressed mycobacteria,” <i>Science</i>, vol. 339, no. 6115. American Association for the Advancement of Science, pp. 91–95, 2013."},"oa_version":"None","date_created":"2018-12-11T11:46:48Z","type":"journal_article","volume":339},{"acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council, the Government of the Republic of Panama, the Interdisciplinary Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC BY 2.0\r\n","quality_controlled":"1","month":"10","pubrep_id":"941","oa_version":"Published Version","citation":{"apa":"Ward, M., Lycett, S., Avila, D., Bollback, J. P., &#38; Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-222\">https://doi.org/10.1186/1471-2148-13-222</a>","mla":"Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, 222, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-222\">10.1186/1471-2148-13-222</a>.","ama":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. <i>BMC Evolutionary Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-13-222\">10.1186/1471-2148-13-222</a>","ista":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 13(1), 222.","chicago":"Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-222\">https://doi.org/10.1186/1471-2148-13-222</a>.","short":"M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013).","ieee":"M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, 2013."},"date_created":"2018-12-11T11:46:49Z","publication":"BMC Evolutionary Biology","type":"journal_article","oa":1,"day":"09","status":"public","article_number":"222","date_published":"2013-10-09T00:00:00Z","doi":"10.1186/1471-2148-13-222","intvolume":"        13","abstract":[{"lang":"eng","text":"Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:08Z","file":[{"checksum":"52cf48a7c1794676ae8b0029573a84a9","date_updated":"2020-07-14T12:46:36Z","file_name":"IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf","relation":"main_file","file_id":"4722","creator":"system","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:08:59Z","file_size":1150052}],"author":[{"first_name":"Melissa","last_name":"Ward","full_name":"Ward, Melissa"},{"last_name":"Lycett","full_name":"Lycett, Samantha","first_name":"Samantha"},{"first_name":"Dorita","full_name":"Avila, Dorita","last_name":"Avila"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"first_name":"Andrew","last_name":"Leigh Brown","full_name":"Leigh Brown, Andrew"}],"language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"1","scopus_import":1,"year":"2013","has_accepted_license":"1","volume":13,"department":[{"_id":"JoBo"}],"title":"Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza","ddc":["576"],"file_date_updated":"2020-07-14T12:46:36Z","publication_status":"published","_id":"500","publisher":"BioMed Central","publist_id":"7320"},{"month":"12","pubrep_id":"940","quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"journal_article","publication":"Journal of Mammalogy","date_created":"2018-12-11T11:46:49Z","citation":{"apa":"Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy, B., … Santos, F. (2013). A new species of tapir from the Amazon. <i>Journal of Mammalogy</i>. Oxford University Press. <a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">https://doi.org/10.1644/12-MAMM-A-169.1</a>","mla":"Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” <i>Journal of Mammalogy</i>, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45, doi:<a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">10.1644/12-MAMM-A-169.1</a>.","ama":"Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon. <i>Journal of Mammalogy</i>. 2013;94(6):1331-1345. doi:<a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">10.1644/12-MAMM-A-169.1</a>","ista":"Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of Mammalogy. 94(6), 1331–1345.","chicago":"Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A New Species of Tapir from the Amazon.” <i>Journal of Mammalogy</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">https://doi.org/10.1644/12-MAMM-A-169.1</a>.","short":"M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy, R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.","ieee":"M. Cozzuol <i>et al.