[{"date_updated":"2026-06-22T14:05:53Z","year":"2017","volume":71,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"page":"845 - 858","oa":1,"_id":"1063","ec_funded":1,"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"oa_version":"Submitted Version","department":[{"_id":"NiBa"}],"external_id":{"isi":["000398545200003"],"biorxivid":["10.1101/081042"]},"author":[{"first_name":"Hildegard","last_name":"Uecker","full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations."}],"publication_identifier":{"issn":["0014-3820"]},"publist_id":"6327","scopus_import":"1","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","issue":"4","type":"journal_article","day":"01","status":"public","das_tickbox":"1","main_file_link":[{"url":"https://doi.org/10.1101/081042","open_access":"1"}],"date_created":"2018-12-11T11:49:57Z","doi":"10.1111/evo.13191","citation":{"ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley, 2017. https://doi.org/10.1111/evo.13191.","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley, pp. 845–858, 2017.","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution, vol. 71, no. 4, Wiley, 2017, pp. 845–58, doi:10.1111/evo.13191.","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. Wiley. https://doi.org/10.1111/evo.13191","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","short":"H. Uecker, Evolution 71 (2017) 845–858."},"date_published":"2017-04-01T00:00:00Z","intvolume":" 71","publisher":"Wiley","language":[{"iso":"eng"}],"month":"04","publication":"Evolution","biorxivid":1,"quality_controlled":"1","article_processing_charge":"No"},{"volume":43,"year":"2017","publication_status":"published","related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"id":"8350","relation":"dissertation_contains","status":"public"}]},"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-22T22:30:04Z","department":[{"_id":"CaHe"},{"_id":"CaGu"},{"_id":"GaTk"}],"external_id":{"isi":["000413443700011"]},"author":[{"first_name":"Vanessa","last_name":"Barone","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","last_name":"Lang"},{"last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"full_name":"Pradhan, Saurabh","first_name":"Saurabh","last_name":"Pradhan"},{"first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke","last_name":"Sako","first_name":"Keisuke"},{"full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","last_name":"Sikora"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"abstract":[{"lang":"eng","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."}],"page":"198 - 211","_id":"735","ec_funded":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"252DD2A6-B435-11E9-9278-68D0E5697425","grant_number":"I2058","name":"Cell segregation in gastrulation: the role of cell fate specification"}],"oa_version":"None","day":"23","type":"journal_article","status":"public","doi":"10.1016/j.devcel.2017.09.014","date_created":"2018-12-11T11:48:13Z","publication_identifier":{"issn":["1534-5807"]},"publist_id":"6934","scopus_import":"1","corr_author":"1","issue":"2","title":"An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate","publisher":"Cell Press","language":[{"iso":"eng"}],"month":"10","publication":"Developmental Cell","quality_controlled":"1","article_processing_charge":"No","citation":{"ama":"Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 2017;43(2):198-211. doi:10.1016/j.devcel.2017.09.014","ieee":"V. Barone et al., “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” Developmental Cell, vol. 43, no. 2. Cell Press, pp. 198–211, 2017.","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.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.09.014.","mla":"Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell, vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:10.1016/j.devcel.2017.09.014.","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.","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. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.09.014","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_published":"2017-10-23T00:00:00Z","intvolume":" 43"},{"arxiv":1,"date_created":"2018-12-11T11:47:39Z","main_file_link":[{"url":"https://arxiv.org/abs/1705.00317","open_access":"1"}],"doi":"10.1007/978-3-319-63390-9_3","status":"public","type":"conference","day":"01","title":"Non-polynomial worst case analysis of recursive programs","publist_id":"7149","publication_identifier":{"isbn":["978-331963389-3"]},"scopus_import":"1","editor":[{"first_name":"Rupak","last_name":"Majumdar","full_name":"Majumdar, Rupak"},{"full_name":"Kunčak, Viktor","first_name":"Viktor","last_name":"Kunčak"}],"quality_controlled":"1","article_processing_charge":"No","month":"01","publisher":"Springer","language":[{"iso":"eng"}],"intvolume":" 10427","citation":{"ista":"Chatterjee K, Fu H, Goharshady AK. 2017. Non-polynomial worst case analysis of recursive programs. CAV: Computer Aided Verification, LNCS, vol. 10427, 41–63.","apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2017). Non-polynomial worst case analysis of recursive programs. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 41–63). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_3","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 41–63.","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst case analysis of recursive programs. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:41-63. doi:10.1007/978-3-319-63390-9_3","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst Case Analysis of Recursive Programs.” edited by Rupak Majumdar and Viktor Kunčak, 10427:41–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63390-9_3.