[{"title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","day":"11","department":[{"_id":"DaZi"}],"author":[{"first_name":"Zsuzsanna","full_name":"Mérai, Zsuzsanna","last_name":"Mérai"},{"first_name":"Nina","full_name":"Chumak, Nina","last_name":"Chumak"},{"first_name":"Marcelina","last_name":"García-Aguilar","full_name":"García-Aguilar, Marcelina"},{"full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh","first_name":"Tzung-Fu"},{"full_name":"Nishimura, Toshiro","last_name":"Nishimura","first_name":"Toshiro"},{"first_name":"Vera K.","last_name":"Schoft","full_name":"Schoft, Vera K."},{"first_name":"János","full_name":"Bindics, János","last_name":"Bindics"},{"first_name":"Lucyna","last_name":"Ślusarz","full_name":"Ślusarz, Lucyna"},{"first_name":"Stéphanie","last_name":"Arnoux","full_name":"Arnoux, Stéphanie"},{"first_name":"Susanne","last_name":"Opravil","full_name":"Opravil, Susanne"},{"first_name":"Karl","full_name":"Mechtler, Karl","last_name":"Mechtler"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."},{"last_name":"Tamaru","full_name":"Tamaru, Hisashi","first_name":"Hisashi"}],"oa_version":"Published Version","intvolume":"       111","date_updated":"2021-12-14T08:23:26Z","abstract":[{"lang":"eng","text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction."}],"date_created":"2021-06-07T07:23:43Z","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}],"status":"public","article_processing_charge":"No","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication":"Proceedings of the National Academy of Sciences","pmid":1,"scopus_import":"1","month":"11","_id":"9479","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","citation":{"apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171."},"type":"journal_article","volume":111,"oa":1,"date_published":"2014-11-11T00:00:00Z","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1418564111","issue":"45","article_type":"original","extern":"1","external_id":{"pmid":["25344531"]},"page":"16166-16171","quality_controlled":"1","year":"2014"},{"article_type":"review","extern":"1","date_published":"2014-05-04T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Elsevier","doi":"10.1016/j.tplants.2014.01.014","issue":"5","quality_controlled":"1","year":"2014","page":"320-326","external_id":{"pmid":["24618094 "]},"_id":"9519","pmid":1,"scopus_import":"1","month":"05","type":"journal_article","volume":19,"publication_status":"published","citation":{"apa":"Kim, M. Y., &#38; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>","ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. 2014;19(5):320-326. doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>","ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” <i>Trends in Plant Science</i>, vol. 19, no. 5. Elsevier, pp. 320–326, 2014.","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>.","mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>.","ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326.","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","date_created":"2021-06-07T14:38:09Z","status":"public","publication":"Trends in Plant Science","publication_identifier":{"eissn":["1878-4372"],"issn":["1360-1385"]},"department":[{"_id":"DaZi"}],"day":"04","title":"DNA methylation as a system of plant genomic immunity","abstract":[{"text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression.","lang":"eng"}],"oa_version":"None","date_updated":"2021-12-14T08:24:48Z","intvolume":"        19","author":[{"first_name":"M. Yvonne","full_name":"Kim, M. Yvonne","last_name":"Kim"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel"}]},{"oa_version":"Published Version","date_updated":"2025-09-29T12:02:47Z","citation":{"short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014).","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>.","mla":"Lovrics, Anna, et al. <i>Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","ieee":"A. Lovrics <i>et al.</i>, “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.","ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &#38; Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>"},"type":"research_data_reference","author":[{"full_name":"Lovrics, Anna","last_name":"Lovrics","first_name":"Anna"},{"full_name":"Gao, Yu","last_name":"Gao","first_name":"Yu"},{"first_name":"Bianka","full_name":"Juhász, Bianka","last_name":"Juhász"},{"last_name":"Bock","full_name":"Bock, István","first_name":"István"},{"first_name":"Helen M.","full_name":"Byrne, Helen M.","last_name":"Byrne"},{"first_name":"András","last_name":"Dinnyés","full_name":"Dinnyés, András"},{"last_name":"Kovács","full_name":"Kovács, Krisztián","first_name":"Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9722","department":[{"_id":"JoCs"}],"title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2","month":"11","day":"14","year":"2014","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2004"}]},"article_processing_charge":"No","date_created":"2021-07-26T14:35:00Z","status":"public","date_published":"2014-11-14T00:00:00Z","doi":"10.1371/journal.pone.0111430.s006","publisher":"Public Library of Science"},{"article_processing_charge":"No","publisher":"Public Library of Science","date_published":"2014-09-11T00:00:00Z","doi":"10.1371/journal.pcbi.1003818.s001","date_created":"2021-07-28T08:13:57Z","status":"public","related_material":{"record":[{"status":"public","id":"2039","relation":"used_in_publication"}]},"year":"2014","department":[{"_id":"KrCh"}],"_id":"9739","day":"11","month":"09","title":"Detailed proofs for “The time scale of evolutionary innovation”","type":"research_data_reference","oa_version":"Published Version","citation":{"ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., &#38; Novak, M. (2014). Detailed proofs for “The time scale of evolutionary innovation.” Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time scale of evolutionary innovation.” 2014. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak. “Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>.","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for “The time scale of evolutionary innovation”, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Detailed Proofs for “The Time Scale of Evolutionary Innovation.”</i> Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014)."},"date_updated":"2025-09-29T11:53:46Z","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ben","last_name":"Adlam","full_name":"Adlam, Ben"},{"last_name":"Novak","full_name":"Novak, Martin","first_name":"Martin"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.vm0vc"}],"date_created":"2021-07-28T08:38:40Z","status":"public","oa":1,"publisher":"Dryad","doi":"10.5061/dryad.vm0vc","date_published":"2014-11-13T00:00:00Z","article_processing_charge":"No","year":"2014","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1993"}]},"title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","month":"11","day":"13","_id":"9740","department":[{"_id":"SyCr"}],"author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Konrad","full_name":"Konrad, Matthias"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse"},{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Tragust, Simon","last_name":"Tragust"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","citation":{"apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2014). Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Dryad. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host.” Dryad, 2014.","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad, <a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","mla":"Konrad, Matthias, et al. <i>Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014)."},"date_updated":"2025-09-23T07:55:02Z","corr_author":"1","abstract":[{"lang":"eng","text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens."}],"type":"research_data_reference"},{"related_material":{"record":[{"status":"public","id":"2036","relation":"used_in_publication"}]},"year":"2014","article_processing_charge":"No","publisher":"Dryad","doi":"10.5061/dryad.85dn7","date_published":"2014-08-21T00:00:00Z","status":"public","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.85dn7","open_access":"1"}],"date_created":"2021-07-28T08:48:06Z","abstract":[{"lang":"eng","text":"In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments."}],"type":"research_data_reference","date_updated":"2025-09-29T11:54:45Z","citation":{"apa":"Lagator, M., Colegrave, N., &#38; Neve, P. (2014). Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Dryad. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>","ama":"Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.” Dryad, 2014.","mla":"Lagator, Mato, et al. <i>Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>.","ista":"Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses, Dryad, <a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>.","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>.","short":"M. Lagator, N. Colegrave, P. Neve, (2014)."},"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Lagator, Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"first_name":"Nick","last_name":"Colegrave","full_name":"Colegrave, Nick"},{"first_name":"Paul","full_name":"Neve, Paul","last_name":"Neve"}],"department":[{"_id":"CaGu"}],"_id":"9741","month":"08","day":"21","title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses"},{"date_updated":"2025-09-29T11:46:47Z","citation":{"ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","apa":"Lagator, M., Morgan, A., Neve, P., &#38; Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>","mla":"Lagator, Mato, et al. <i>Data from: Role of Sex and Migration in Adaptation to Sink Environments</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>.","ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, <a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014)."