[{"isi":1,"external_id":{"isi":["000428239300010"]},"date_updated":"2023-09-11T14:11:35Z","year":"2018","citation":{"ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” <i>Algorithmica</i>, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” <i>Algorithmica</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00453-017-0369-2\">https://doi.org/10.1007/s00453-017-0369-2</a>.","ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. <i>Algorithmica</i>. 2018;80(5):1604-1633. doi:<a href=\"https://doi.org/10.1007/s00453-017-0369-2\">10.1007/s00453-017-0369-2</a>","apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-017-0369-2\">https://doi.org/10.1007/s00453-017-0369-2</a>","ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” <i>Algorithmica</i>, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:<a href=\"https://doi.org/10.1007/s00453-017-0369-2\">10.1007/s00453-017-0369-2</a>.","short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633."},"abstract":[{"text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys.","lang":"eng"}],"doi":"10.1007/s00453-017-0369-2","day":"01","ddc":["576"],"volume":80,"author":[{"last_name":"Oliveto","first_name":"Pietro","full_name":"Oliveto, Pietro"},{"last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pérez Heredia","first_name":"Jorge","full_name":"Pérez Heredia, Jorge"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova","first_name":"Barbora"}],"issue":"5","_id":"723","scopus_import":"1","title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","pubrep_id":"1014","intvolume":"        80","publication_status":"published","date_created":"2018-12-11T11:48:09Z","article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:54Z","page":"1604 - 1633","ec_funded":1,"quality_controlled":"1","publisher":"Springer","date_published":"2018-05-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publist_id":"6957","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","file":[{"date_created":"2018-12-12T10:08:14Z","file_size":691245,"checksum":"7d92f5d7be81e387edeec4f06442791c","date_updated":"2020-07-14T12:47:54Z","content_type":"application/pdf","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","relation":"main_file","access_level":"open_access","file_id":"4674","creator":"system"}],"publication":"Algorithmica","has_accepted_license":"1","month":"05","oa_version":"Published Version","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}]},{"publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_created":"2018-12-11T11:46:35Z","article_processing_charge":"No","title":"Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity","intvolume":"         2","_id":"457","scopus_import":"1","author":[{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","first_name":"Maros","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479"},{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz","last_name":"Lang","first_name":"Moritz"},{"last_name":"Refardt","first_name":"Dominik","full_name":"Refardt, Dominik"},{"full_name":"Levin, Bruce","last_name":"Levin","first_name":"Bruce"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"issue":"2","publisher":"Springer Nature","page":"359 - 366","quality_controlled":"1","ec_funded":1,"doi":"10.1038/s41559-017-0424-z","day":"01","abstract":[{"lang":"eng","text":"Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages"}],"date_updated":"2023-09-15T12:04:57Z","citation":{"ama":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. <i>Nature Ecology and Evolution</i>. 2018;2(2):359-366. doi:<a href=\"https://doi.org/10.1038/s41559-017-0424-z\">10.1038/s41559-017-0424-z</a>","apa":"Pleska, M., Lang, M., Refardt, D., Levin, B., &#38; Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. <i>Nature Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-017-0424-z\">https://doi.org/10.1038/s41559-017-0424-z</a>","ieee":"M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” <i>Nature Ecology and Evolution</i>, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018.","chicago":"Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” <i>Nature Ecology and Evolution</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41559-017-0424-z\">https://doi.org/10.1038/s41559-017-0424-z</a>.","short":"M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.","mla":"Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” <i>Nature Ecology and Evolution</i>, vol. 2, no. 2, Springer Nature, 2018, pp. 359–66, doi:<a href=\"https://doi.org/10.1038/s41559-017-0424-z\">10.1038/s41559-017-0424-z</a>.","ista":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2(2), 359–366."},"year":"2018","isi":1,"external_id":{"isi":["000426516400027"]},"volume":2,"oa_version":"None","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"251BCBEC-B435-11E9-9278-68D0E5697425","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","grant_number":"RGY0079/2011"},{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"month":"02","publication":"Nature Ecology and Evolution","language":[{"iso":"eng"}],"publist_id":"7364","date_published":"2018-02-01T00:00:00Z","type":"journal_article","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"202"}]},"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication":"Journal of Biotechnology","acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"None","month":"02","language":[{"iso":"eng"}],"date_published":"2018-02-20T00:00:00Z","type":"journal_article","publist_id":"7317","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"503","scopus_import":"1","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C"}],"publication_status":"published","department":[{"_id":"CaGu"}],"article_processing_charge":"No","date_created":"2018-12-11T11:46:50Z","title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","intvolume":"       268","page":"40 - 52","quality_controlled":"1","publisher":"Elsevier","date_updated":"2023-09-13T08:24:51Z","citation":{"ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” <i>Journal of Biotechnology</i>, vol. 268. Elsevier, pp. 40–52, 2018.","chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>.","apa":"Tomasek, K., Bergmiller, T., &#38; Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. 