</i>, “A new species of tapir from the Amazon,” <i>Journal of Mammalogy</i>, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013."},"oa_version":"Published Version","day":"01","oa":1,"intvolume":"        94","date_published":"2013-12-01T00:00:00Z","doi":"10.1644/12-MAMM-A-169.1","status":"public","language":[{"iso":"eng"}],"author":[{"full_name":"Cozzuol, Mario","last_name":"Cozzuol","first_name":"Mario"},{"full_name":"Clozato, Camila","last_name":"Clozato","first_name":"Camila"},{"first_name":"Elizete","full_name":"Holanda, Elizete","last_name":"Holanda"},{"first_name":"Flávio","last_name":"Rodrigues","full_name":"Rodrigues, Flávio"},{"last_name":"Nienow","full_name":"Nienow, Samuel","first_name":"Samuel"},{"first_name":"Benoit","full_name":"De Thoisy, Benoit","last_name":"De Thoisy"},{"first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793"},{"last_name":"Santos","full_name":"Santos, Fabrício","first_name":"Fabrício"}],"file":[{"checksum":"8007815078dccac21ecd1cf73a269dc6","date_updated":"2020-07-14T12:46:36Z","file_name":"IST-2018-940-v1+1_2013_Redondo_A_new.pdf","date_created":"2018-12-12T10:12:59Z","file_size":1040765,"relation":"main_file","file_id":"4980","creator":"system","content_type":"application/pdf","access_level":"open_access"}],"date_updated":"2021-01-12T08:01:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region."}],"volume":94,"has_accepted_license":"1","year":"2013","scopus_import":1,"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"issue":"6","page":"1331 - 1345","title":"A new species of tapir from the Amazon","department":[{"_id":"JoBo"}],"publist_id":"7319","publisher":"Oxford University Press","_id":"501","publication_status":"published","file_date_updated":"2020-07-14T12:46:36Z","ddc":["570"]},{"department":[{"_id":"KrPi"}],"title":"Short blind signatures","page":"627 - 661","day":"22","publication_status":"published","status":"public","_id":"502","publist_id":"7318","intvolume":"        21","date_published":"2013-11-22T00:00:00Z","publisher":"IOS Press","doi":"10.3233/JCS-130477","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Blind signatures allow users to obtain signatures on messages hidden from the signer; moreover, the signer cannot link the resulting message/signature pair to the signing session. This paper presents blind signature schemes, in which the number of interactions between the user and the signer is minimal and whose blind signatures are short. Our schemes are defined over bilinear groups and are proved secure in the common-reference-string model without random oracles and under standard assumptions: CDH and the decision-linear assumption. (We also give variants over asymmetric groups based on similar assumptions.) The blind signatures are Waters signatures, which consist of 2 group elements. Moreover, we instantiate partially blind signatures, where the message consists of a part hidden from the signer and a commonly known public part, and schemes achieving perfect blindness. We propose new variants of blind signatures, such as signer-friendly partially blind signatures, where the public part can be chosen by the signer without prior agreement, 3-party blind signatures, as well as blind signatures on multiple aggregated messages provided by independent sources. We also extend Waters signatures to non-binary alphabets by proving a new result on the underlying hash function. "}],"quality_controlled":"1","date_updated":"2021-01-12T08:01:09Z","author":[{"first_name":"Olivier","full_name":"Blazy, Olivier","last_name":"Blazy"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg","first_name":"Georg"},{"first_name":"David","full_name":"Pointcheval, David","last_name":"Pointcheval"},{"first_name":"Damien","full_name":"Vergnaud, Damien","last_name":"Vergnaud"}],"month":"11","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:46:50Z","oa_version":"None","citation":{"ama":"Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. Short blind signatures. <i>Journal of Computer Security</i>. 