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst case analysis of recursive programs,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 41–63.","mla":"Chatterjee, Krishnendu, et al. Non-Polynomial Worst Case Analysis of Recursive Programs. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 41–63, doi:10.1007/978-3-319-63390-9_3."},"date_published":"2017-01-01T00:00:00Z","conference":{"end_date":"2017-07-28","name":"CAV: Computer Aided Verification","start_date":"2017-07-24","location":"Heidelberg, Germany"},"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"id":"7014","relation":"later_version","status":"public"},{"relation":"dissertation_contains","status":"public","id":"8934"}]},"publication_status":"published","volume":10427,"year":"2017","date_updated":"2026-06-22T22:30:11Z","alternative_title":["LNCS"],"abstract":[{"text":"We study the problem of developing efficient approaches for proving worst-case bounds of non-deterministic recursive programs. Ranking functions are sound and complete for proving termination and worst-case bounds of non-recursive programs. First, we apply ranking functions to recursion, resulting in measure functions, and show that they provide a sound and complete approach to prove worst-case bounds of non-deterministic recursive programs. Our second contribution is the synthesis of measure functions in non-polynomial forms. We show that non-polynomial measure functions with logarithm and exponentiation can be synthesized through abstraction of logarithmic or exponentiation terms, Farkas’ Lemma, and Handelman’s Theorem using linear programming. While previous methods obtain worst-case polynomial bounds, our approach can synthesize bounds of the form O(n log n) as well as O(nr) where r is not an integer. We present experimental results to demonstrate that our approach can efficiently obtain worst-case bounds of classical recursive algorithms such as Merge-Sort, Closest-Pair, Karatsuba’s algorithm and Strassen’s algorithm.","lang":"eng"}],"external_id":{"arxiv":["1705.00317"],"isi":["000431900900003"]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir","last_name":"Goharshady","first_name":"Amir"}],"department":[{"_id":"KrCh"}],"oa_version":"Submitted Version","project":[{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"}],"_id":"639","ec_funded":1,"oa":1,"page":"41 - 63"},{"quality_controlled":"1","article_processing_charge":"No","publisher":"Springer","language":[{"iso":"eng"}],"month":"01","intvolume":" 10482","conference":{"location":"Pune, India","start_date":"2017-10-03","end_date":"2017-10-06","name":"ATVA: Automated Technology for Verification and Analysis"},"citation":{"ama":"Chatterjee K, Goharshady AK, Pavlogiannis A. JTDec: A tool for tree decompositions in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:10.1007/978-3-319-68167-2_4","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for tree decompositions in soot,” presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “JTDec: A Tool for Tree Decompositions in Soot.” edited by Deepak D’Souza, 10482:59–66. Springer, 2017. https://doi.org/10.1007/978-3-319-68167-2_4.","mla":"Chatterjee, Krishnendu, et al. JTDec: A Tool for Tree Decompositions in Soot. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:10.1007/978-3-319-68167-2_4.","apa":"Chatterjee, K., Goharshady, A. K., & Pavlogiannis, A. (2017). JTDec: A tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66). Presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India: Springer. https://doi.org/10.1007/978-3-319-68167-2_4","ista":"Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree decompositions in soot. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 10482, 59–66.","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66."},"date_published":"2017-01-01T00:00:00Z","has_accepted_license":"1","status":"public","doi":"10.1007/978-3-319-68167-2_4","date_created":"2018-12-11T11:49:22Z","day":"01","type":"conference","title":"JTDec: A tool for tree decompositions in soot","editor":[{"last_name":"D'Souza","first_name":"Deepak","full_name":"D'Souza, Deepak"}],"publication_identifier":{"issn":["0302-9743"]},"publist_id":"6468","scopus_import":"1","ddc":["005"],"corr_author":"1","external_id":{"isi":["000723567800004"]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Goharshady, Amir","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir","last_name":"Goharshady"},{"first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"The notion of treewidth of graphs has been exploited for faster algorithms for several problems arising in verification and program analysis. Moreover, various notions of balanced tree decompositions have been used for improved algorithms supporting dynamic updates and analysis of concurrent programs. In this work, we present a tool for constructing tree-decompositions of CFGs obtained from Java methods, which is implemented as an extension to the widely used Soot framework. The experimental results show that our implementation on real-world Java benchmarks is very efficient. Our tool also provides the first implementation for balancing tree-decompositions. In summary, we present the first tool support for exploiting treewidth in the static analysis problems on Java programs.","lang":"eng"}],"department":[{"_id":"KrCh"}],"project":[{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"_id":"949","ec_funded":1,"oa_version":"Submitted Version","page":"59 - 