2018;268:40-52. doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>","ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>, vol. 268, Elsevier, 2018, pp. 40–52, doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>."},"year":"2018","isi":1,"external_id":{"isi":["000425715100006"]},"doi":"10.1016/j.jbiotec.2018.01.008","day":"20","abstract":[{"text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry.","lang":"eng"}],"volume":268,"acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n"},{"article_processing_charge":"No","date_created":"2018-12-12T12:31:35Z","department":[{"_id":"CaGu"}],"oa_version":"Published Version","title":"Time-lapse microscopy data","month":"02","has_accepted_license":"1","license":"https://creativecommons.org/publicdomain/zero/1.0/","_id":"5569","datarep_id":"74","author":[{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller"},{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090"}],"publisher":"Institute of Science and Technology Austria","keyword":["microscopy","microfluidics"],"file_date_updated":"2020-07-14T12:47:04Z","day":"07","doi":"10.15479/AT:ISTA:74","publist_id":"7385","oa":1,"abstract":[{"lang":"eng","text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic."}],"year":"2018","citation":{"ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>.","short":"T. Bergmiller, N. Nikolic, (2018).","mla":"Bergmiller, Tobias, and Nela Nikolic. <i>Time-Lapse Microscopy Data</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>.","chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:74\">https://doi.org/10.15479/AT:ISTA:74</a>.","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","apa":"Bergmiller, T., &#38; Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:74\">https://doi.org/10.15479/AT:ISTA:74</a>","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>"},"date_updated":"2024-02-21T13:44:45Z","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"type":"research_data","date_published":"2018-02-07T00:00:00Z","file":[{"file_id":"5637","creator":"system","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:04Z","content_type":"application/zip","file_name":"IST-2018-74-v1+2_15-11-05.zip","date_created":"2018-12-12T13:04:39Z","file_size":3558703796,"checksum":"61ebb92213cfffeba3ddbaff984b81af"},{"file_name":"IST-2018-74-v1+3_15-07-31.zip","content_type":"application/zip","date_updated":"2020-07-14T12:47:04Z","checksum":"bf26649af310ef6892d68576515cde6d","file_size":1830422606,"date_created":"2018-12-12T13:04:55Z","creator":"system","file_id":"5638","access_level":"open_access","relation":"main_file"},{"relation":"main_file","access_level":"open_access","file_id":"5639","creator":"system","date_created":"2018-12-12T13:05:11Z","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","file_size":2140849248,"date_updated":"2020-07-14T12:47:04Z","content_type":"application/zip","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip"}],"ddc":["579"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"record":[{"id":"438","relation":"research_paper","status":"public"}]}},{"oa_version":"Published Version","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"article_processing_charge":"No","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_created":"2018-12-12T12:31:40Z","month":"07","title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","_id":"5585","has_accepted_license":"1","author":[{"full_name":"Igler, Claudia","first_name":"Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato","full_name":"Lagator, Mato"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"datarep_id":"108","publisher":"Institute of Science and Technology Austria","ec_funded":1,"file_date_updated":"2020-07-14T12:47:07Z","doi":"10.15479/AT:ISTA:108","day":"20","abstract":[{"text":"Mean repression values and standard error of the mean are given for all operator mutant libraries.","lang":"eng"}],"oa":1,"date_updated":"2024-03-25T23:30:27Z","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"citation":{"apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., &#38; Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:108\">https://doi.org/10.15479/AT:ISTA:108</a>","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:108\">https://doi.org/10.15479/AT:ISTA:108</a>.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","mla":"Igler, Claudia, et al. <i>Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>.","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>."},"year":"2018","date_published":"2018-07-20T00:00:00Z","type":"research_data","file":[{"creator":"system","file_id":"5611","access_level":"open_access","relation":"main_file","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_name":"IST-2018-108-v1+1_data_figures.xlsx","date_updated":"2020-07-14T12:47:07Z","checksum":"1435781526c77413802adee0d4583cce","file_size":16507,"date_created":"2018-12-12T13:02:45Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"67"},{"id":"6371","relation":"research_paper","status":"public"}]},"status":"public"},{"date_updated":"2023-09-19T14:29:32Z","year":"2018","citation":{"short":"M. Morri, I. Sanchez-Romero, A.-M. Tichy, S. Kainrath, E.J. Gerrard, P. Hirschfeld, J. Schwarz, H.L. Janovjak, Nature Communications 9 (2018).","mla":"Morri, Maurizio, et al. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.” <i>Nature Communications</i>, vol. 9, no. 1, 1950, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-04342-1\">10.1038/s41467-018-04342-1</a>.","ista":"Morri M, Sanchez-Romero I, Tichy A-M, Kainrath S, Gerrard EJ, Hirschfeld P, Schwarz J, Janovjak HL. 2018. Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. 9(1), 1950.","ama":"Morri M, Sanchez-Romero I, Tichy A-M, et al. Optical functionalization of human class A orphan G-protein-coupled receptors. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-04342-1\">10.1038/s41467-018-04342-1</a>","apa":"Morri, M., Sanchez-Romero, I., Tichy, A.-M., Kainrath, S., Gerrard, E. J., Hirschfeld, P., … Janovjak, H. L. (2018). Optical functionalization of human class A orphan G-protein-coupled receptors. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-04342-1\">https://doi.org/10.1038/s41467-018-04342-1</a>","ieee":"M. Morri <i>et al.