2013;21(5):627-661. doi:<a href=\"https://doi.org/10.3233/JCS-130477\">10.3233/JCS-130477</a>","mla":"Blazy, Olivier, et al. “Short Blind Signatures.” <i>Journal of Computer Security</i>, vol. 21, no. 5, IOS Press, 2013, pp. 627–61, doi:<a href=\"https://doi.org/10.3233/JCS-130477\">10.3233/JCS-130477</a>.","apa":"Blazy, O., Fuchsbauer, G., Pointcheval, D., &#38; Vergnaud, D. (2013). Short blind signatures. <i>Journal of Computer Security</i>. IOS Press. <a href=\"https://doi.org/10.3233/JCS-130477\">https://doi.org/10.3233/JCS-130477</a>","short":"O. Blazy, G. Fuchsbauer, D. Pointcheval, D. Vergnaud, Journal of Computer Security 21 (2013) 627–661.","ieee":"O. Blazy, G. Fuchsbauer, D. Pointcheval, and D. Vergnaud, “Short blind signatures,” <i>Journal of Computer Security</i>, vol. 21, no. 5. IOS Press, pp. 627–661, 2013.","ista":"Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. 2013. Short blind signatures. Journal of Computer Security. 21(5), 627–661.","chicago":"Blazy, Olivier, Georg Fuchsbauer, David Pointcheval, and Damien Vergnaud. “Short Blind Signatures.” <i>Journal of Computer Security</i>. IOS Press, 2013. <a href=\"https://doi.org/10.3233/JCS-130477\">https://doi.org/10.3233/JCS-130477</a>."},"publication":"Journal of Computer Security","year":"2013","issue":"5","scopus_import":1,"volume":21,"type":"journal_article"},{"type":"journal_article","volume":15,"scopus_import":1,"issue":"2","publication":"Green Chemistry","year":"2013","oa_version":"None","citation":{"ista":"Greimel K, Perz V, Koren K, Feola R, Temel A, Sohar C, Herrero Acero E, Klimant I, Guebitz G. 2013. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 15(2), 381–388.","chicago":"Greimel, Katrin, Veronika Perz, Klaus Koren, Roland Feola, Armin Temel, Christian Sohar, Enrique Herrero Acero, Ingo Klimant, and Georg Guebitz. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” <i>Green Chemistry</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c2gc36666e\">https://doi.org/10.1039/c2gc36666e</a>.","ieee":"K. Greimel <i>et al.</i>, “Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins,” <i>Green Chemistry</i>, vol. 15, no. 2. Royal Society of Chemistry, pp. 381–388, 2013.","short":"K. Greimel, V. Perz, K. Koren, R. Feola, A. Temel, C. Sohar, E. Herrero Acero, I. Klimant, G. Guebitz, Green Chemistry 15 (2013) 381–388.","apa":"Greimel, K., Perz, V., Koren, K., Feola, R., Temel, A., Sohar, C., … Guebitz, G. (2013). Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. <i>Green Chemistry</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c2gc36666e\">https://doi.org/10.1039/c2gc36666e</a>","mla":"Greimel, Katrin, et al. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” <i>Green Chemistry</i>, vol. 15, no. 2, Royal Society of Chemistry, 2013, pp. 381–88, doi:<a href=\"https://doi.org/10.1039/c2gc36666e\">10.1039/c2gc36666e</a>.","ama":"Greimel K, Perz V, Koren K, et al. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. <i>Green Chemistry</i>. 2013;15(2):381-388. doi:<a href=\"https://doi.org/10.1039/c2gc36666e\">10.1039/c2gc36666e</a>"},"date_created":"2018-12-11T11:46:51Z","language":[{"iso":"eng"}],"author":[{"first_name":"Katrin","last_name":"Greimel","full_name":"Greimel, Katrin"},{"first_name":"Veronika","full_name":"Perz, Veronika","last_name":"Perz"},{"first_name":"Klaus","last_name":"Koren","full_name":"Koren, Klaus","id":"382FBD6A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Feola","full_name":"Feola, Roland","first_name":"Roland"},{"last_name":"Temel","full_name":"Temel, Armin","first_name":"Armin"},{"first_name":"Christian","full_name":"Sohar, Christian","last_name":"Sohar"},{"full_name":"Herrero Acero, Enrique","last_name":"Herrero