[{"month":"10","external_id":{"isi":["000362056300005"]},"publication":"Journal of Theoretical Biology","oa":1,"article_processing_charge":"No","publisher":"Elsevier","corr_author":"1","has_accepted_license":"1","ddc":["570"],"day":"21","volume":383,"abstract":[{"text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ","lang":"eng"}],"scopus_import":"1","project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"fulldoi":"https://doi.org/10.1016/j.jtbi.2015.07.011","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"journal_article","publist_id":"5629","language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","status":"public","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"citation":{"chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” <i>Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>.","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” <i>Journal of Theoretical Biology</i>, vol. 383, Elsevier, 2015, pp. 28–43, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>.","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. <i>Journal of Theoretical Biology</i>. 2015;383:28-43. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>","ieee":"T. Paixao <i>et al.</i>, “Toward a unifying framework for evolutionary processes,” <i>Journal of Theoretical Biology</i>, vol. 383. Elsevier, pp. 28–43, 2015."},"quality_controlled":"1","_id":"1542","tmp":{"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)","short":"CC BY-NC-ND (4.0)"},"date_updated":"2026-07-07T13:12:13Z","intvolume":"       383","date_created":"2018-12-11T11:52:37Z","pubrep_id":"483","date_published":"2015-10-21T00:00:00Z","publication_status":"published","author":[{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","first_name":"Tiago"},{"full_name":"Badkobeh, Golnaz","last_name":"Badkobeh","first_name":"Golnaz"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"first_name":"Doğan","last_name":"Çörüş","full_name":"Çörüş, Doğan"},{"last_name":"Dang","first_name":"Duccuong","full_name":"Dang, Duccuong"},{"full_name":"Friedrich, Tobias","last_name":"Friedrich","first_name":"Tobias"},{"full_name":"Lehre, Per","last_name":"Lehre","first_name":"Per"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"first_name":"Andrew","last_name":"Sutton","full_name":"Sutton, Andrew"},{"full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","access_level":"open_access","file_id":"5244","content_type":"application/pdf","file_size":595307,"date_updated":"2020-07-14T12:45:01Z","checksum":"33b60ecfea60764756a9ee9df5eb65ca","relation":"main_file","date_created":"2018-12-12T10:16:53Z","creator":"system"}],"page":"28 - 43","title":"Toward a unifying framework for evolutionary processes","das_tickbox":"1","isi":1,"file_date_updated":"2020-07-14T12:45:01Z","doi":"10.1016/j.jtbi.2015.07.011"},{"related_material":{"record":[{"relation":"research_data","status":"public","id":"9712"},{"id":"1131","status":"public","relation":"dissertation_contains"}]},"month":"11","oa":1,"article_processing_charge":"No","publication":"PLoS Genetics","external_id":{"isi":["000366179000022"]},"ddc":["576"],"has_accepted_license":"1","publisher":"Public Library of Science","abstract":[{"text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics.","lang":"eng"}],"scopus_import":"1","day":"06","volume":11,"fulldoi":"https://doi.org/10.1371/journal.pgen.1005639","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"year":"2015","license":"https://creativecommons.org/licenses/by/4.0/","issue":"11","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","ec_funded":1,"oa_version":"Published Version","publist_id":"5483","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"citation":{"ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” <i>PLoS Genetics</i>, vol. 11, no. 11. Public Library of Science, 2015.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. 2015;11(11). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>, vol. 11, no. 11, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>."},"status":"public","intvolume":"        11","date_created":"2018-12-11T11:53:21Z","quality_controlled":"1","date_updated":"2026-07-29T11:31:13Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"1666","pubrep_id":"463","author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","last_name":"Tugrul","first_name":"Murat","full_name":"Tugrul, Murat"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"publication_status":"published","file":[{"date_created":"2018-12-12T10:07:58Z","creator":"system","date_updated":"2020-07-14T12:45:10Z","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","relation":"main_file","file_size":2580778,"content_type":"application/pdf","file_id":"4657","access_level":"open_access","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf"}],"date_published":"2015-11-06T00:00:00Z","file_date_updated":"2020-07-14T12:45:10Z","title":"Dynamics of transcription factor binding site evolution","isi":1,"doi":"10.1371/journal.pgen.1005639"},{"month":"04","related_material":{"record":[{"id":"9747","relation":"research_data","status":"public"}]},"article_processing_charge":"No","oa":1,"external_id":{"isi":["000340470600012"]},"publication":"Evolution","has_accepted_license":"1","ddc":["570"],"acknowledgement":"The authors are grateful to the Leverhulme Trust (F/00 215/AW) for funding this work.","corr_author":"1","publisher":"Wiley","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"}],"scopus_import":"1","volume":68,"day":"25","year":"2014","fulldoi":"https://doi.org/10.1111/evo.12440","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"8","article_type":"original","type":"journal_article","oa_version":"Published Version","language":[{"iso":"eng"}],"publist_id":"4954","citation":{"apa":"Lagator, M., Morgan, A., Neve, P., &#38; Colegrave, N. (2014). Role of sex and migration in adaptation to sink environments. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12440\">https://doi.org/10.1111/evo.12440</a>","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Role of Sex and Migration in Adaptation to Sink Environments.” <i>Evolution</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/evo.12440\">https://doi.org/10.1111/evo.12440</a>.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, Evolution 68 (2014) 2296–2305.","ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Role of sex and migration in adaptation to sink environments. Evolution. 68(8), 2296–2305.","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Role of sex and migration in adaptation to sink environments. <i>Evolution</i>. 2014;68(8):2296-2305. doi:<a href=\"https://doi.org/10.1111/evo.12440\">10.1111/evo.12440</a>","mla":"Lagator, Mato, et al. “Role of Sex and Migration in Adaptation to Sink Environments.” <i>Evolution</i>, vol. 68, no. 8, Wiley, 2014, pp. 2296–305, doi:<a href=\"https://doi.org/10.1111/evo.12440\">10.1111/evo.12440</a>.","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Role of sex and migration in adaptation to sink environments,” <i>Evolution</i>, vol. 68, no. 8. Wiley, pp. 2296–2305, 2014."