</i>, “Optical functionalization of human class A orphan G-protein-coupled receptors,” <i>Nature Communications</i>, vol. 9, no. 1. Springer Nature, 2018.","chicago":"Morri, Maurizio, Inmaculada Sanchez-Romero, Alexandra-Madelaine Tichy, Stephanie Kainrath, Elliot J. Gerrard, Priscila Hirschfeld, Jan Schwarz, and Harald L Janovjak. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-04342-1\">https://doi.org/10.1038/s41467-018-04342-1</a>."},"isi":1,"external_id":{"isi":["000432280000006"]},"doi":"10.1038/s41467-018-04342-1","day":"01","abstract":[{"text":"G-protein-coupled receptors (GPCRs) form the largest receptor family, relay environmental stimuli to changes in cell behavior and represent prime drug targets. Many GPCRs are classified as orphan receptors because of the limited knowledge on their ligands and coupling to cellular signaling machineries. Here, we engineer a library of 63 chimeric receptors that contain the signaling domains of human orphan and understudied GPCRs functionally linked to the light-sensing domain of rhodopsin. Upon stimulation with visible light, we identify activation of canonical cell signaling pathways, including cAMP-, Ca2+-, MAPK/ERK-, and Rho-dependent pathways, downstream of the engineered receptors. For the human pseudogene GPR33, we resurrect a signaling function that supports its hypothesized role as a pathogen entry site. These results demonstrate that substituting unknown chemical activators with a light switch can reveal information about protein function and provide an optically controlled protein library for exploring the physiology and therapeutic potential of understudied GPCRs.","lang":"eng"}],"volume":9,"ddc":["570"],"_id":"5984","scopus_import":"1","author":[{"last_name":"Morri","first_name":"Maurizio","full_name":"Morri, Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inmaculada","last_name":"Sanchez-Romero","full_name":"Sanchez-Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tichy, Alexandra-Madelaine","last_name":"Tichy","first_name":"Alexandra-Madelaine"},{"id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","first_name":"Stephanie","full_name":"Kainrath, Stephanie"},{"last_name":"Gerrard","first_name":"Elliot J.","full_name":"Gerrard, Elliot J."},{"id":"435ACB3A-F248-11E8-B48F-1D18A9856A87","last_name":"Hirschfeld","first_name":"Priscila","full_name":"Hirschfeld, Priscila"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","last_name":"Schwarz","first_name":"Jan"},{"last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"issue":"1","publication_status":"published","date_created":"2019-02-14T10:50:24Z","article_processing_charge":"No","department":[{"_id":"HaJa"},{"_id":"CaGu"},{"_id":"MiSi"}],"title":"Optical functionalization of human class A orphan G-protein-coupled receptors","intvolume":"         9","ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:14Z","publisher":"Springer Nature","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2018-12-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["2041-1723"]},"oa":1,"file":[{"date_updated":"2020-07-14T12:47:14Z","file_name":"2018_Springer_Morri.pdf","content_type":"application/pdf","date_created":"2019-02-14T10:58:29Z","file_size":1349914,"checksum":"8325fcc194264af4749e662a73bf66b5","file_id":"5985","creator":"kschuh","relation":"main_file","access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","publication":"Nature Communications","has_accepted_license":"1","oa_version":"Published Version","project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"month":"12","article_number":"1950","language":[{"iso":"eng"}]},{"file_date_updated":"2020-07-14T12:45:06Z","ec_funded":1,"quality_controlled":"1","publisher":"Springer Nature","author":[{"last_name":"De Martino","first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andersson Anna","last_name":"Mc","full_name":"Mc, Andersson Anna"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"issue":"1","_id":"161","scopus_import":"1","title":"Statistical mechanics for metabolic networks during steady state growth","intvolume":"         9","publication_status":"published","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"article_processing_charge":"No","date_created":"2018-12-11T11:44:57Z","ddc":["570"],"volume":9,"isi":1,"external_id":{"isi":["000440149300021"]},"date_updated":"2024-02-21T13:45:39Z","year":"2018","citation":{"ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” <i>Nature Communications</i>, vol. 9, no. 1. Springer Nature, 2018.","chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>.","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., &#38; Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>","ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>."},"abstract":[{"text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells.","lang":"eng"}],"doi":"10.1038/s41467-018-05417-9","day":"30","language":[{"iso":"eng"}],"publication":"Nature Communications","has_accepted_license":"1","month":"07","article_number":"2988","oa_version":"Published Version","project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5587"}]},"file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"5728","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","file_size":1043205,"date_created":"2018-12-17T16:44:28Z","content_type":"application/pdf","file_name":"2018_NatureComm_DeMartino.pdf","date_updated":"2020-07-14T12:45:06Z"}],"date_published":"2018-07-30T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publist_id":"7760","oa":1},{"doi":"10.1371/journal.pbio.2005971.s008","day":"16","date_published":"2018-08-16T00:00:00Z","type":"research_data_reference","date_updated":"2023-09-13T08:45:41Z","citation":{"ama":"Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Numerical data used in figures. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">https://doi.org/10.1371/journal.pbio.2005971.s008</a>","ieee":"W. Chaudhry <i>et al.</i>, “Numerical data used in figures.” Public Library of Science, 2018.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.” Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">https://doi.org/10.1371/journal.pbio.2005971.s008</a>.