[{"oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","page":"10666 - 10671","date_created":"2018-12-11T11:48:41Z","date_published":"2017-10-03T00:00:00Z","doi":"10.1073/pnas.1713372114","year":"2017","isi":1,"publication":"PNAS","day":"03","project":[{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"}],"external_id":{"pmid":["28923953"],"isi":["000412130500061"]},"article_processing_charge":"No","publist_id":"6827","author":[{"last_name":"De Vos","full_name":"De Vos, Marjon","first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","last_name":"Zagórski","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alan","last_name":"Mcnally","full_name":"Mcnally, Alan"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","citation":{"chicago":"Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1713372114.","ista":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671.","mla":"de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.","ieee":"M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017.","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.","apa":"de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114","ama":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 2017;114(40):10666-10671. doi:10.1073/pnas.1713372114"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/"}],"scopus_import":"1","intvolume":" 114","month":"10","abstract":[{"lang":"eng","text":"Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. "}],"pmid":1,"oa_version":"Submitted Version","ec_funded":1,"volume":114,"issue":"40","publication_status":"published","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"822","department":[{"_id":"ToBo"}],"date_updated":"2023-09-26T16:18:48Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Vos, Marjon de, Alexandre Dawid, Vanda Šunderlíková, and Sander Tans. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510282112.","ista":"de Vos M, Dawid A, Šunderlíková V, Tans S. 2015. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 112(48), 14906–14911.","mla":"de Vos, Marjon, et al. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS, vol. 112, no. 48, National Academy of Sciences, 2015, pp. 14906–11, doi:10.1073/pnas.1510282112.","apa":"de Vos, M., Dawid, A., Šunderlíková, V., & Tans, S. (2015). Breaking evolutionary constraint with a tradeoff ratchet. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510282112","ama":"de Vos M, Dawid A, Šunderlíková V, Tans S. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 2015;112(48):14906-14911. doi:10.1073/pnas.1510282112","ieee":"M. de Vos, A. Dawid, V. Šunderlíková, and S. Tans, “Breaking evolutionary constraint with a tradeoff ratchet,” PNAS, vol. 112, no. 48. National Academy of Sciences, pp. 14906–14911, 2015.","short":"M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911."},"date_updated":"2021-01-12T06:51:40Z","title":"Breaking evolutionary constraint with a tradeoff ratchet","department":[{"_id":"ToBo"}],"publist_id":"5600","author":[{"id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","first_name":"Marjon","full_name":"De Vos, Marjon","last_name":"De Vos"},{"full_name":"Dawid, Alexandre","last_name":"Dawid","first_name":"Alexandre"},{"last_name":"Šunderlíková","full_name":"Šunderlíková, Vanda","first_name":"Vanda"},{"full_name":"Tans, Sander","last_name":"Tans","first_name":"Sander"}],"_id":"1571","status":"public","type":"journal_article","day":"01","publication":"PNAS","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","volume":112,"doi":"10.1073/pnas.1510282112","issue":"48","date_published":"2015-12-01T00:00:00Z","date_created":"2018-12-11T11:52:47Z","page":"14906 - 14911","oa_version":"None","acknowledgement":"This work is part of the research program of the Foundation for Fundamental Research on Matter, which is part of the Netherlands Organization for Scientific Research (NWO). M.G.J.d.V. was (partially) funded by NWO Earth and Life Sciences (ALW), project 863.14.015. We thank D. M. Weinreich, J. A. G. M. de Visser, T. Paixão, J. Polechová, T. Friedlander, and A. E. Mayo for reading and commenting on earlier versions of the manuscript and B. Houchmandzadeh, O. Rivoire, and M. Hemery for discussions and suggestions on the Markov computation. Furthermore, we thank F. J. Poelwijk for sharing plasmid pCascade5 and pRD007 and Y. Yokobayashi for sharing plasmid pINV-110. We also thank the anonymous reviewers for remarks on the initial version of the manuscript.","abstract":[{"lang":"eng","text":"Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype-environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor-operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that crossenvironmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance."}],"month":"12","intvolume":" 112","scopus_import":1,"quality_controlled":"1","publisher":"National Academy of Sciences"},{"oa":1,"quality_controlled":"1","publisher":"Cell Press","date_created":"2018-12-11T11:56:24Z","date_published":"2014-04-24T00:00:00Z","doi":"10.1016/j.chembiol.2014.04.004","page":"439 - 440","publication":"Chemistry and Biology","day":"24","year":"2014","title":"Suppressive drug interactions between antifungals","external_id":{"pmid":["24766845"]},"author":[{"id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","first_name":"Marjon","last_name":"De Vos","full_name":"De Vos, Marjon"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"publist_id":"4747","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"de Vos, M., & Bollenbach, M. T. (2014). Suppressive drug interactions between antifungals. Chemistry and Biology. Cell Press. https://doi.org/10.1016/j.chembiol.2014.04.004","ama":"de Vos M, Bollenbach MT. Suppressive drug interactions between antifungals. Chemistry and Biology. 2014;21(4):439-440. doi:10.1016/j.chembiol.2014.04.004","short":"M. de Vos, M.T. Bollenbach, Chemistry and Biology 21 (2014) 439–440.","ieee":"M. de Vos and M. T. Bollenbach, “Suppressive drug interactions between antifungals,” Chemistry and Biology, vol. 21, no. 4. Cell Press, pp. 439–440, 2014.","mla":"de Vos, Marjon, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” Chemistry and Biology, vol. 21, no. 4, Cell Press, 2014, pp. 439–40, doi:10.1016/j.chembiol.2014.04.004.","ista":"de Vos M, Bollenbach MT. 2014. Suppressive drug interactions between antifungals. Chemistry and Biology. 21(4), 439–440.","chicago":"Vos, Marjon de, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” Chemistry and Biology. Cell Press, 2014. https://doi.org/10.1016/j.chembiol.2014.04.004."},"intvolume":" 21","month":"04","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/24766845"}],"scopus_import":1,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this issue of Chemistry & Biology, Cokol and colleagues report a systematic study of drug interactions between antifungal compounds. Suppressive drug interactions occur more frequently than previously realized and come in different flavors with interesting implications."}],"issue":"4","volume":21,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["10745521"]},"status":"public","type":"journal_article","_id":"2220","department":[{"_id":"ToBo"}],"date_updated":"2021-01-12T06:56:06Z"},{"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"412","_id":"2810","department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:45:48Z","date_updated":"2021-01-12T06:59:52Z","ddc":["570"],"scopus_import":1,"month":"06","intvolume":" 9","abstract":[{"lang":"eng","text":"The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data."}],"oa_version":"Published Version","volume":9,"issue":"6","license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","file":[{"checksum":"7a4736dd80496d29ff6908b6f2329b4e","file_id":"4713","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-412-v1+1_journal.pgen.1003580.pdf","date_created":"2018-12-12T10:08:51Z","creator":"system","file_size":474655,"date_updated":"2020-07-14T12:45:48Z"}],"language":[{"iso":"eng"}],"article_number":"e1003580","publist_id":"4075","author":[{"id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","first_name":"Marjon","full_name":"De Vos, Marjon","last_name":"De Vos"},{"full_name":"Poelwijk, Frank","last_name":"Poelwijk","first_name":"Frank"},{"full_name":"Battich, Nico","last_name":"Battich","first_name":"Nico"},{"first_name":"Joseph","last_name":"Ndika","full_name":"Ndika, Joseph"},{"first_name":"Sander","full_name":"Tans, Sander","last_name":"Tans"}],"title":"Environmental dependence of genetic constraint","citation":{"chicago":"Vos, Marjon de, Frank Poelwijk, Nico Battich, Joseph Ndika, and Sander Tans. “Environmental Dependence of Genetic Constraint.” PLoS Genetics. Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003580.","ista":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. 2013. Environmental dependence of genetic constraint. PLoS Genetics. 9(6), e1003580.","mla":"de Vos, Marjon, et al. “Environmental Dependence of Genetic Constraint.” PLoS Genetics, vol. 9, no. 6, e1003580, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003580.","ieee":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, and S. Tans, “Environmental dependence of genetic constraint,” PLoS Genetics, vol. 9, no. 6. Public Library of Science, 2013.","short":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, S. Tans, PLoS Genetics 9 (2013).","ama":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. Environmental dependence of genetic constraint. PLoS Genetics. 2013;9(6). doi:10.1371/journal.pgen.1003580","apa":"de Vos, M., Poelwijk, F., Battich, N., Ndika, J., & Tans, S. (2013). Environmental dependence of genetic constraint. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1003580"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"date_published":"2013-06-27T00:00:00Z","doi":"10.1371/journal.pgen.1003580","date_created":"2018-12-11T11:59:43Z","has_accepted_license":"1","year":"2013","day":"27","publication":"PLoS Genetics"}]