},"department":[{"_id":"CaGu"}],"status":"public","date_created":"2018-12-11T11:55:36Z","intvolume":"        68","_id":"2083","date_updated":"2025-09-29T11:46:47Z","quality_controlled":"1","page":"2296 - 2305","author":[{"full_name":"Lagator, Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"last_name":"Morgan","first_name":"Andrew","full_name":"Morgan, Andrew"},{"full_name":"Neve, Paul","first_name":"Paul","last_name":"Neve"},{"first_name":"Nick","last_name":"Colegrave","full_name":"Colegrave, Nick"}],"publication_status":"published","file":[{"file_name":"2014_Evolution_Lagator.pdf","access_level":"open_access","file_id":"7845","content_type":"application/pdf","file_size":467254,"relation":"main_file","date_updated":"2020-07-14T12:45:28Z","checksum":"8d459b07e4a11bb5fde92d969184fe48","creator":"dernst","date_created":"2020-05-14T16:40:31Z"}],"date_published":"2014-04-25T00:00:00Z","doi":"10.1111/evo.12440","file_date_updated":"2020-07-14T12:45:28Z","isi":1,"title":"Role of sex and migration in adaptation to sink environments"},{"quality_controlled":"1","article_number":"e106247","date_updated":"2025-09-29T13:05:10Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"1894","intvolume":"         9","date_created":"2018-12-11T11:54:35Z","status":"public","department":[{"_id":"CaGu"}],"citation":{"ieee":"A. Grabowska <i>et al.</i>, “Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” <i>PLoS One</i>, vol. 9, no. 9. Public Library of Science, 2014.","mla":"Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” <i>PLoS One</i>, vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0106247\">10.1371/journal.pone.0106247</a>.","ista":"Grabowska A, Wywiał E, Dunin Horkawicz S, Łasica A, Wösten M, Nagy-Staron AA, Godlewska R, Bocian Ostrzycka K, Pieńkowska K, Łaniewski P, Bujnicki J, Van Putten J, Jagusztyn Krynicka E. 2014. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 9(9), e106247.","ama":"Grabowska A, Wywiał E, Dunin Horkawicz S, et al. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. <i>PLoS One</i>. 2014;9(9). doi:<a href=\"https://doi.org/10.1371/journal.pone.0106247\">10.1371/journal.pone.0106247</a>","short":"A. Grabowska, E. Wywiał, S. Dunin Horkawicz, A. Łasica, M. Wösten, A.A. Nagy-Staron, R. Godlewska, K. Bocian Ostrzycka, K. Pieńkowska, P. Łaniewski, J. Bujnicki, J. Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014).","apa":"Grabowska, A., Wywiał, E., Dunin Horkawicz, S., Łasica, A., Wösten, M., Nagy-Staron, A. A., … Jagusztyn Krynicka, E. (2014). Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0106247\">https://doi.org/10.1371/journal.pone.0106247</a>","chicago":"Grabowska, Anna, Ewa Wywiał, Stanislaw Dunin Horkawicz, Anna Łasica, Marc Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” <i>PLoS One</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0106247\">https://doi.org/10.1371/journal.pone.0106247</a>."},"publist_id":"5201","language":[{"iso":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:20Z","isi":1,"title":"Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA","doi":"10.1371/journal.pone.0106247","publication_status":"published","author":[{"last_name":"Grabowska","first_name":"Anna","full_name":"Grabowska, Anna"},{"first_name":"Ewa","last_name":"Wywiał","full_name":"Wywiał, Ewa"},{"first_name":"Stanislaw","last_name":"Dunin Horkawicz","full_name":"Dunin Horkawicz, Stanislaw"},{"full_name":"Łasica, Anna","last_name":"Łasica","first_name":"Anna"},{"full_name":"Wösten, Marc","last_name":"Wösten","first_name":"Marc"},{"full_name":"Nagy-Staron, Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","first_name":"Anna A"},{"full_name":"Godlewska, Renata","first_name":"Renata","last_name":"Godlewska"},{"full_name":"Bocian Ostrzycka, Katarzyna","last_name":"Bocian Ostrzycka","first_name":"Katarzyna"},{"full_name":"Pieńkowska, Katarzyna","first_name":"Katarzyna","last_name":"Pieńkowska"},{"first_name":"Paweł","last_name":"Łaniewski","full_name":"Łaniewski, Paweł"},{"full_name":"Bujnicki, Janusz","first_name":"Janusz","last_name":"Bujnicki"},{"last_name":"Van Putten","first_name":"Jos","full_name":"Van Putten, Jos"},{"first_name":"Elzbieta","last_name":"Jagusztyn Krynicka","full_name":"Jagusztyn Krynicka, Elzbieta"}],"date_published":"2014-09-02T00:00:00Z","file":[{"content_type":"application/pdf","file_size":4248801,"relation":"main_file","date_updated":"2020-07-14T12:45:20Z","checksum":"7d02c3da7f72b82bb5d7932d80c3251f","creator":"system","date_created":"2018-12-12T10:16:19Z","file_name":"IST-2016-438-v1+1_journal.pone.0106247.pdf","access_level":"open_access","file_id":"5205"}],"pubrep_id":"438","day":"02","volume":9,"scopus_import":"1","abstract":[{"lang":"eng","text":"Background: Bacterial Dsb enzymes are involved in the oxidative folding of many proteins, through the formation of disulfide bonds between their cysteine residues. The Dsb protein network has been well characterized in cells of the model microorganism Escherichia coli. To gain insight into the functioning of the Dsb system in epsilon-Proteobacteria, where it plays an important role in the colonization process, we studied two homologs of the main Escherichia coli Dsb oxidase (EcDsbA) that are present in the cells of the enteric pathogen Campylobacter jejuni, the most frequently reported bacterial cause of human enteritis in the world. Methods and Results: Phylogenetic analysis suggests the horizontal transfer of the epsilon-Proteobacterial DsbAs from a common ancestor to gamma-Proteobacteria, which then gave rise to the DsbL lineage. Phenotype and enzymatic assays suggest that the two C. jejuni DsbAs play different roles in bacterial cells and have divergent substrate spectra. CjDsbA1 is essential for the motility and autoagglutination phenotypes, while CjDsbA2 has no impact on those processes. CjDsbA1 plays a critical role in the oxidative folding that ensures the activity of alkaline phosphatase CjPhoX, whereas CjDsbA2 is crucial for the activity of arylsulfotransferase CjAstA, encoded within the dsbA2-dsbB-astA operon. Conclusions: Our results show that CjDsbA1 is the primary thiol-oxidoreductase affecting life processes associated with bacterial spread and host colonization, as well as ensuring the oxidative folding of particular protein substrates. In contrast, CjDsbA2 activity does not affect the same processes and so far its oxidative folding activity has been demonstrated for one substrate, arylsulfotransferase CjAstA. The results suggest the cooperation between CjDsbA2 and CjDsbB. In the case of the CjDsbA1, this cooperation is not exclusive and there is probably another protein to be identified in C. jejuni cells that acts to re-oxidize CjDsbA1. Altogether the data presented here constitute the considerable insight to the Epsilonproteobacterial Dsb systems, which have been poorly understood so far."