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).","mla":"Chaudhry, Waqas, et al. <i>Numerical Data Used in Figures</i>. Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Numerical data used in figures, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>."},"year":"2018","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"82"}]},"month":"08","title":"Numerical data used in figures","oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"CaGu"}],"date_created":"2021-08-06T12:43:44Z","author":[{"last_name":"Chaudhry","first_name":"Waqas","full_name":"Chaudhry, Waqas"},{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","last_name":"Pleska","first_name":"Maros"},{"last_name":"Shah","first_name":"Nilang","full_name":"Shah, Nilang"},{"full_name":"Weiss, Howard","first_name":"Howard","last_name":"Weiss"},{"full_name":"Mccall, Ingrid","last_name":"Mccall","first_name":"Ingrid"},{"full_name":"Meyer, Justin","first_name":"Justin","last_name":"Meyer"},{"last_name":"Gupta","first_name":"Animesh","full_name":"Gupta, Animesh"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"first_name":"Bruce","last_name":"Levin","full_name":"Levin, Bruce"}],"_id":"9810","publisher":"Public Library of Science"},{"publisher":"Oxford University Press","page":"2918-2931","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:27Z","publication_status":"published","department":[{"_id":"CaGu"}],"date_created":"2018-12-11T11:46:29Z","article_processing_charge":"Yes (in subscription journal)","title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","pubrep_id":"971","intvolume":"        46","_id":"438","scopus_import":"1","author":[{"first_name":"Nela","last_name":"Nikolic","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"first_name":"Alexandra","last_name":"Vandervelde","full_name":"Vandervelde, Alexandra"},{"last_name":"Albanese","first_name":"Tanino","full_name":"Albanese, Tanino"},{"last_name":"Gelens","first_name":"Lendert","full_name":"Gelens, Lendert"},{"full_name":"Moll, Isabella","first_name":"Isabella","last_name":"Moll"}],"issue":"6","volume":46,"ddc":["576"],"doi":"10.1093/nar/gky079","day":"06","abstract":[{"lang":"eng","text":"The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress."}],"date_updated":"2024-02-21T13:44:45Z","citation":{"short":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll, Nucleic Acids Research 46 (2018) 2918–2931.","mla":"Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” <i>Nucleic Acids Research</i>, vol. 46, no. 6, Oxford University Press, 2018, pp. 2918–31, doi:<a href=\"https://doi.org/10.1093/nar/gky079\">10.1093/nar/gky079</a>.","ista":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 46(6), 2918–2931.","ama":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. <i>Nucleic Acids Research</i>. 2018;46(6):2918-2931. doi:<a href=\"https://doi.org/10.1093/nar/gky079\">10.1093/nar/gky079</a>","apa":"Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., &#38; Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gky079\">https://doi.org/10.1093/nar/gky079</a>","ieee":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I. Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations,” <i>Nucleic Acids Research</i>, vol. 46, no. 6. Oxford University Press, pp. 2918–2931, 2018.","chicago":"Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” <i>Nucleic Acids Research</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/nar/gky079\">https://doi.org/10.1093/nar/gky079</a>."},"year":"2018","isi":1,"external_id":{"isi":["000429009500021"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"month":"04","publication":"Nucleic Acids Research","has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:46:27Z","file_name":"IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:15:30Z","file_size":5027978,"checksum":"3ff4f545c27e11a4cd20ccb30778793e","file_id":"5151","creator":"system","access_level":"open_access","relation":"main_file"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","id":"5569","relation":"popular_science"}]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2018-04-06T00:00:00Z","type":"journal_article"},{"title":"Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis","intvolume":"       104","publication_status":"published","date_created":"2018-12-11T11:50:03Z","department":[{"_id":"CaGu"}],"article_processing_charge":"No","author":[{"last_name":"Fang","first_name":"Chong","full_name":"Fang, Chong"},{"orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","first_name":"Anna A","last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Grafe","full_name":"Grafe, Martin"},{"first_name":"Ralf","last_name":"Heermann","full_name":"Heermann, Ralf"},{"full_name":"Jung, Kirsten","last_name":"Jung","first_name":"Kirsten"},{"full_name":"Gebhard, Susanne","last_name":"Gebhard","first_name":"Susanne"},{"first_name":"Thorsten","last_name":"Mascher","full_name":"Mascher, Thorsten"}],"issue":"1","_id":"1084","scopus_import":"1","publisher":"Wiley-Blackwell","page":"16 - 31","quality_controlled":"1","abstract":[{"lang":"eng","text":"BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities."}],"doi":"10.1111/mmi.13597","day":"01","isi":1,"external_id":{"isi":["000398059200002"]},"date_updated":"2023-09-20T11:48:43Z","year":"2017","citation":{"ama":"Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. <i>Molecular Microbiology</i>. 2017;104(1):16-31. doi:<a href=\"https://doi.org/10.1111/mmi.13597\">10.1111/mmi.13597</a>","apa":"Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., &#38; Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. <i>Molecular Microbiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mmi.13597\">https://doi.org/10.1111/mmi.13597</a>","chicago":"Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” <i>Molecular Microbiology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/mmi.13597\">https://doi.org/10.1111/mmi.13597</a>.","ieee":"C. Fang <i>et al.</i>, “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” <i>Molecular Microbiology</i>, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.","short":"C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31.","mla":"Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” <i>Molecular Microbiology</i>, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:<a href=\"https://doi.org/10.1111/mmi.13597\">10.1111/mmi.13597</a>.","ista":"Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31."