},"oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Morgan, Andrew","last_name":"Morgan","first_name":"Andrew"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"},{"last_name":"Colegrave","full_name":"Colegrave, Nick","first_name":"Nick"}],"_id":"9747","department":[{"_id":"CaGu"}],"title":"Data from: Role of sex and migration in adaptation to sink environments","month":"04","day":"17","year":"2014","related_material":{"record":[{"relation":"used_in_publication","id":"2083","status":"public"}]},"article_processing_charge":"No","status":"public","oa":1,"date_created":"2021-07-28T15:32:55Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s42n1"}],"date_published":"2014-04-17T00:00:00Z","publisher":"Dryad","doi":"10.5061/dryad.s42n1"},{"year":"2014","related_material":{"record":[{"id":"2277","relation":"used_in_publication","status":"public"}]},"article_processing_charge":"No","oa":1,"status":"public","date_created":"2021-07-30T08:13:52Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.246qg"}],"publisher":"Dryad","date_published":"2014-11-07T00:00:00Z","doi":"10.5061/dryad.246qg","citation":{"short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>.","mla":"Simmons, Kristina, et al. <i>Data from: Transformation of Stimulus Correlations by the Retina</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad, <a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","ieee":"K. Simmons <i>et al.</i>, “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>","ama":"Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>"},"date_updated":"2025-09-29T14:27:23Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible."}],"type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Kristina","last_name":"Simmons","full_name":"Simmons, Kristina"},{"first_name":"Jason","full_name":"Prentice, Jason","last_name":"Prentice"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik"},{"first_name":"Jan","full_name":"Homann, Jan","last_name":"Homann"},{"first_name":"Heather","full_name":"Yee, Heather","last_name":"Yee"},{"first_name":"Stephanie","last_name":"Palmer","full_name":"Palmer, Stephanie"},{"first_name":"Philip","full_name":"Nelson, Philip","last_name":"Nelson"},{"first_name":"Vijay","full_name":"Balasubramanian, Vijay","last_name":"Balasubramanian"}],"_id":"9752","department":[{"_id":"GaTk"}],"title":"Data from: Transformation of stimulus correlations by the retina","day":"07","month":"11"},{"article_processing_charge":"No","doi":"10.5061/dryad.nc0gc","publisher":"Dryad","date_published":"2014-10-08T00:00:00Z","status":"public","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.nc0gc"}],"date_created":"2021-07-30T08:24:11Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2284"}]},"year":"2014","department":[{"_id":"SyCr"}],"_id":"9753","day":"08","month":"10","title":"Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","type":"research_data_reference","abstract":[{"text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal - originally described for honeybees as “hygienic behaviour” – is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.","lang":"eng"}],"date_updated":"2025-09-29T14:24:12Z","citation":{"short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014).","chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>.","ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies, Dryad, <a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>.","mla":"Tragust, Simon, et al. <i>Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>.","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., &#38; Cremer, S. (2014). Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. Dryad. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies.” Dryad, 2014."},"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Tragust","full_name":"Tragust, Simon","first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ugelvig, Line V","last_name":"Ugelvig","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"},{"first_name":"Michel","last_name":"Chapuisat","full_name":"Chapuisat, Michel"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}]},{"series_title":"SpringerBriefs in Applied Sciences and Technology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2022-03-04T07:47:54Z","citation":{"ieee":"H. Edelsbrunner, <i>A Short Course in Computational Geometry and Topology</i>, 1st ed. Cham: Springer Nature, 2014.","apa":"Edelsbrunner, H. (2014). <i>A Short Course in Computational Geometry and Topology</i> (1st ed.). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>","ama":"Edelsbrunner H. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. Cham: Springer Nature; 2014. doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>","short":"H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st ed., Springer Nature, Cham, 2014.","chicago":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. SpringerBriefs in Applied Sciences and Technology. Cham: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>.","ista":"Edelsbrunner H. 2014. A Short Course in Computational Geometry and Topology 1st ed., Cham: Springer Nature, IX, 110p.","mla":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed., Springer Nature, 2014, doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>."