}],"publisher":"Public Library of Science","has_accepted_license":"1","ddc":["570"],"external_id":{"isi":["000341231500064"]},"publication":"PLoS One","oa":1,"article_processing_charge":"No","month":"09","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"9","fulldoi":"https://doi.org/10.1371/journal.pone.0106247","year":"2014"},{"status":"public","citation":{"short":"I. Milenković, T. Petrov, G. Kovács, Dementia and Geriatric Cognitive Disorders 38 (2014) 375–388.","chicago":"Milenković, Ivan, Tatjana Petrov, and Gábor Kovács. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.” <i>Dementia and Geriatric Cognitive Disorders</i>. Karger Publishers, 2014. <a href=\"https://doi.org/10.1159/000365548\">https://doi.org/10.1159/000365548</a>.","apa":"Milenković, I., Petrov, T., &#38; Kovács, G. (2014). Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. <i>Dementia and Geriatric Cognitive Disorders</i>. Karger Publishers. <a href=\"https://doi.org/10.1159/000365548\">https://doi.org/10.1159/000365548</a>","ieee":"I. Milenković, T. Petrov, and G. Kovács, “Patterns of hippocampal tau pathology differentiate neurodegenerative dementias,” <i>Dementia and Geriatric Cognitive Disorders</i>, vol. 38, no. 5–6. Karger Publishers, pp. 375–388, 2014.","mla":"Milenković, Ivan, et al. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.” <i>Dementia and Geriatric Cognitive Disorders</i>, vol. 38, no. 5–6, Karger Publishers, 2014, pp. 375–88, doi:<a href=\"https://doi.org/10.1159/000365548\">10.1159/000365548</a>.","ista":"Milenković I, Petrov T, Kovács G. 2014. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. 38(5–6), 375–388.","ama":"Milenković I, Petrov T, Kovács G. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. <i>Dementia and Geriatric Cognitive Disorders</i>. 2014;38(5-6):375-388. doi:<a href=\"https://doi.org/10.1159/000365548\">10.1159/000365548</a>"},"main_file_link":[{"url":"https://kops.uni-konstanz.de/bitstream/123456789/42127/1/Milenkovic_2-17ivylo2up0798.pdf","open_access":"1"}],"department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"publist_id":"5181","oa_version":"Published Version","_id":"1913","date_updated":"2026-06-18T18:13:04Z","quality_controlled":"1","date_created":"2018-12-11T11:54:41Z","intvolume":"        38","doi":"10.1159/000365548","isi":1,"title":"Patterns of hippocampal tau pathology differentiate neurodegenerative dementias","page":"375 - 388","publication_status":"published","author":[{"last_name":"Milenković","first_name":"Ivan","full_name":"Milenković, Ivan"},{"first_name":"Tatjana","orcid":"0000-0002-9041-0905","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana"},{"full_name":"Kovács, Gábor","first_name":"Gábor","last_name":"Kovács"}],"pmid":1,"date_published":"2014-11-07T00:00:00Z","external_id":{"isi":["000344049900011"],"pmid":["25195847"]},"publication":"Dementia and Geriatric Cognitive Disorders","article_processing_charge":"No","oa":1,"month":"11","volume":38,"day":"07","abstract":[{"lang":"eng","text":"Deposits of phosphorylated tau protein and convergence of pathology in the hippocampus are the hallmarks of neurodegenerative tauopathies. Thus we aimed to evaluate whether regional and cellular vulnerability patterns in the hippocampus distinguish tauopathies or are influenced by their concomitant presence. Methods: We created a heat map of phospho-tau (AT8) immunoreactivity patterns in 24 hippocampal subregions/layers in individuals with Alzheimer's disease (AD)-related neurofibrillary degeneration (n = 40), Pick's disease (n = 8), progressive supranuclear palsy (n = 7), corticobasal degeneration (n = 6), argyrophilic grain disease (AGD, n = 18), globular glial tauopathy (n = 5), and tau-astrogliopathy of the elderly (n = 10). AT8 immunoreactivity patterns were compared by mathematical analysis. Results: Our study reveals disease-specific hot spots and regional selective vulnerability for these disorders. The pattern of hippocampal AD-related tau pathology is strongly influenced by concomitant AGD. Mathematical analysis reveals that hippocampal involvement in primary tauopathies is distinguishable from early-stage AD-related neurofibrillary degeneration. Conclusion: Our data demonstrate disease-specific AT8 immunoreactivity patterns and hot spots in the hippocampus even in tauopathies, which primarily do not affect the hippocampus. These hot spots can be shifted to other regions by the co-occurrence of tauopathies like AGD. Our observations support the notion that globular glial tauopathies and tau-astrogliopathy of the elderly are distinct entities."}],"scopus_import":"1","publication_identifier":{"issn":["1420-8008"]},"publisher":"Karger Publishers","ddc":["570"],"acknowledgement":"This study was supported by the European Commission’s 7th Framework Programme under GA No. 278486, ‘DEVELAGE’.","issue":"5-6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","fulldoi":"https://doi.org/10.1159/000365548","type":"journal_article","article_type":"original"},{"language":[{"iso":"eng"}],"publist_id":"4990","oa_version":"Submitted Version","status":"public","citation":{"ama":"Ganguly A, Petrov T, Koeppl H. Markov chain aggregation and its applications to combinatorial reaction networks. <i>Journal of Mathematical Biology</i>. 2014;69(3):767-797. doi:<a href=\"https://doi.org/10.1007/s00285-013-0738-7\">10.1007/s00285-013-0738-7</a>","ista":"Ganguly A, Petrov T, Koeppl H. 2014. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 69(3), 767–797.","mla":"Ganguly, Arnab, et al. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” <i>Journal of Mathematical Biology</i>, vol. 69, no. 3, Springer, 2014, pp. 767–97, doi:<a href=\"https://doi.org/10.1007/s00285-013-0738-7\">10.1007/s00285-013-0738-7</a>.","ieee":"A. Ganguly, T. Petrov, and H. Koeppl, “Markov chain aggregation and its applications to combinatorial reaction networks,” <i>Journal of Mathematical Biology</i>, vol. 69, no. 3. Springer, pp. 767–797, 2014.","apa":"Ganguly, A., Petrov, T., &#38; Koeppl, H. (2014). Markov chain aggregation and its applications to combinatorial reaction networks. <i>Journal of Mathematical Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s00285-013-0738-7\">https://doi.org/10.1007/s00285-013-0738-7</a>","chicago":"Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” <i>Journal of Mathematical Biology</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00285-013-0738-7\">https://doi.org/10.1007/s00285-013-0738-7</a>.","short":"A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014) 767–797."