},"volume":104,"month":"04","oa_version":"None","publication":"Molecular Microbiology","language":[{"iso":"eng"}],"publist_id":"6294","publication_identifier":{"issn":[" 0950382X"]},"date_published":"2017-04-01T00:00:00Z","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public"},{"related_material":{"record":[{"id":"1243","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"561"},{"relation":"part_of_dissertation","id":"457","status":"public"}]},"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"main_file","access_level":"open_access","file_id":"4710","creator":"system","date_created":"2018-12-12T10:08:48Z","checksum":"33cfb59674e91f82e3738396d3fb3776","file_size":18569590,"date_updated":"2020-07-14T12:45:24Z","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","content_type":"application/pdf"},{"date_created":"2019-04-05T08:33:14Z","checksum":"dcc239968decb233e7f98cf1083d8c26","file_size":2801649,"date_updated":"2020-07-14T12:45:24Z","file_name":"2017_Pleska_Maros_Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"6204","creator":"dernst"}],"date_published":"2017-10-01T00:00:00Z","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"supervisor":[{"first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publist_id":"7711","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"10","oa_version":"Published Version","project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"ddc":["576","579"],"acknowledgement":"During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n","date_updated":"2023-09-15T12:04:56Z","year":"2017","citation":{"ama":"Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>","apa":"Pleska, M. (2017). <i>Biology of restriction-modification systems at the single-cell and population level</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","chicago":"Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>.","short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017.","mla":"Pleska, Maros. <i>Biology of Restriction-Modification Systems at the Single-Cell and Population Level</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>.","ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria."},"abstract":[{"lang":"eng","text":"Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions."}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_916","day":"01","file_date_updated":"2020-07-14T12:45:24Z","page":"126","publisher":"Institute of Science and Technology Austria","author":[{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","last_name":"Pleska","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros"}],"_id":"202","title":"Biology of restriction-modification systems at the single-cell and population level","pubrep_id":"916","alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2018-12-11T11:45:10Z","department":[{"_id":"CaGu"}],"article_processing_charge":"No"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"record":[{"relation":"popular_science","id":"5560","status":"public"}]},"date_published":"2017-04-21T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["00368075"]},"publist_id":"7064","language":[{"iso":"eng"}],"publication":"Science","oa_version":"None","project":[{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"month":"04","volume":356,"date_updated":"2024-02-21T13:49:00Z","citation":{"short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.","mla":"Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” <i>Science</i>, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:<a href=\"https://doi.org/10.1126/science.aaf4762\">10.1126/science.aaf4762</a>.","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. <i>Science</i>. 2017;356(6335):311-315. doi:<a href=\"https://doi.org/10.1126/science.aaf4762\">10.1126/science.aaf4762</a>","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf4762\">https://doi.org/10.1126/science.aaf4762</a>","chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aaf4762\">https://doi.org/10.1126/science.aaf4762</a>.","ieee":"T. Bergmiller <i>et al.</i>, “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” <i>Science</i>, vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315, 2017."},"year":"2017","doi":"10.1126/science.aaf4762","day":"21","abstract":[{"lang":"eng","text":"The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria."}],"page":"311 - 315","quality_controlled":"1","publisher":"American Association for the Advancement of Science","article_type":"original","_id":"665","scopus_import":1,"author":[{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2912-6769","full_name":"Andersson, Anna M","first_name":"Anna M","last_name":"Andersson"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X"},{"full_name":"Balleza, Enrique","first_name":"Enrique","last_name":"Balleza"},{"full_name":"Kiviet, Daniel","first_name":"Daniel","last_name":"Kiviet"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet"}],"issue":"6335","publication_status":"published","date_created":"2018-12-11T11:47:48Z","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"article_processing_charge":"No","title":"Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity","intvolume":"       356"},{"file_date_updated":"2020-07-14T12:47:46Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"Public Library of Science","issue":"7","author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","first_name":"Marta","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004"},{"first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"_id":"696","intvolume":"        13","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","pubrep_id":"894","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"date_created":"2018-12-11T11:47:58Z","publication_status":"published","ddc":["576"],"volume":13,"year":"2017","citation":{"ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609."