},"oa_version":"None","publication_status":"published","abstract":[{"text":"This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields.","lang":"eng"}],"type":"book","edition":"1","place":"Cham","title":"A Short Course in Computational Geometry and Topology","alternative_title":["SpringerBriefs in Applied Sciences and Technology"],"scopus_import":"1","day":"01","month":"01","_id":"6853","department":[{"_id":"HeEd"}],"publication_identifier":{"isbn":["9-783-3190-5956-3"],"eissn":["2191-5318"],"eisbn":["9-783-3190-5957-0"],"issn":["2191-530X"]},"page":"IX, 110","year":"2014","quality_controlled":"1","related_material":{"link":[{"relation":"other","description":"available as eBook via catalog IST BookList","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=356106"},{"description":"available via catalog IST BookList","relation":"other","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=373842"}]},"status":"public","date_created":"2019-09-06T09:22:33Z","date_published":"2014-01-01T00:00:00Z","publisher":"Springer Nature","doi":"10.1007/978-3-319-05957-0","language":[{"iso":"eng"}],"article_processing_charge":"No"},{"author":[{"last_name":"Huszár","full_name":"Huszár, Kristóf","first_name":"Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rolinek","full_name":"Rolinek, Michal"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"draft","oa_version":"Published Version","date_updated":"2025-06-26T12:38:53Z","citation":{"mla":"Huszár, Kristóf, and Michal Rolinek. <i>Playful Math - An Introduction to Mathematical Games</i>. IST Austria.","chicago":"Huszár, Kristóf, and Michal Rolinek. <i>Playful Math - An Introduction to Mathematical Games</i>. IST Austria, n.d.","ista":"Huszár K, Rolinek M. Playful Math - An introduction to mathematical games, IST Austria, 5p.","short":"K. Huszár, M. Rolinek, Playful Math - An Introduction to Mathematical Games, IST Austria, n.d.","ama":"Huszár K, Rolinek M. <i>Playful Math - An Introduction to Mathematical Games</i>. IST Austria","apa":"Huszár, K., &#38; Rolinek, M. (n.d.). <i>Playful Math - An introduction to mathematical games</i>. IST Austria.","ieee":"K. Huszár and M. Rolinek, <i>Playful Math - An introduction to mathematical games</i>. IST Austria."},"type":"working_paper","corr_author":"1","title":"Playful Math - An introduction to mathematical games","ddc":["510"],"month":"06","day":"30","has_accepted_license":"1","_id":"7038","department":[{"_id":"VlKo"},{"_id":"UlWa"}],"page":"5","year":"2014","file":[{"date_created":"2019-11-18T15:57:51Z","creator":"dernst","relation":"main_file","file_name":"2014_Playful_Math_Huszar.pdf","access_level":"open_access","checksum":"2b94e5e1f4c3fe8ab89b12806276fb09","file_id":"7039","file_size":511233,"content_type":"application/pdf","date_updated":"2020-07-14T12:47:48Z"}],"date_created":"2019-11-18T15:57:05Z","oa":1,"file_date_updated":"2020-07-14T12:47:48Z","status":"public","language":[{"iso":"eng"}],"publisher":"IST Austria","date_published":"2014-06-30T00:00:00Z","article_processing_charge":"No"},{"_id":"9888","department":[{"_id":"SyCr"}],"title":"Supporting information","day":"06","month":"08","oa_version":"Published Version","citation":{"ista":"Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. Supporting information, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>.","mla":"Wolf, Stephan, et al. <i>Supporting Information</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>.","chicago":"Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “Supporting Information.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">https://doi.org/10.1371/journal.pone.0103989.s003</a>.","short":"S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, (2014).","ieee":"S. Wolf <i>et al.</i>, “Supporting information.” Public Library of Science, 2014.","ama":"Wolf S, Mcmahon D, Lim K, et al. Supporting information. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>","apa":"Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., &#38; Osborne, J. (2014). Supporting information. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">https://doi.org/10.1371/journal.pone.0103989.s003</a>"},"date_updated":"2025-09-29T11:45:40Z","abstract":[{"lang":"eng","text":"Detailed description of the experimental prodedures, data analyses and additional statistical analyses of the results."}],"type":"research_data_reference","author":[{"first_name":"Stephan","last_name":"Wolf","full_name":"Wolf, Stephan"},{"last_name":"Mcmahon","full_name":"Mcmahon, Dino","first_name":"Dino"},{"first_name":"Ka","full_name":"Lim, Ka","last_name":"Lim"},{"last_name":"Pull","full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","orcid":"0000-0003-1122-3982"},{"first_name":"Suzanne","full_name":"Clark, Suzanne","last_name":"Clark"},{"first_name":"Robert","full_name":"Paxton, Robert","last_name":"Paxton"},{"first_name":"Juliet","full_name":"Osborne, Juliet","last_name":"Osborne"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","date_created":"2021-08-11T14:17:53Z","status":"public","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0103989.s003","year":"2014","related_material":{"record":[{"relation":"used_in_publication","id":"2086","status":"public"}]}},{"article_type":"original","date_published":"2014-06-03T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Wiley","doi":"10.1111/evo.12373","issue":"6","quality_controlled":"1","year":"2014","page":"1775-1791","external_id":{"pmid":["24495000"],"isi":["000337558900019"]},"_id":"9931","pmid":1,"scopus_import":"1","month":"06","volume":68,"type":"journal_article","publication_status":"published","citation":{"apa":"Dhar, R., Bergmiller, T., &#38; Wagner, A. (2014). Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12373\">https://doi.org/10.1111/evo.12373</a>","ama":"Dhar R, Bergmiller T, Wagner A. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. <i>Evolution</i>. 2014;68(6):1775-1791. doi:<a href=\"https://doi.org/10.1111/evo.12373\">10.1111/evo.12373</a>","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes,” <i>Evolution</i>, vol. 68, no. 6. Wiley, pp. 1775–1791, 2014.","mla":"Dhar, Riddhiman, et al. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” <i>Evolution</i>, vol. 68, no. 6, Wiley, 2014, pp. 1775–91, doi:<a href=\"https://doi.org/10.1111/evo.12373\">10.1111/evo.12373</a>.","ista":"Dhar R, Bergmiller T, Wagner A. 2014. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution. 68(6), 1775–1791.","chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” <i>Evolution</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/evo.12373\">https://doi.org/10.1111/evo.12373</a>.","short":"R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 1775–1791."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","acknowledgement":"We thank the Functional Genomics Center Zurich for its service in generating sequencing data, M. Ackermann and E. Hayden for helpful discussions, A. de Visser for comments on earlier versions of this manuscript, and M. Moser for help with quantitative PCR. This work was supported by Swiss National Science Foundation (grant 315230–129708), as well as through the YeastX project of SystemsX.ch, and the University Priority Research Program in Systems Biology at the University of Zurich. RD acknowledges support from the Forschungskredit program of the University of Zurich. The authors declare no conflict of interest.","date_created":"2021-08-17T09:03:09Z","status":"public","related_material":{"record":[{"relation":"research_data","id":"9932","status":"public"}]},"publication":"Evolution","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"department":[{"_id":"CaGu"}],"isi":1,"day":"03","title":"Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","abstract":[{"lang":"eng","text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, subfunctionalization, and neofunctionalization. Little experimental data exist on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region."}],"oa_version":"None","date_updated":"2025-09-29T13:20:48Z","intvolume":"        68","author":[{"first_name":"Riddhiman","last_name":"Dhar","full_name":"Dhar, Riddhiman"},{"full_name":"Bergmiller, Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"full_name":"Wagner, Andreas","last_name":"Wagner","first_name":"Andreas"}]},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Dhar, Riddhiman","last_name":"Dhar","first_name":"Riddhiman"},{"full_name":"Bergmiller, Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"full_name":"Wagner, Andreas","last_name":"Wagner","first_name":"Andreas"}],"type":"research_data_reference","abstract":[{"lang":"eng","text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region."}],"date_updated":"2025-09-29T13:20:47Z","citation":{"short":"R. Dhar, T. Bergmiller, A. Wagner, (2014).","chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.jc402\">https://doi.org/10.5061/dryad.jc402</a>.","ista":"Dhar R, Bergmiller T, Wagner A. 2014. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes, Dryad, <a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>.","mla":"Dhar, Riddhiman, et al. <i>Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>.","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.” Dryad, 2014.","ama":"Dhar R, Bergmiller T, Wagner A. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>","apa":"Dhar, R., Bergmiller, T., &#38; Wagner, A. (2014). Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Dryad. <a href=\"https://doi.org/10.5061/dryad.jc402\">https://doi.org/10.5061/dryad.jc402</a>"},"oa_version":"Published Version","day":"27","month":"01","title":"Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","department":[{"_id":"CaGu"}],"_id":"9932","related_material":{"record":[{"status":"public","id":"9931","relation":"used_in_publication"}]},"year":"2014","publisher":"Dryad","doi":"10.5061/dryad.jc402","date_published":"2014-01-27T00:00:00Z","oa":1,"status":"public","main_file_link":[{"url":"https://doi.org/10.5061/dryad.jc402","open_access":"1"}],"date_created":"2021-08-17T09:11:40Z","article_processing_charge":"No"},{"author":[{"full_name":"Stroeymeyt, Nathalie","last_name":"Stroeymeyt","first_name":"Nathalie"},{"first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez"},{"orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"oa_version":"None","intvolume":"         