},"department":[{"_id":"CaGu"},{"_id":"ToHe"}],"main_file_link":[{"url":"http://arxiv.org/abs/1303.4532","open_access":"1"}],"_id":"2056","date_updated":"2025-09-29T11:50:22Z","quality_controlled":"1","date_created":"2018-12-11T11:55:28Z","intvolume":"        69","page":"767 - 797","date_published":"2014-11-20T00:00:00Z","author":[{"first_name":"Arnab","last_name":"Ganguly","full_name":"Ganguly, Arnab"},{"full_name":"Petrov, Tatjana","last_name":"Petrov","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana"},{"last_name":"Koeppl","first_name":"Heinz","full_name":"Koeppl, Heinz"}],"publication_status":"published","doi":"10.1007/s00285-013-0738-7","isi":1,"title":"Markov chain aggregation and its applications to combinatorial reaction networks","month":"11","publication":"Journal of Mathematical Biology","external_id":{"arxiv":["1303.4532"],"isi":["000340588700008"]},"article_processing_charge":"No","arxiv":1,"oa":1,"publisher":"Springer","acknowledgement":"T. Petrov is supported by SystemsX.ch—the Swiss Inititative for Systems Biology.","volume":69,"day":"20","scopus_import":"1","abstract":[{"lang":"eng","text":"We consider a continuous-time Markov chain (CTMC) whose state space is partitioned into aggregates, and each aggregate is assigned a probability measure. A sufficient condition for defining a CTMC over the aggregates is presented as a variant of weak lumpability, which also characterizes that the measure over the original process can be recovered from that of the aggregated one. We show how the applicability of de-aggregation depends on the initial distribution. The application section is devoted to illustrate how the developed theory aids in reducing CTMC models of biochemical systems particularly in connection to protein-protein interactions. We assume that the model is written by a biologist in form of site-graph-rewrite rules. Site-graph-rewrite rules compactly express that, often, only a local context of a protein (instead of a full molecular species) needs to be in a certain configuration in order to trigger a reaction event. This observation leads to suitable aggregate Markov chains with smaller state spaces, thereby providing sufficient reduction in computational complexity. This is further exemplified in two case studies: simple unbounded polymerization and early EGFR/insulin crosstalk."}],"year":"2014","fulldoi":"https://doi.org/10.1007/s00285-013-0738-7","issue":"3","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article"},{"publisher":"Dryad","date_created":"2021-07-28T15:32:55Z","abstract":[{"lang":"eng","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."}],"day":"17","date_updated":"2025-09-29T11:46:47Z","_id":"9747","oa_version":"Published Version","related_material":{"record":[{"id":"2083","status":"public","relation":"used_in_publication"}]},"month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s42n1"}],"department":[{"_id":"CaGu"}],"oa":1,"article_processing_charge":"No","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.","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>.","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>.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (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>","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>."},"status":"public","author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"full_name":"Morgan, Andrew","first_name":"Andrew","last_name":"Morgan"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"},{"full_name":"Colegrave, Nick","last_name":"Colegrave","first_name":"Nick"}],"date_published":"2014-04-17T00:00:00Z","title":"Data from: Role of sex and migration in adaptation to sink environments","doi":"10.5061/dryad.s42n1","type":"research_data_reference","fulldoi":"https://doi.org/10.5061/dryad.s42n1","year":"2014","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"isi":1,"title":"Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","doi":"10.1111/evo.12373","date_published":"2014-06-03T00:00:00Z","author":[{"first_name":"Riddhiman","last_name":"Dhar","full_name":"Dhar, Riddhiman"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"first_name":"Andreas","last_name":"Wagner","full_name":"Wagner, Andreas"}],"publication_status":"published","pmid":1,"page":"1775-1791","intvolume":"        68","date_created":"2021-08-17T09:03:09Z","quality_controlled":"1","date_updated":"2025-09-29T13:20:48Z","_id":"9931","department":[{"_id":"CaGu"}],"citation":{"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>.","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>","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.","short":"R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 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>.","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>"},"status":"public","oa_version":"None","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","issue":"6","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1111/evo.12373","year":"2014","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"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."}],"scopus_import":"1","day":"03","volume":68,"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.","publisher":"Wiley","article_processing_charge":"No","external_id":{"isi":["000337558900019"],"pmid":["24495000"]},"publication":"Evolution","related_material":{"record":[{"status":"public","relation":"research_data","id":"9932"}]},"month":"06"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2014","fulldoi":"https://doi.org/10.5061/dryad.jc402","type":"research_data_reference","doi":"10.5061/dryad.jc402","title":"Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","date_published":"2014-01-27T00:00:00Z","author":[{"full_name":"Dhar, Riddhiman","last_name":"Dhar","first_name":"Riddhiman"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"first_name":"Andreas","last_name":"Wagner","full_name":"Wagner, Andreas"}],"status":"public","article_processing_charge":"No","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>.","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>","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>","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>."},"oa":1,"department":[{"_id":"CaGu"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.jc402","open_access":"1"}],"month":"01","related_material":{"record":[{"id":"9931","status":"public","relation":"used_in_publication"}]},"oa_version":"Published Version","_id":"9932","date_updated":"2025-09-29T13:20:47Z","day":"27","date_created":"2021-08-17T09:11:40Z","abstract":[{"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.","lang":"eng"}],"publisher":"Dryad"},{"date_published":"2014-09-17T00:00:00Z","author":[{"full_name":"Lagator, Mato","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator"},{"full_name":"Colegrave, Nick","first_name":"Nick","last_name":"Colegrave"},{"last_name":"Neve","first_name":"Paul","full_name":"Neve, Paul"}],"publication_status":"published","isi":1,"title":"Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","doi":"10.1098/rspb.2014.1679","quality_controlled":"1","article_number":"20141679","date_updated":"2026-08-12T06:26:10Z","_id":"2036","intvolume":"       281","date_created":"2018-12-11T11:55:21Z","publist_id":"5019","language":[{"iso":"eng"}],"oa_version":"Submitted Version","status":"public","department":[{"_id":"CaGu"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211454/"}],"citation":{"ieee":"M. Lagator, N. Colegrave, and P. Neve, “Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 281, no. 1794. Royal Society, 2014.","mla":"Lagator, Mato, et al. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 281, no. 1794, 20141679, Royal Society, 2014, doi:<a href=\"https://doi.org/10.1098/rspb.2014.1679\">10.1098/rspb.2014.1679</a>.","ista":"Lagator M, Colegrave N, Neve P. 2014. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20141679.","ama":"Lagator M, Colegrave N, Neve P. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2014;281(1794). doi:<a href=\"https://doi.org/10.1098/rspb.2014.1679\">10.1098/rspb.2014.1679</a>","short":"M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, 2014. <a href=\"https://doi.org/10.1098/rspb.2014.1679\">https://doi.org/10.1098/rspb.2014.1679</a>.","apa":"Lagator, M., Colegrave, N., &#38; Neve, P. (2014). Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rspb.2014.1679\">https://doi.org/10.1098/rspb.2014.1679</a>"},"type":"journal_article","fulldoi":"https://doi.org/10.1098/rspb.2014.1679","year":"2014","issue":"1794","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Royal Society","acknowledgement":"The project was supported by Leverhulme Trust.","day":"17","volume":281,"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. "}],"scopus_import":"1","related_material":{"record":[{"id":"9741","status":"public","relation":"research_data"}]},"month":"09","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","external_id":{"isi":["000341922700009"]},"oa":1,"article_processing_charge":"No"},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2036"}]},"month":"08","oa_version":"Published Version","status":"public","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.85dn7"}],"department":[{"_id":"CaGu"}],"article_processing_charge":"No","citation":{"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>","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>.","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>.","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.","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>.","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>","short":"M. Lagator, N. Colegrave, P. Neve, (2014)."},"publisher":"Dryad","day":"21","_id":"9741","date_updated":"2026-08-12T06:26:09Z","abstract":[{"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.","lang":"eng"}],"date_created":"2021-07-28T08:48:06Z","fulldoi":"https://doi.org/10.5061/dryad.85dn7","year":"2014","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","full_name":"Lagator, Mato"},{"full_name":"Colegrave, Nick","last_name":"Colegrave","first_name":"Nick"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"}],"date_published":"2014-08-21T00:00:00Z","type":"research_data_reference","title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","doi":"10.5061/dryad.85dn7"},{"pubrep_id":"564","doi":"10.1145/2463372.2463568","title":"Can quantitative and population genetics help us understand evolutionary computation?","file_date_updated":"2020-07-14T12:45:45Z","page":"1573 - 1580","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Paixao, Tiago","first_name":"Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","file":[{"file_name":"IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf","access_level":"open_access","file_id":"5159","file_size":475844,"content_type":"application/pdf","checksum":"9d9be9090ce5c20766e0eb076ace5b98","date_updated":"2020-07-14T12:45:45Z","relation":"main_file","date_created":"2018-12-12T10:15:38Z","creator":"system"}],"date_published":"2013-07-01T00:00:00Z","citation":{"short":"N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.","chicago":"Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” In <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, 1573–80. ACM, 2013. <a href=\"https://doi.org/10.1145/2463372.2463568\">https://doi.org/10.1145/2463372.2463568</a>.","apa":"Barton, N. H., &#38; Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i> (pp. 1573–1580). Amsterdam, Netherlands: ACM. <a href=\"https://doi.org/10.1145/2463372.2463568\">https://doi.org/10.1145/2463372.2463568</a>","ieee":"N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i>, Amsterdam, Netherlands, 2013, pp. 1573–1580.","mla":"Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2013, pp. 1573–80, doi:<a href=\"https://doi.org/10.1145/2463372.2463568\">10.1145/2463372.2463568</a>.","ama":"Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2013:1573-1580. doi:<a href=\"https://doi.org/10.1145/2463372.2463568\">10.1145/2463372.2463568</a>","ista":"Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580."},"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"status":"public","oa_version":"Submitted Version","ec_funded":1,"language":[{"iso":"eng"}],"publist_id":"4174","date_created":"2018-12-11T11:59:14Z","date_updated":"2024-10-09T20:55:12Z","_id":"2718","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"fulldoi":"https://doi.org/10.1145/2463372.2463568","conference":{"end_date":"2013-07-10","location":"Amsterdam, Netherlands","name":"GECCO: Genetic and evolutionary computation conference","start_date":"2013-07-06"},"type":"conference","oa":1,"publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","month":"07","abstract":[{"text":"Even though both population and quantitative genetics, and evolutionary computation, deal with the same questions, they have developed largely independently of each other. I review key results from each field, emphasising those that apply independently of the (usually unknown) relation between genotype and phenotype. The infinitesimal model provides a simple framework for predicting the response of complex traits to selection, which in biology has proved remarkably successful. This allows one to choose the schedule of population sizes and selection intensities that will maximise the response to selection, given that the total number of individuals realised, C = ∑t Nt, is constrained. This argument shows that for an additive trait (i.e., determined by the sum of effects of the genes), the optimum population size and the maximum possible response (i.e., the total change in trait mean) are both proportional to √C.","lang":"eng"}],"scopus_import":1,"day":"01","ddc":["570"],"has_accepted_license":"1","publisher":"ACM","corr_author":"1"},{"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"citation":{"ieee":"T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i>, Amsterdam, Netherlands, 2013, pp. 845–852.","mla":"Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2013, pp. 845–52, doi:<a href=\"https://doi.org/10.1145/2463372.2463470\">10.1145/2463372.2463470</a>.","ama":"Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2013:845-852. doi:<a href=\"https://doi.org/10.1145/2463372.2463470\">10.1145/2463372.2463470</a>","ista":"Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852.","short":"T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.","apa":"Paixao, T., &#38; Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i> (pp. 845–852). Amsterdam, Netherlands: ACM. <a href=\"https://doi.org/10.1145/2463372.2463470\">https://doi.org/10.1145/2463372.2463470</a>","chicago":"Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, 845–52. ACM, 2013. <a href=\"https://doi.org/10.1145/2463372.2463470\">https://doi.org/10.1145/2463372.2463470</a>."