},"date_updated":"2024-03-25T23:30:14Z","abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"day":"18","doi":"10.1371/journal.pcbi.1005609","language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"PLoS Computational Biology","article_number":"e1005609","month":"07","project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"9849","relation":"research_data","status":"public"},{"id":"9850","relation":"research_data","status":"public"},{"id":"9851","relation":"research_data","status":"public"},{"id":"9852","relation":"research_data","status":"public"},{"id":"6263","relation":"dissertation_contains","status":"public"}]},"file":[{"content_type":"application/pdf","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","date_updated":"2020-07-14T12:47:46Z","file_size":3775716,"checksum":"9143c290fa6458ed2563bff4b295554a","date_created":"2018-12-12T10:15:01Z","creator":"system","file_id":"5117","relation":"main_file","access_level":"open_access"}],"type":"journal_article","date_published":"2017-07-18T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publist_id":"7004","oa":1,"publication_identifier":{"issn":["1553734X"]}},{"has_accepted_license":"1","publication":"eLife","article_number":"e25100","month":"07","oa_version":"Published Version","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2017-07-25T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publist_id":"6990","publication_identifier":{"issn":["2050084X"]},"status":"public","related_material":{"record":[{"relation":"popular_science","id":"5564","status":"public"},{"status":"public","relation":"dissertation_contains","id":"26"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:47:48Z","content_type":"application/pdf","file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","date_created":"2018-12-12T10:12:54Z","checksum":"6b908b5db9f61f6820ebd7f8fa815571","file_size":2092088,"file_id":"4975","creator":"system","access_level":"open_access","relation":"main_file"},{"creator":"system","file_id":"4976","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","date_updated":"2020-07-14T12:47:48Z","file_size":3428681,"checksum":"ca21530389b720243552678125fdba35","date_created":"2018-12-12T10:12:55Z"}],"author":[{"first_name":"Magdalena","last_name":"Steinrück","orcid":"0000-0003-1229-9719","full_name":"Steinrück, Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"_id":"704","intvolume":"         6","pubrep_id":"890","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","department":[{"_id":"CaGu"}],"date_created":"2018-12-11T11:48:01Z","publication_status":"published","file_date_updated":"2020-07-14T12:47:48Z","quality_controlled":"1","publisher":"eLife Sciences Publications","year":"2017","citation":{"ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","mla":"Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>, vol. 6, e25100, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>.","short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>.","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","apa":"Steinrück, M., &#38; Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>","ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>"},"date_updated":"2024-03-25T23:30:14Z","abstract":[{"text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data.","lang":"eng"}],"day":"25","doi":"10.7554/eLife.25100","ddc":["576"],"volume":6},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"id":"8350","relation":"dissertation_contains","status":"public"}]},"publist_id":"6934","publication_identifier":{"issn":["15345807"]},"type":"journal_article","date_published":"2017-10-23T00:00:00Z","language":[{"iso":"eng"}],"month":"10","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Cell segregation in gastrulation: the role of cell fate specification","grant_number":"I2058","_id":"252DD2A6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"None","publication":"Developmental Cell","volume":43,"abstract":[{"text":"Cell-cell contact formation constitutes an essential step in evolution, leading to the differentiation of specialized cell types. However, remarkably little is known about whether and how the interplay between contact formation and fate specification affects development. Here, we identify a positive feedback loop between cell-cell contact duration, morphogen signaling, and mesendoderm cell-fate specification during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for ppl cell-fate specification. We further show that Nodal signaling promotes ppl cell-cell contact duration, generating a positive feedback loop between ppl cell-cell contact duration and cell-fate specification. Finally, by combining mathematical modeling and experimentation, we show that this feedback determines whether anterior axial mesendoderm cells become ppl or, instead, turn into endoderm. Thus, the interdependent activities of cell-cell signaling and contact formation control fate diversification within the developing embryo.","lang":"eng"}],"day":"23","doi":"10.1016/j.devcel.2017.09.014","external_id":{"isi":["000413443700011"]},"isi":1,"year":"2017","citation":{"chicago":"Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour, Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">https://doi.org/10.1016/j.devcel.2017.09.014</a>.","ieee":"V. Barone <i>et al.</i>, “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” <i>Developmental Cell</i>, vol. 43, no. 2. Cell Press, pp. 198–211, 2017.","ama":"Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. <i>Developmental Cell</i>. 2017;43(2):198-211. doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">10.1016/j.devcel.2017.09.014</a>","apa":"Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K., … Heisenberg, C.-P. J. (2017). An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">https://doi.org/10.1016/j.devcel.2017.09.014</a>","ista":"Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 43(2), 198–211.","mla":"Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” <i>Developmental Cell</i>, vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">10.1016/j.devcel.2017.09.014</a>.","short":"V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora, C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211."