Acero","first_name":"Enrique"},{"last_name":"Klimant","full_name":"Klimant, Ingo","first_name":"Ingo"},{"last_name":"Guebitz","full_name":"Guebitz, Georg","first_name":"Georg"}],"month":"02","date_updated":"2021-01-12T08:01:11Z","quality_controlled":"1","abstract":[{"lang":"eng","text":"Alkyd resins are polyesters containing unsaturated fatty acids that are used as binding agents in paints and coatings. Chemical drying of these polyesters is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective, yet they have been proven to be carcinogenic. Therefore, strategies to replace the cobalt-based catalyst by environmentally friendlier and less toxic alternatives are under development. Here, we demonstrate for the first time that a laccase-mediator system can effectively replace the heavy-metal catalyst and cross-link alkyd resins. Interestingly, the biocatalytic reaction does not only work in aqueous media, but also in a solid film, where enzyme diffusion is limited. Within the catalytic cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase, which is uniformly distributed within the drying film as evidenced by confocal laser scanning microscopy. During gradual build-up of molecular weight, there is a concomitant decrease of the oxygen content in the film. A new optical sensor to follow oxygen consumption during the cross-linking reaction was developed and validated with state of the art techniques. A remarkable feature is the low sample amount required, which allows faster screening of new catalysts."}],"acknowledgement":"This study was performed within the Austrian Centre of Indus-\r\ntrial Biotechnology ACIB and the COST Action 868. This work\r\nhas been supported by the Federal Ministry of Economy,\r\nFamily and Youth (BMWFJ), the Federal Ministry of Tra\r\nffi\r\nc,\r\nInnovation and Technology (bmvit), the Styrian Business\r\nPromotion Agency SFG, the Standortagentur Tirol and ZIT\r\n–\r\nTechnology  Agency  of  the  City  of  Vienna  through  the\r\nCOMET-Funding Program managed by the Austrian Research\r\nPromotion Agency FFG. Dr Massimiliano Cardinale (Institute of\r\nEnvironmental Biotechnology, TU Graz) is gratefully acknowl-\r\nedged for technical support with the CLSM measurements.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Royal Society of Chemistry","doi":"10.1039/c2gc36666e","date_published":"2013-02-01T00:00:00Z","publist_id":"7313","intvolume":"        15","_id":"505","status":"public","publication_status":"published","day":"01","title":"Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins","page":"381 - 388","department":[{"_id":"HaJa"}]},{"oa":1,"external_id":{"pmid":["23975898"]},"day":"01","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/","open_access":"1"}],"status":"public","date_published":"2013-08-01T00:00:00Z","doi":"10.1105/tpc.113.114264","intvolume":"        25","quality_controlled":"1","month":"08","oa_version":"Submitted Version","citation":{"apa":"Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013). Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114264\">https://doi.org/10.1105/tpc.113.114264</a>","mla":"Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” <i>Plant Cell</i>, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:<a href=\"https://doi.org/10.1105/tpc.113.114264\">10.1105/tpc.113.114264</a>.","ama":"Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. <i>Plant Cell</i>. 2013;25(8):2970-2985. doi:<a href=\"https://doi.org/10.1105/tpc.113.114264\">10.1105/tpc.113.114264</a>","chicago":"Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt, Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114264\">https://doi.org/10.1105/tpc.113.114264</a>.","ista":"Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985.","short":"S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml, G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985.","ieee":"S. Kim <i>et al.</i>, “Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis,” <i>Plant Cell</i>, vol. 25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013."