},"publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","status":"public","ec_funded":1,"oa_version":"None","publist_id":"4173","month":"07","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Prediction of the evolutionary process is a long standing problem both in the theory of evolutionary biology and evolutionary computation (EC). It has long been realized that heritable variation is crucial to both the response to selection and the success of genetic algorithms. However, not all variation contributes in the same way to the response. Quantitative genetics has developed a large body of work trying to estimate and understand how different components of the variance in fitness in the population contribute to the response to selection. We illustrate how to apply some concepts of quantitative genetics to the analysis of genetic algorithms. In particular, we derive estimates for the short term prediction of the response to selection and we use variance decomposition to gain insight on local aspects of the landscape. Finally, we propose a new population based genetic algorithm that uses these methods to improve its operation."}],"date_created":"2018-12-11T11:59:15Z","scopus_import":1,"quality_controlled":"1","day":"01","_id":"2719","date_updated":"2024-10-09T20:55:12Z","corr_author":"1","publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1145/2463372.2463470","project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152"}],"conference":{"start_date":"2013-07-06","end_date":"2013-07-10","name":"GECCO: Genetic and evolutionary computation conference","location":"Amsterdam, Netherlands"},"year":"2013","title":"A variance decomposition approach to the analysis of genetic algorithms","doi":"10.1145/2463372.2463470","type":"conference","author":[{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao","full_name":"Paixao, Tiago"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"date_published":"2013-07-01T00:00:00Z","publication_status":"published","page":"845 - 852"},{"date_updated":"2025-09-29T14:08:19Z","_id":"2720","quality_controlled":"1","date_created":"2018-12-11T11:59:15Z","intvolume":"       195","language":[{"iso":"eng"}],"publist_id":"4172","oa_version":"Submitted Version","ec_funded":1,"status":"public","citation":{"short":"H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.","chicago":"Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” <i>Genetics</i>. Genetics Society of America, 2013. <a href=\"https://doi.org/10.1534/genetics.113.153536\">https://doi.org/10.1534/genetics.113.153536</a>.","apa":"Long, H., Paixao, T., Azevedo, R., &#38; Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.113.153536\">https://doi.org/10.1534/genetics.113.153536</a>","ieee":"H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” <i>Genetics</i>, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013.","ama":"Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. <i>Genetics</i>. 2013;195(2):527-540. doi:<a href=\"https://doi.org/10.1534/genetics.113.153536\">10.1534/genetics.113.153536</a>","ista":"Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.","mla":"Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” <i>Genetics</i>, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:<a href=\"https://doi.org/10.1534/genetics.113.153536\">10.1534/genetics.113.153536</a>."},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/"}],"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"page":"527-540","date_published":"2013-10-01T00:00:00Z","pmid":1,"author":[{"full_name":"Long, Hongan","last_name":"Long","first_name":"Hongan"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao","full_name":"Paixao, Tiago"},{"full_name":"Azevedo, Ricardo","first_name":"Ricardo","last_name":"Azevedo"},{"full_name":"Zufall, Rebecca","first_name":"Rebecca","last_name":"Zufall"}],"publication_status":"published","doi":"10.1534/genetics.113.153536","isi":1,"title":"Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila","publisher":"Genetics Society of America","volume":195,"day":"01","scopus_import":"1","abstract":[{"text":"Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is &lt;10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.","lang":"eng"}],"month":"10","publication":"Genetics","external_id":{"pmid":["23934880"],"isi":["000325286200020"]},"article_processing_charge":"No","oa":1,"type":"journal_article","year":"2013","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.1534/genetics.113.153536","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"2"},{"fulldoi":"https://doi.org/10.1098/rspb.2012.3035","year":"2013","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"1759","article_type":"original","type":"journal_article","related_material":{"record":[{"id":"9751","status":"public","relation":"research_data"}]},"month":"05","oa":1,"article_processing_charge":"No","external_id":{"isi":["000317482100005"],"pmid":["23516238"]},"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","corr_author":"1","publisher":"The Royal Society","publication_identifier":{"eissn":["1471-2954"]},"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 with 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."}],"scopus_import":"1","day":"22","volume":280,"author":[{"last_name":"Refardt","first_name":"Dominik","full_name":"Refardt, Dominik"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"full_name":"Kümmerli, Rolf","last_name":"Kümmerli","first_name":"Rolf"}],"pmid":1,"publication_status":"published","date_published":"2013-05-22T00:00:00Z","isi":1,"title":"Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection","doi":"10.1098/rspb.2012.3035","oa_version":"Submitted Version","publist_id":"3939","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619501/","open_access":"1"}],"citation":{"apa":"Refardt, D., Bergmiller, T., &#38; Kümmerli, R. (2013). Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2012.3035\">https://doi.org/10.1098/rspb.2012.3035</a>","chicago":"Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society, 2013. <a href=\"https://doi.org/10.1098/rspb.2012.3035\">https://doi.org/10.1098/rspb.2012.3035</a>.","short":"D. Refardt, T. Bergmiller, R. Kümmerli, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","mla":"Refardt, Dominik, et al. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1759, The Royal Society, 2013, doi:<a href=\"https://doi.org/10.1098/rspb.2012.3035\">10.1098/rspb.2012.3035</a>.","ista":"Refardt D, Bergmiller T, Kümmerli R. 2013. Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1759).","ama":"Refardt D, Bergmiller T, Kümmerli R. Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2013;280(1759). doi:<a href=\"https://doi.org/10.1098/rspb.2012.3035\">10.1098/rspb.2012.3035</a>","ieee":"D. Refardt, T. Bergmiller, and R. Kümmerli, “Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1759. The Royal Society, 2013."},"status":"public","intvolume":"       280","date_created":"2018-12-11T11:59:56Z","quality_controlled":"1","date_updated":"2025-09-29T13:41:12Z","_id":"2853"},{"publication_status":"published","date_published":"2013-01-04T00:00:00Z","author":[{"last_name":"Wakamoto","first_name":"Yurichi","full_name":"Wakamoto, Yurichi"},{"full_name":"Dhar, Neraaj","last_name":"Dhar","first_name":"Neraaj"},{"full_name":"Chait, Remy P","first_name":"Remy P","orcid":"0000-0003-0876-3187","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schneider","first_name":"Katrin","full_name":"Schneider, Katrin"},{"full_name":"Signorino Gelo, François","last_name":"Signorino Gelo","first_name":"François"},{"full_name":"Leibler, Stanislas","first_name":"Stanislas","last_name":"Leibler"},{"full_name":"Mckinney, John","first_name":"John","last_name":"Mckinney"}],"page":"91 - 95","isi":1,"title":"Dynamic persistence of antibiotic-stressed mycobacteria","doi":"10.1126/science.1229858","quality_controlled":"1","_id":"499","date_updated":"2025-09-30T07:29:30Z","intvolume":"       339","date_created":"2018-12-11T11:46:48Z","publist_id":"7321","language":[{"iso":"eng"}],"oa_version":"None","status":"public","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"citation":{"short":"Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.","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>.","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>","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.","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>","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."},"type":"journal_article","fulldoi":"https://doi.org/10.1126/science.1229858","year":"2013","issue":"6115","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Association for the Advancement of Science","day":"04","volume":339,"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."}],"scopus_import":"1","month":"01","external_id":{"isi":["000312985800059"]},"publication":"Science","article_processing_charge":"No"},{"doi":"10.5061/dryad.b1q2n","title":"Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection","type":"research_data_reference","author":[{"full_name":"Refardt, Dominik","last_name":"Refardt","first_name":"Dominik"},{"full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kümmerli, Rolf","last_name":"Kümmerli","first_name":"Rolf"}],"date_published":"2013-03-21T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2013","fulldoi":"https://doi.org/10.5061/dryad.b1q2n","date_created":"2021-07-30T08:08:09Z","abstract":[{"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.","lang":"eng"}],"_id":"9751","date_updated":"2025-09-29T13:41:12Z","day":"21","publisher":"Dryad","citation":{"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>.","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>","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>.","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.","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>","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)."},"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.b1q2n","open_access":"1"}],"oa":1,"department":[{"_id":"CaGu"}],"status":"public","oa_version":"Published Version","month":"03","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2853"}]}},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"2","year":"2012","project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"}],"fulldoi":"https://doi.org/10.1109/TCBB.2012.91","type":"journal_article","article_processing_charge":"No","external_id":{"pmid":["22778152"],"isi":["000323504100006"]},"publication":"IEEE ACM Transactions on Computational Biology and Bioinformatics","month":"07","abstract":[{"text":"We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only &quot;significant&quot; mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.","lang":"eng"}],"scopus_import":"1","volume":10,"day":"03","corr_author":"1","publisher":"IEEE","doi":"10.1109/TCBB.2012.91","title":"The propagation approach for computing biochemical reaction networks","isi":1,"page":"310 - 322","pmid":1,"author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"3B43276C-F248-11E8-B48F-1D18A9856A87","last_name":"Mateescu","first_name":"Maria","full_name":"Mateescu, Maria"}],"publication_status":"published","date_published":"2012-07-03T00:00:00Z","citation":{"mla":"Henzinger, Thomas A., and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2, IEEE, 2012, pp. 310–22, doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>.","ista":"Henzinger TA, Mateescu M. 2012. The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. 10(2), 310–322.","ama":"Henzinger TA, Mateescu M. The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. 2012;10(2):310-322. doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>","ieee":"T. A. Henzinger and M. Mateescu, “The propagation approach for computing biochemical reaction networks,” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2. IEEE, pp. 310–322, 2012.","apa":"Henzinger, T. A., &#38; Mateescu, M. (2012). The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>","chicago":"Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE, 2012. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>.","short":"T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology and Bioinformatics 10 (2012) 310–322."