},"date_updated":"2024-03-25T23:30:21Z","publisher":"Cell Press","ec_funded":1,"quality_controlled":"1","page":"198 - 211","intvolume":"        43","title":"An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate","date_created":"2018-12-11T11:48:13Z","department":[{"_id":"CaHe"},{"_id":"CaGu"},{"_id":"GaTk"}],"article_processing_charge":"No","publication_status":"published","issue":"2","author":[{"id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","first_name":"Vanessa","last_name":"Barone"},{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz","last_name":"Lang","first_name":"Moritz"},{"first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pradhan, Saurabh","first_name":"Saurabh","last_name":"Pradhan"},{"full_name":"Shamipour, Shayan","first_name":"Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke","first_name":"Keisuke","last_name":"Sako","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"scopus_import":"1","_id":"735"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2017-05-20T00:00:00Z","type":"journal_article","oa":1,"publist_id":"7279","file":[{"file_id":"5007","creator":"system","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:46:39Z","content_type":"application/pdf","file_name":"IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf","date_created":"2018-12-12T10:13:24Z","checksum":"d66fee867e7cdbfa3fe276c2fb0778bb","file_size":1668557}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication":"Angewandte Chemie","has_accepted_license":"1","oa_version":"Published Version","project":[{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564"},{"_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"month":"05","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:01:33Z","citation":{"ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 129(16), 4679–4682.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682.","mla":"Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” <i>Angewandte Chemie</i>, vol. 129, no. 16, Wiley, 2017, pp. 4679–82, doi:<a href=\"https://doi.org/10.1002/ange.201611998\">10.1002/ange.201611998</a>.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” <i>Angewandte Chemie</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/ange.201611998\">https://doi.org/10.1002/ange.201611998</a>.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” <i>Angewandte Chemie</i>, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., &#38; Janovjak, H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. <i>Angewandte Chemie</i>. Wiley. <a href=\"https://doi.org/10.1002/ange.201611998\">https://doi.org/10.1002/ange.201611998</a>","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. <i>Angewandte Chemie</i>. 2017;129(16):4679-4682. doi:<a href=\"https://doi.org/10.1002/ange.201611998\">10.1002/ange.201611998</a>"},"year":"2017","doi":"10.1002/ange.201611998","day":"20","abstract":[{"text":"Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. ","lang":"ger"}],"volume":129,"ddc":["571"],"_id":"538","author":[{"last_name":"Kainrath","first_name":"Stephanie","full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stadler, Manuela","first_name":"Manuela","last_name":"Stadler"},{"first_name":"Eva","last_name":"Gschaider-Reichhart","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Distel","full_name":"Distel, Martin"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak"}],"issue":"16","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"date_created":"2018-12-11T11:47:02Z","pubrep_id":"932","title":"Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen","intvolume":"       129","page":"4679 - 4682","ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:39Z","publisher":"Wiley"},{"publisher":"Public Library of Science","quality_controlled":"1","ec_funded":1,"file_date_updated":"2020-07-14T12:46:46Z","publication_status":"published","date_created":"2018-12-11T11:47:04Z","department":[{"_id":"CaGu"}],"pubrep_id":"959","title":"Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations","intvolume":"        13","_id":"541","scopus_import":1,"author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090"},{"full_name":"Schreiber, Frank","last_name":"Schreiber","first_name":"Frank"},{"full_name":"Dal Co, Alma","first_name":"Alma","last_name":"Dal Co"},{"full_name":"Kiviet, Daniel","first_name":"Daniel","last_name":"Kiviet"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Littmann, Sten","first_name":"Sten","last_name":"Littmann"},{"last_name":"Kuypers","first_name":"Marcel","full_name":"Kuypers, Marcel"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"issue":"12","volume":13,"ddc":["576","579"],"doi":"10.1371/journal.pgen.1007122","day":"18","abstract":[{"lang":"eng","text":"While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed."}],"date_updated":"2023-02-23T14:10:34Z","citation":{"short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).","mla":"Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” <i>PLoS Genetics</i>, vol. 13, no. 12, e1007122, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122\">10.1371/journal.pgen.1007122</a>.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007122\">https://doi.org/10.1371/journal.pgen.1007122</a>","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. <i>PLoS Genetics</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122\">10.1371/journal.pgen.1007122</a>","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” <i>PLoS Genetics</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pgen.1007122\">https://doi.org/10.1371/journal.pgen.1007122</a>.","ieee":"N. Nikolic <i>et al.</i>, “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” <i>PLoS Genetics</i>, vol. 13, no. 12. Public Library of Science, 2017."