},"date_created":"2018-12-11T11:46:52Z","publication":"Plant Cell","type":"journal_article","department":[{"_id":"JiFr"}],"title":"Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis","page":"2970 - 2985","publication_status":"published","_id":"507","publisher":"American Society of Plant Biologists","publist_id":"7312","abstract":[{"lang":"eng","text":"Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:12Z","author":[{"last_name":"Kim","full_name":"Kim, Soo","first_name":"Soo"},{"first_name":"Zheng","full_name":"Xu, Zheng","last_name":"Xu"},{"first_name":"Kyungyoung","last_name":"Song","full_name":"Song, Kyungyoung"},{"full_name":"Kim, Dae","last_name":"Kim","first_name":"Dae"},{"last_name":"Kang","full_name":"Kang, Hyangju","first_name":"Hyangju"},{"first_name":"Ilka","last_name":"Reichardt","full_name":"Reichardt, Ilka"},{"first_name":"Eun","full_name":"Sohn, Eun","last_name":"Sohn"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Gerd","last_name":"Juergens","full_name":"Juergens, Gerd"},{"last_name":"Hwang","full_name":"Hwang, Inhwan","first_name":"Inhwan"}],"pmid":1,"language":[{"iso":"eng"}],"issue":"8","scopus_import":1,"year":"2013","volume":25},{"date_published":"2013-09-01T00:00:00Z","doi":"10.1093/molbev/mst119","intvolume":"        30","status":"public","external_id":{"pmid":["23821607"]},"day":"01","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/","open_access":"1"}],"oa":1,"type":"journal_article","publication":"Molecular Biology and Evolution","oa_version":"Submitted Version","citation":{"apa":"Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett, L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/mst119\">https://doi.org/10.1093/molbev/mst119</a>","mla":"Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” <i>Molecular Biology and Evolution</i>, vol. 30, no. 9, Oxford University Press, 2013, pp. 2157–67, doi:<a href=\"https://doi.org/10.1093/molbev/mst119\">10.1093/molbev/mst119</a>.","ama":"Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. <i>Molecular Biology and Evolution</i>. 2013;30(9):2157-2167. doi:<a href=\"https://doi.org/10.1093/molbev/mst119\">10.1093/molbev/mst119</a>","chicago":"Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen, Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/molbev/mst119\">https://doi.org/10.1093/molbev/mst119</a>.","ista":"Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M, Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 30(9), 2157–2167.","ieee":"E. Tarazona Santos <i>et al.</i>, “Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” <i>Molecular Biology and Evolution</i>, vol. 30, no. 9. Oxford University Press, pp. 2157–2167, 2013.","short":"E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett, A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich, M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167."},"date_created":"2018-12-11T11:46:52Z","month":"09","quality_controlled":"1","publisher":"Oxford University Press","publist_id":"7310","_id":"508","publication_status":"published","title":"Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications","page":"2157 - 2167","department":[{"_id":"JoBo"}],"volume":30,"scopus_import":1,"issue":"9","year":"2013","pmid":1,"language":[{"iso":"eng"}],"author":[{"last_name":"Tarazona Santos","full_name":"Tarazona Santos, Eduardo","first_name":"Eduardo"},{"first_name":"Moara","last_name":"Machado","full_name":"Machado, Moara"},{"full_name":"Magalhães, Wagner","last_name":"Magalhães","first_name":"Wagner"},{"last_name":"Chen","full_name":"Chen, Renee","first_name":"Renee"},{"full_name":"Lyon, Fernanda","last_name":"Lyon","first_name":"Fernanda"},{"last_name":"Burdett","full_name":"Burdett, Laurie","first_name":"Laurie"},{"first_name":"Andrew","full_name":"Crenshaw, Andrew","last_name":"Crenshaw"},{"first_name":"Cristina","full_name":"Fabbri, Cristina","last_name":"Fabbri"},{"full_name":"Pereira, Latife","last_name":"Pereira","first_name":"Latife"},{"first_name":"Laelia","last_name":"Pinto","full_name":"Pinto, Laelia"},{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","first_name":"Rodrigo