5","date_updated":"2026-07-01T22:31:12Z","abstract":[{"lang":"eng","text":"Selection for disease control is believed to have contributed to shape the organisation of insect societies — leading to interaction patterns that mitigate disease transmission risk within colonies, conferring them ‘organisational immunity’. Recent studies combining epidemiological models with social network analysis have identified general properties of interaction networks that may hinder propagation of infection within groups. These can be prophylactic and/or induced upon pathogen exposure. Here we review empirical evidence for these two types of organisational immunity in social insects and describe the individual-level behaviours that underlie it. We highlight areas requiring further investigation, and emphasise the need for tighter links between theory and empirical research and between individual-level and collective-level analyses."}],"title":"Organisational immunity in social insects","day":"01","isi":1,"department":[{"_id":"SyCr"}],"project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"6383"},{"status":"public","id":"6435","relation":"dissertation_contains"}]},"publication":"Current Opinion in Insect Science","date_created":"2018-12-11T11:55:08Z","status":"public","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","citation":{"chicago":"Stroeymeyt, Nathalie, Barbara E Casillas Perez, and Sylvia Cremer. “Organisational Immunity in Social Insects.” <i>Current Opinion in Insect Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">https://doi.org/10.1016/j.cois.2014.09.001</a>.","mla":"Stroeymeyt, Nathalie, et al. “Organisational Immunity in Social Insects.” <i>Current Opinion in Insect Science</i>, vol. 5, no. 1, Elsevier, 2014, pp. 1–15, doi:<a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">10.1016/j.cois.2014.09.001</a>.","ista":"Stroeymeyt N, Casillas Perez BE, Cremer S. 2014. Organisational immunity in social insects. Current Opinion in Insect Science. 5(1), 1–15.","short":"N. Stroeymeyt, B.E. Casillas Perez, S. Cremer, Current Opinion in Insect Science 5 (2014) 1–15.","apa":"Stroeymeyt, N., Casillas Perez, B. E., &#38; Cremer, S. (2014). Organisational immunity in social insects. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">https://doi.org/10.1016/j.cois.2014.09.001</a>","ama":"Stroeymeyt N, Casillas Perez BE, Cremer S. Organisational immunity in social insects. <i>Current Opinion in Insect Science</i>. 2014;5(1):1-15. doi:<a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">10.1016/j.cois.2014.09.001</a>","ieee":"N. Stroeymeyt, B. E. Casillas Perez, and S. Cremer, “Organisational immunity in social insects,” <i>Current Opinion in Insect Science</i>, vol. 5, no. 1. Elsevier, pp. 1–15, 2014."},"type":"journal_article","volume":5,"corr_author":"1","publist_id":"5080","scopus_import":"1","month":"11","_id":"1999","external_id":{"isi":["000209578900002"]},"page":"1 - 15","quality_controlled":"1","year":"2014","publisher":"Elsevier","doi":"10.1016/j.cois.2014.09.001","language":[{"iso":"eng"}],"date_published":"2014-11-01T00:00:00Z","issue":"1"},{"date_created":"2022-03-21T07:13:49Z","file_date_updated":"2022-03-21T12:12:56Z","status":"public","article_processing_charge":"No","publication_identifier":{"issn":["2223-7747"]},"publication":"Plants","title":"Calcium: The missing link in auxin action","ddc":["580"],"day":"21","has_accepted_license":"1","department":[{"_id":"JiFr"}],"author":[{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"}],"oa_version":"Published Version","intvolume":"         2","date_updated":"2024-10-09T21:01:52Z","abstract":[{"lang":"eng","text":"Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. "}],"file":[{"file_id":"10916","checksum":"fb4ff2e820e344e253c9197544610be6","access_level":"open_access","file_name":"2013_Plants_Vanneste.pdf","date_updated":"2022-03-21T12:12:56Z","content_type":"application/pdf","file_size":670188,"date_created":"2022-03-21T12:12:56Z","creator":"dernst","relation":"main_file","success":1}],"oa":1,"date_published":"2013-10-21T00:00:00Z","publisher":"MDPI","language":[{"iso":"eng"}],"doi":"10.3390/plants2040650","issue":"4","article_type":"original","keyword":["Plant Science","Ecology","Ecology","Evolution","Behavior and Systematics"],"external_id":{"pmid":["27137397"]},"page":"650-675","quality_controlled":"1","year":"2013","pmid":1,"scopus_import":"1","month":"10","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"_id":"10895","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","citation":{"ama":"Vanneste S, Friml J. Calcium: The missing link in auxin action. <i>Plants</i>. 2013;2(4):650-675. doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>","apa":"Vanneste, S., &#38; Friml, J. (2013). Calcium: The missing link in auxin action. <i>Plants</i>. MDPI. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>","ieee":"S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” <i>Plants</i>, vol. 2, no. 4. MDPI, pp. 650–675, 2013.","chicago":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>. MDPI, 2013. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>.","mla":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>.","ista":"Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675.","short":"S. Vanneste, J. Friml, Plants 2 (2013) 650–675."},"corr_author":"1","volume":2,"type":"journal_article"},{"publication_status":"published","citation":{"apa":"Edelsbrunner, H. (2013). Persistent homology in image processing. In <i>Graph-Based Representations in Pattern Recognition</i> (Vol. 7877, pp. 182–183). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>","ama":"Edelsbrunner H. Persistent homology in image processing. In: <i>Graph-Based Representations in Pattern Recognition</i>. Vol 7877. LNCS. Berlin, Heidelberg: Springer Nature; 2013:182-183. doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>","ieee":"H. Edelsbrunner, “Persistent homology in image processing,” in <i>Graph-Based Representations in Pattern Recognition</i>, Vienna, Austria, 2013, vol. 7877, pp. 182–183.","ista":"Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNCS vol. 7877, 182–183.","mla":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” <i>Graph-Based Representations in Pattern Recognition</i>, vol. 7877, Springer Nature, 2013, pp. 182–83, doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>.","chicago":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In <i>Graph-Based Representations in Pattern Recognition</i>, 7877:182–83. LNCS. Berlin, Heidelberg: Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>.","short":"H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition, Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183."},"corr_author":"1","type":"conference","volume":7877,"series_title":"LNCS","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10897","scopus_import":"1","month":"06","quality_controlled":"1","year":"2013","page":"182-183","date_published":"2013-06-01T00:00:00Z","publisher":"Springer Nature","doi":"10.1007/978-3-642-38221-5_19","language":[{"iso":"eng"}],"oa_version":"None","date_updated":"2025-04-15T08:37:54Z","intvolume":"      7877","abstract":[{"lang":"eng","text":"Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing."}],"author":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"department":[{"_id":"HeEd"}],"project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"title":"Persistent homology in image processing","place":"Berlin, Heidelberg","day":"01","publication":"Graph-Based Representations in Pattern Recognition","ec_funded":1,"conference":{"end_date":"2013-05-17","name":"GbRPR: Graph-based Representations in Pattern Recognition","start_date":"2013-05-15","location":"Vienna, Austria"},"publication_identifier":{"issn":["0302-9743"],"eisbn":["9783642382215"],"eissn":["1611-3349"],"isbn":["9783642382208"]},"article_processing_charge":"No","date_created":"2022-03-21T07:30:33Z","status":"public","acknowledgement":"This research is partially supported by the European Science Foundation (ESF) under the Research Network Programme, the European Union under the Toposys Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053."},{"article_processing_charge":"No","date_created":"2022-03-21T07:33:22Z","status":"public","acknowledgement":"This work has been supported by the European Research Council advanced grant on Quantitative Reactive Modeling (QUAREM) and the National Research Network RiSE on Rigorous Systems Engineering (Austrian Science Fund S11402-N23 and S11404-N23).","publication":"Proceedings of the ACM International Conference on Computing Frontiers - CF '13","ec_funded":1,"conference":{"name":"CF: Conference on Computing Frontiers","end_date":"2013-05-16","start_date":"2013-05-14","location":"Ischia, Italy"},"publication_identifier":{"isbn":["978-145032053-5"]},"department":[{"_id":"ToHe"}],"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"}],"title":"Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation","day":"14","article_number":"17","oa_version":"None","date_updated":"2025-05-14T11:23:58Z","abstract":[{"text":"A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered.","lang":"eng"}],"author":[{"last_name":"Haas","full_name":"Haas, Andreas","first_name":"Andreas"},{"first_name":"Michael","full_name":"Lippautz, Michael","last_name":"Lippautz"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Hannes","last_name":"Payer","full_name":"Payer, Hannes"},{"first_name":"Ana","full_name":"Sokolova, Ana","last_name":"Sokolova"},{"first_name":"Christoph M.","last_name":"Kirsch","full_name":"Kirsch, Christoph M."},{"full_name":"Sezgin, Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali"}],"language":[{"iso":"eng"}],"publisher":"ACM","date_published":"2013-05-14T00:00:00Z","doi":"10.1145/2482767.2482789","issue":"5","quality_controlled":"1","year":"2013","_id":"10898","scopus_import":"1","month":"05","publication_status":"published","citation":{"short":"A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch, A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, ACM, 2013.","ista":"Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin A. 2013. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17.","chicago":"Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>.","mla":"Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, no. 5, 17, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>.","ama":"Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In: <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM; 2013. doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>","apa":"Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch, C. M., &#38; Sezgin, A. (2013). Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. Ischia, Italy: ACM. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>","ieee":"A. Haas <i>et al.</i>, “Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation,” in <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, Ischia, Italy, 2013, no. 5."},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"10899","department":[{"_id":"NiBa"}],"title":"Differentiation","day":"01","scopus_import":"1","month":"01","date_updated":"2024-10-09T21:02:37Z","citation":{"short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","ista":"Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.","mla":"Barton, Nicholas H. “Differentiation.” <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–15, doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>.","chicago":"Barton, Nicholas H. “Differentiation.” In <i>Encyclopedia of Biodiversity</i>, 2nd ed., 508–15. Elsevier, 2013. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>.","apa":"Barton, N. H. (2013). Differentiation. In <i>Encyclopedia of Biodiversity</i> (2nd ed., pp. 508–515). Elsevier. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>","ama":"Barton NH. Differentiation. In: <i>Encyclopedia of Biodiversity</i>. 2nd ed. Elsevier; 2013:508-515. doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>","ieee":"N. H. Barton, “Differentiation,” in <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–515."},"oa_version":"None","publication_status":"published","type":"book_chapter","edition":"2","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"article_processing_charge":"No","keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"],"status":"public","date_created":"2022-03-21T07:46:22Z","publisher":"Elsevier","doi":"10.1016/b978-0-12-384719-5.00031-9","date_published":"2013-01-01T00:00:00Z","language":[{"iso":"eng"}],"year":"2013","quality_controlled":"1","publication":"Encyclopedia of Biodiversity","publication_identifier":{"isbn":["978-0-12-384720-1"]},"page":"508-515"},{"publication_identifier":{"isbn":["9781627034258"],"eissn":["1940-6029"],"eisbn":["9781627034265"],"issn":["1064-3745"]},"publication":"Chemokines","acknowledgement":"We would like to thank Alexander Eichner and Ingrid de Vries for discussion and critical reading of the manuscript, and Mary Frank for assistance with the recording of videos and images in Fig. 1. M.S. is supported through funding from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt Foundation for funding.","date_created":"2022-03-21T07:47:41Z","status":"public","article_processing_charge":"No","author":[{"full_name":"Weber, Michele","last_name":"Weber","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt"}],"abstract":[{"lang":"eng","text":"Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays."}],"oa_version":"None","date_updated":"2024-10-09T21:02:37Z","intvolume":"      1013","day":"03","alternative_title":["Methods in Molecular Biology"],"title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","place":"Totowa, NJ","department":[{"_id":"MiSi"}],"page":"215-226","external_id":{"pmid":["23625502"]},"quality_controlled":"1","year":"2013","doi":"10.1007/978-1-62703-426-5_14","date_published":"2013-04-03T00:00:00Z","publisher":"Humana Press","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","series_title":"MIMB","editor":[{"first_name":"Astrid","last_name":"Cardona","full_name":"Cardona, Astrid"},{"full_name":"Ubogu, Eroboghene","last_name":"Ubogu","first_name":"Eroboghene"}],"type":"book_chapter","corr_author":"1","volume":1013,"publication_status":"published","citation":{"ieee":"M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in <i>Chemokines</i>, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.","apa":"Weber, M., &#38; Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona &#38; E. Ubogu (Eds.), <i>Chemokines</i> (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>","ama":"Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. <i>Chemokines</i>. Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>","short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226.","mla":"Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26, doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>.","chicago":"Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ: Humana Press, 2013. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>.","ista":"Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology, vol. 1013, 215–226."},"pmid":1,"month":"04","scopus_import":"1","_id":"10900"}]