},"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"status":"public","oa_version":"None","ec_funded":1,"language":[{"iso":"eng"}],"publist_id":"4625","date_created":"2018-12-11T11:56:52Z","intvolume":"        10","_id":"2302","date_updated":"2025-09-29T14:17:43Z","quality_controlled":"1"},{"volume":86,"day":"09","scopus_import":"1","abstract":[{"lang":"eng","text":"We examine whether the Escherichia coli chromosome is folded into a self-adherent nucleoprotein complex, or alternately is a confined but otherwise unconstrained self-avoiding polymer. We address this through in vivo visualization, using an inducible GFP fusion to the nucleoid-associated protein Fis to non-specifically decorate the entire chromosome. For a range of different growth conditions, the chromosome is a compact structure that does not fill the volume of the cell, and which moves from the new pole to the cell centre. During rapid growth, chromosome segregation occurs well before cell division, with daughter chromosomes coupled by a thin inter-daughter filament before complete segregation, whereas during slow growth chromosomes stay adjacent until cell division occurs. Image correlation analysis indicates that sub-nucleoid structure is stable on a 1min timescale, comparable to the timescale for redistribution time measured for GFP-Fis after photobleaching. Optical deconvolution and writhe calculation analysis indicate that the nucleoid has a large-scale coiled organization rather than being an amorphous mass. Our observations are consistent with the chromosome having a self-adherent filament organization."}],"publisher":"Wiley-Blackwell","acknowledgement":"We thank Professor Philippe Cluzel and Mr Lance Min for providing advice and materials. Jeannette Chau provided technical support. Work at NU was supported by NSF Grants DMR-0715099, MCB-1022117, DMR-1206868, DMR-0520513 and DMR-1121262 (NU-MRSEC), by NIH-NCI Grant U54CA143869-01 (NU-PS-OC) and by the Chicago Biomedical Consortium with support from the Searle Funds at the Chicago Community Trust. Work at UCLA was supported by NIH Grant GM038509.","publication":"Molecular Microbiology","external_id":{"isi":["000312557000005"]},"article_processing_charge":"No","oa":1,"month":"11","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"6","year":"2012","fulldoi":"https://doi.org/10.1111/mmi.12071","_id":"2943","date_updated":"2025-09-30T08:13:13Z","quality_controlled":"1","date_created":"2018-12-11T12:00:28Z","intvolume":"        86","status":"public","citation":{"apa":"Hadizadeh Yazdi, N., Guet, C. C., Johnson, R., &#38; Marko, J. (2012). Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. <i>Molecular Microbiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mmi.12071\">https://doi.org/10.1111/mmi.12071</a>","chicago":"Hadizadeh Yazdi, Nastaran, Calin C Guet, Reid Johnson, and John Marko. “Variation of the Folding and Dynamics of the Escherichia Coli Chromosome with Growth Conditions.” <i>Molecular Microbiology</i>. Wiley-Blackwell, 2012. <a href=\"https://doi.org/10.1111/mmi.12071\">https://doi.org/10.1111/mmi.12071</a>.","short":"N. Hadizadeh Yazdi, C.C. Guet, R. Johnson, J. Marko, Molecular Microbiology 86 (2012) 1318–1333.","mla":"Hadizadeh Yazdi, Nastaran, et al. “Variation of the Folding and Dynamics of the Escherichia Coli Chromosome with Growth Conditions.” <i>Molecular Microbiology</i>, vol. 86, no. 6, Wiley-Blackwell, 2012, pp. 1318–33, doi:<a href=\"https://doi.org/10.1111/mmi.12071\">10.1111/mmi.12071</a>.","ista":"Hadizadeh Yazdi N, Guet CC, Johnson R, Marko J. 2012. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. 86(6), 1318–1333.","ama":"Hadizadeh Yazdi N, Guet CC, Johnson R, Marko J. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. <i>Molecular Microbiology</i>. 2012;86(6):1318-1333. doi:<a href=\"https://doi.org/10.1111/mmi.12071\">10.1111/mmi.12071</a>","ieee":"N. Hadizadeh Yazdi, C. C. Guet, R. Johnson, and J. Marko, “Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions,” <i>Molecular Microbiology</i>, vol. 86, no. 6. Wiley-Blackwell, pp. 1318–1333, 2012."},"department":[{"_id":"CaGu"}],"main_file_link":[{"open_access":"1","url":"http://europepmc.org/articles/pmc3524407"}],"language":[{"iso":"eng"}],"publist_id":"3790","oa_version":"Submitted Version","doi":"10.1111/mmi.12071","title":"Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions","isi":1,"page":"1318 - 1333","date_published":"2012-11-09T00:00:00Z","author":[{"last_name":"Hadizadeh Yazdi","first_name":"Nastaran","full_name":"Hadizadeh Yazdi, Nastaran"},{"full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Reid","first_name":"Reid","last_name":"Johnson"},{"full_name":"Marko, John","last_name":"Marko","first_name":"John"}],"publication_status":"published"},{"department":[{"_id":"CaGu"}],"citation":{"ieee":"T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” <i>PLoS Genetics</i>, vol. 8, no. 6. Public Library of Science, 2012.","mla":"Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” <i>PLoS Genetics</i>, vol. 8, no. 6, e1002803, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002803\">10.1371/journal.pgen.1002803</a>.","ama":"Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation of essential genes correlate with their compensability. <i>PLoS Genetics</i>. 2012;8(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002803\">10.1371/journal.pgen.1002803</a>","ista":"Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803.","short":"T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).","apa":"Bergmiller, T., Ackermann, M., &#38; Silander, O. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002803\">https://doi.org/10.1371/journal.pgen.1002803</a>","chicago":"Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002803\">https://doi.org/10.1371/journal.pgen.1002803</a>."},"status":"public","oa_version":"Published Version","publist_id":"3567","language":[{"iso":"eng"}],"intvolume":"         8","date_created":"2018-12-11T12:01:34Z","quality_controlled":"1","article_number":"e1002803","date_updated":"2025-09-30T07:57:16Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"3130","pubrep_id":"386","file_date_updated":"2020-07-14T12:46:01Z","title":"Patterns of evolutionary conservation of essential genes correlate with their compensability","isi":1,"doi":"10.1371/journal.pgen.1002803","date_published":"2012-06-28T00:00:00Z","file":[{"checksum":"f8506fb579eda6fc5613ba9bf421b86a","date_updated":"2020-07-14T12:46:01Z","relation":"main_file","date_created":"2018-12-12T10:12:52Z","creator":"system","content_type":"application/pdf","file_size":2674138,"access_level":"open_access","file_id":"4973","file_name":"IST-2015-386-v1+1_journal.pgen.1002803.pdf"}],"publication_status":"published","author":[{"full_name":"Bergmiller, Tobias","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","last_name":"Bergmiller"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"},{"last_name":"Silander","first_name":"Olin","full_name":"Silander, Olin"}],"oa":1,"article_processing_charge":"No","external_id":{"isi":["000305961000055"]},"publication":"PLoS Genetics","month":"06","abstract":[{"text":"Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.","lang":"eng"}],"scopus_import":"1","day":"28","volume":8,"acknowledgement":"We thank Alex Boehm for discussions and comments.","has_accepted_license":"1","ddc":["576"],"corr_author":"1","publisher":"Public Library of Science","issue":"6","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1371/journal.pgen.1002803","year":"2012","type":"journal_article"}]