A","orcid":"0000-0002-5837-2793"},{"first_name":"Ben","full_name":"Sestanovich, Ben","last_name":"Sestanovich"},{"last_name":"Yeager","full_name":"Yeager, Meredith","first_name":"Meredith"},{"last_name":"Chanock","full_name":"Chanock, Stephen","first_name":"Stephen"}],"date_updated":"2021-01-12T08:01:12Z","abstract":[{"text":"The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","doi":"10.1105/tpc.113.114058","date_published":"2013-08-01T00:00:00Z","intvolume":"        25","oa":1,"external_id":{"pmid":["23975899"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784593/","open_access":"1"}],"day":"01","oa_version":"Submitted Version","citation":{"mla":"Di Rubbo, Simone, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” <i>Plant Cell</i>, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2986–97, doi:<a href=\"https://doi.org/10.1105/tpc.113.114058\">10.1105/tpc.113.114058</a>.","apa":"Di Rubbo, S., Irani, N., Kim, S., Xu, Z., Gadeyne, A., Dejonghe, W., … Russinova, E. (2013). The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114058\">https://doi.org/10.1105/tpc.113.114058</a>","ama":"Di Rubbo S, Irani N, Kim S, et al. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. <i>Plant Cell</i>. 2013;25(8):2986-2997. doi:<a href=\"https://doi.org/10.1105/tpc.113.114058\">10.1105/tpc.113.114058</a>","chicago":"Di Rubbo, Simone, Niloufer Irani, Soo Kim, Zheng Xu, Astrid Gadeyne, Wim Dejonghe, Isabelle Vanhoutte, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114058\">https://doi.org/10.1105/tpc.113.114058</a>.","ista":"Di Rubbo S, Irani N, Kim S, Xu Z, Gadeyne A, Dejonghe W, Vanhoutte I, Persiau G, Eeckhout D, Simon S, Song K, Kleine Vehn J, Friml J, De Jaeger G, Van Damme D, Hwang I, Russinova E. 2013. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 25(8), 2986–2997.","ieee":"S. Di Rubbo <i>et al.</i>, “The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis,” <i>Plant Cell</i>, vol. 25, no. 8. American Society of Plant Biologists, pp. 2986–2997, 2013.","short":"S. Di Rubbo, N. Irani, S. Kim, Z. Xu, A. Gadeyne, W. Dejonghe, I. Vanhoutte, G. Persiau, D. Eeckhout, S. Simon, K. Song, J. Kleine Vehn, J. Friml, G. De Jaeger, D. Van Damme, I. Hwang, E. Russinova, Plant Cell 25 (2013) 2986–2997."},"date_created":"2018-12-11T11:46:52Z","publication":"Plant Cell","type":"journal_article","quality_controlled":"1","month":"08","publication_status":"published","_id":"509","publisher":"American Society of Plant Biologists","publist_id":"7311","department":[{"_id":"JiFr"}],"title":"The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis","page":"2986 - 2997","scopus_import":1,"issue":"8","year":"2013","volume":25,"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. "}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:13Z","author":[{"full_name":"Di Rubbo, Simone","last_name":"Di Rubbo","first_name":"Simone"},{"last_name":"Irani","full_name":"Irani, Niloufer","first_name":"Niloufer"},{"last_name":"Kim","full_name":"Kim, Soo","first_name":"Soo"},{"first_name":"Zheng","full_name":"Xu, Zheng","last_name":"Xu"},{"full_name":"Gadeyne, Astrid","last_name":"Gadeyne","first_name":"Astrid"},{"first_name":"Wim","last_name":"Dejonghe","full_name":"Dejonghe, Wim"},{"full_name":"Vanhoutte, Isabelle","last_name":"Vanhoutte","first_name":"Isabelle"},{"last_name":"Persiau","full_name":"Persiau, Geert","first_name":"Geert"},{"first_name":"Dominique","last_name":"Eeckhout","full_name":"Eeckhout, Dominique"},{"orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu"},{"first_name":"Kyungyoung","last_name":"Song","full_name":"Song, Kyungyoung"},{"full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí"},{"full_name":"De Jaeger, Geert","last_name":"De Jaeger","first_name":"Geert"},{"first_name":"Daniël","full_name":"Van Damme, Daniël","last_name":"Van Damme"},{"first_name":"Inhwan","full_name":"Hwang, Inhwan","last_name":"Hwang"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"}],"pmid":1,"language":[{"iso":"eng"}]}]