},"year":"2017","language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"month":"12","article_number":"e1007122","publication":"PLoS Genetics","has_accepted_license":"1","file":[{"checksum":"22426d9382f21554bad5fa5967afcfd0","file_size":1308475,"date_created":"2018-12-12T10:14:35Z","content_type":"application/pdf","file_name":"IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf","date_updated":"2020-07-14T12:46:46Z","access_level":"open_access","relation":"main_file","creator":"system","file_id":"5088"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"record":[{"relation":"research_data","id":"9844","status":"public"},{"relation":"research_data","id":"9845","status":"public"},{"id":"9846","relation":"research_data","status":"public"}]},"publication_identifier":{"issn":["15537390"]},"publist_id":"7275","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2017-12-18T00:00:00Z","type":"journal_article"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["571"],"related_material":{"record":[{"status":"public","id":"665","relation":"research_paper"}]},"status":"public","file":[{"access_level":"open_access","relation":"main_file","file_id":"5603","creator":"system","date_created":"2018-12-12T13:02:38Z","checksum":"d77859af757ac8025c50c7b12b52eaf3","file_size":6773204,"date_updated":"2020-07-14T12:47:03Z","file_name":"IST-2017-53-v1+1_Data_MDE.zip","content_type":"application/zip"}],"type":"research_data","date_published":"2017-03-10T00:00:00Z","year":"2017","citation":{"apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:53\">https://doi.org/10.15479/AT:ISTA:53</a>","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>","chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:53\">https://doi.org/10.15479/AT:ISTA:53</a>.","ieee":"T. Bergmiller <i>et al.</i>, “Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity.” Institute of Science and Technology Austria, 2017.","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, (2017).","mla":"Bergmiller, Tobias, et al. <i>Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>.","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"date_updated":"2024-02-21T13:49:00Z","oa":1,"abstract":[{"lang":"eng","text":"This repository contains the data collected for the manuscript \"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity\".\r\nThe data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication.\r\nData is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic \"mother machine\" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication."}],"day":"10","doi":"10.15479/AT:ISTA:53","keyword":["single cell microscopy","mother machine microfluidic device","AcrAB-TolC pump","multi-drug efflux","Escherichia coli"],"file_date_updated":"2020-07-14T12:47:03Z","publisher":"Institute of Science and Technology Austria","datarep_id":"53","author":[{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller"},{"id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","last_name":"Andersson","first_name":"Anna M","full_name":"Andersson, Anna M","orcid":"0000-0003-2912-6769"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek","first_name":"Kathrin"},{"full_name":"Balleza, Enrique","first_name":"Enrique","last_name":"Balleza"},{"full_name":"Kiviet, Daniel","first_name":"Daniel","last_name":"Kiviet"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","_id":"5560","month":"03","title":"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity","article_processing_charge":"No","date_created":"2018-12-12T12:31:32Z","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"oa_version":"Published Version"},{"date_published":"2017-04-11T00:00:00Z","type":"research_data","date_updated":"2024-02-21T13:47:28Z","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"citation":{"mla":"Steinrück, Magdalena, and Calin C. Guet. <i>Fastq Files for “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:65\">10.15479/AT:ISTA:65</a>.","short":"M. Steinrück, C.C. Guet, (2017).","ista":"Steinrück M, Guet CC. 2017. Fastq files for ‘Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:65\">10.15479/AT:ISTA:65</a>.","ama":"Steinrück M, Guet CC. Fastq files for “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:65\">10.15479/AT:ISTA:65</a>","apa":"Steinrück, M., &#38; Guet, C. C. (2017). 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grant)","grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425"},{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"publication":"Biology Letters","language":[{"iso":"eng"}],"oa":1,"publist_id":"7253","publication_identifier":{"issn":["1744-9561"]},"date_published":"2017-12-01T00:00:00Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"9847","relation":"research_data"},{"relation":"dissertation_contains","id":"202","status":"public"}]},"status":"public","main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2017.0646","open_access":"1"}],"title":"Effects of mutations in phage restriction sites during escape from restriction–modification","intvolume":"        13","publication_status":"published","article_processing_charge":"No","date_created":"2018-12-11T11:47:11Z","department":[{"_id":"CaGu"}],"author":[{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","last_name":"Pleska","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"issue":"12","pmid":1,"_id":"561","scopus_import":"1","article_type":"original","publisher":"The Royal Society","quality_controlled":"1","abstract":[{"text":"Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage l and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape.","lang":"eng"}],"doi":"10.1098/rsbl.2017.0646","day":"01","external_id":{"pmid":["29237814"]},"date_updated":"2023-09-07T11:59:32Z","year":"2017","citation":{"chicago":"Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” <i>Biology Letters</i>. The Royal Society, 2017. <a href=\"https://doi.org/10.1098/rsbl.2017.0646\">https://doi.org/10.1098/rsbl.2017.0646</a>.","ieee":"M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” <i>Biology Letters</i>, vol. 13, no. 12. The Royal Society, 2017.","apa":"Pleska, M., &#38; Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. <i>Biology Letters</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsbl.2017.0646\">https://doi.org/10.1098/rsbl.2017.0646</a>","ama":"Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. <i>Biology Letters</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0646\">10.1098/rsbl.2017.0646</a>","ista":"Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646.","mla":"Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” <i>Biology Letters</i>, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0646\">10.1098/rsbl.2017.0646</a>.","short":"M. Pleska, C.C. Guet, Biology Letters 13 (2017)."},"acknowledgement":"This work was funded by an HFSP Young Investigators' grant RGY0079/2011 (C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria.","volume":13}]