66","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"file":[{"file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","date_updated":"2020-07-14T12:48:16Z","file_size":948514,"relation":"main_file","content_type":"application/pdf","file_id":"4835","access_level":"open_access","creator":"system","checksum":"a0d9f5f94dc594c4e71e78525c9942f1","date_created":"2018-12-12T10:10:45Z"}],"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":10482,"year":"2017","pubrep_id":"845","publication_status":"published","date_updated":"2026-06-22T22:30:11Z","alternative_title":["LNCS"],"file_date_updated":"2020-07-14T12:48:16Z"},{"title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","issue":"16","ddc":["540"],"corr_author":"1","publist_id":"6362","scopus_import":"1","publication_identifier":{"issn":["1433-7851"]},"date_created":"2018-12-11T11:49:46Z","doi":"10.1002/anie.201611998","has_accepted_license":"1","status":"public","type":"journal_article","day":"20","acknowledgement":"This work was supported by a grant from the European Union􏰝s Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 56","date_published":"2017-03-20T00:00:00Z","citation":{"apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201611998","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie - International Edition 56 (2017) 4608–4611.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition. Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie - International Edition, vol. 56, no. 16. Wiley-Blackwell, pp. 4608–4611, 2017.","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998","mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition, vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:10.1002/anie.201611998."},"article_processing_charge":"No","quality_controlled":"1","publication":"Angewandte Chemie - International Edition","month":"03","language":[{"iso":"eng"}],"publisher":"Wiley-Blackwell","date_updated":"2026-06-22T22:30:15Z","file_date_updated":"2019-01-18T09:39:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"file":[{"access_level":"open_access","date_created":"2019-01-18T09:39:55Z","success":1,"creator":"dernst","file_name":"2017_communications_Kainrath.pdf","relation":"main_file","file_id":"5845","content_type":"application/pdf","date_updated":"2019-01-18T09:39:55Z","file_size":2614942}],"related_material":{"record":[{"id":"418","relation":"dissertation_contains","status":"public"},{"id":"7680","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","volume":56,"year":"2017","oa_version":"Published Version","project":[{"grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets"}],"_id":"1028","ec_funded":1,"oa":1,"page":"4608-4611","abstract":[{"text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes.","lang":"eng"}],"author":[{"id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6709-2195","full_name":"Kainrath, Stephanie","last_name":"Kainrath","first_name":"Stephanie"},{"first_name":"Manuela","last_name":"Stadler","full_name":"Stadler, Manuela"},{"first_name":"Eva","last_name":"Gschaider-Reichhart","full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Distel, Martin","first_name":"Martin","last_name":"Distel"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak"}],"external_id":{"isi":["000398154000038"]},"department":[{"_id":"CaGu"},{"_id":"HaJa"}]},{"date_updated":"2026-06-22T22:30:17Z","file_date_updated":"2020-07-14T12:47:46Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9849"},{"status":"public","relation":"research_data","id":"9850"},{"id":"9851","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9852"},{"id":"6263","relation":"dissertation_contains","status":"public"}]},"file":[{"file_id":"5117","content_type":"application/pdf","relation":"main_file","file_size":3775716,"date_updated":"2020-07-14T12:47:46Z","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","date_created":"2018-12-12T10:15:01Z","checksum":"9143c290fa6458ed2563bff4b295554a","creator":"system","access_level":"open_access"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2017","volume":13,"pubrep_id":"894","publication_status":"published","_id":"696","ec_funded":1,"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","call_identifier":"FP7"}],"oa_version":"Published Version","article_type":"original","oa":1,"external_id":{"isi":["000406619800014"]},"author":[{"last_name":"Lukacisinova","first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004"},{"orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago"}],"abstract":[{"lang":"eng","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."}],"department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","issue":"7","scopus_import":"1","publist_id":"7004","publication_identifier":{"issn":["1553-734X"]},"corr_author":"1","ddc":["576"],"has_accepted_license":"1","status":"public","date_created":"2018-12-11T11:47:58Z","doi":"10.1371/journal.pcbi.1005609","day":"18","type":"journal_article","intvolume":" 13","article_number":"e1005609","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7. Public Library of Science, 2017.","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609","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.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017)."},"date_published":"2017-07-18T00:00:00Z","publication":"PLoS Computational Biology","quality_controlled":"1","article_processing_charge":"No","publisher":"Public Library of Science","language":[{"iso":"eng"}],"month":"07"},{"ec_funded":1,"_id":"1027","project":[{"call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","article_type":"original","page":"90 - 97","oa":1,"author":[{"last_name":"Lukacisinova","first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach"}],"external_id":{"isi":["000408077400015"]},"abstract":[{"lang":"eng","text":"The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance."}],"department":[{"_id":"ToBo"}],"date_updated":"2026-06-22T22:30:17Z","file_date_updated":"2019-01-18T09:57:57Z","file":[{"content_type":"application/pdf","file_id":"5846","relation":"main_file","file_size":858338,"date_updated":"2019-01-18T09:57:57Z","file_name":"2017_CurrentOpinion_Lukaciinova.pdf","date_created":"2019-01-18T09:57:57Z","creator":"dernst","success":1,"access_level":"open_access"}],"related_material":{"record":[{"id":"6263","status":"public","relation":"dissertation_contains"}]},"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":46,"year":"2017","publication_status":"published","pubrep_id":"801","intvolume":" 46","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"date_published":"2017-08-01T00:00:00Z","citation":{"ieee":"M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding of antibiotic resistance evolution,” Current Opinion in Biotechnology, vol. 46. Elsevier, pp. 90–97, 2017.","chicago":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013.","ama":"Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97. doi:10.1016/j.copbio.2017.02.013","mla":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology, vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013.","apa":"Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.013","ista":"Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97."},"publication":"Current Opinion in Biotechnology","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Elsevier","month":"08","title":"Toward a quantitative understanding of antibiotic resistance evolution","corr_author":"1","ddc":["570"],"publist_id":"6364","scopus_import":"1","status":"public","has_accepted_license":"1","doi":"10.1016/j.copbio.2017.02.013","date_created":"2018-12-11T11:49:45Z","type":"journal_article","day":"01"},{"department":[{"_id":"ToBo"}],"external_id":{"isi":["000396318300121"]},"author":[{"id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6549-4177","full_name":"Lukacisin, Martin","last_name":"Lukacisin","first_name":"Martin"},{"first_name":"Matthieu","last_name":"Landon","full_name":"Landon, Matthieu"},{"first_name":"Rishi","last_name":"Jajoo","full_name":"Jajoo, Rishi"}],"abstract":[{"lang":"eng","text":"RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking."}],"oa":1,"_id":"1029","oa_version":"Published Version","year":"2017","volume":12,"publication_status":"published","pubrep_id":"800","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5556"},{"relation":"dissertation_contains","status":"public","id":"6392"}]},"file":[{"access_level":"open_access","creator":"system","date_created":"2018-12-12T10:09:47Z","file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","date_updated":"2018-12-12T10:09:47Z","file_size":3429381,"relation":"main_file","content_type":"application/pdf","file_id":"4772"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2018-12-12T10:09:47Z","date_updated":"2026-06-22T22:30:20Z","publisher":"Public Library of Science","language":[{"iso":"eng"}],"month":"03","publication":"PLoS One","quality_controlled":"1","article_processing_charge":"Yes","citation":{"mla":"Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:10.1371/journal.pone.0174066.","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast,” PLoS One, vol. 12, no. 3. Public Library of Science, 2017.","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0174066.","ama":"Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 2017;12(3). doi:10.1371/journal.pone.0174066","short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2017). Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0174066","ista":"Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 12(3), e0174066."},"date_published":"2017-03-16T00:00:00Z","intvolume":" 12","article_number":"e0174066","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","day":"16","has_accepted_license":"1","status":"public","doi":"10.1371/journal.pone.0174066","date_created":"2018-12-11T11:49:46Z","scopus_import":"1","publist_id":"6361","publication_identifier":{"issn":["1932-6203"]},"ddc":["570"],"title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","issue":"3"},{"date_updated":"2026-06-22T22:30:24Z","publication_status":"published","volume":46,"year":"2017","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"related_material":{"record":[{"id":"6947","status":"public","relation":"dissertation_contains"}]},"page":"519 - 520","oa_version":"None","_id":"664","department":[{"_id":"MiSi"}],"abstract":[{"lang":"eng","text":"Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it."}],"author":[{"id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","last_name":"Assen","first_name":"Frank P"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt"}],"external_id":{"isi":["000399451100002"]},"corr_author":"1","publist_id":"7065","scopus_import":"1","publication_identifier":{"issn":["1074-7613"]},"issue":"4","title":"The dynamic cytokine niche","day":"18","type":"journal_article","doi":"10.1016/j.immuni.2017.04.006","date_created":"2018-12-11T11:47:47Z","status":"public","date_published":"2017-04-18T00:00:00Z","citation":{"short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.","apa":"Assen, F. P., & Sixt, M. K. (2017). The dynamic cytokine niche. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2017.04.006","ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.","mla":"Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” Immunity, vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:10.1016/j.immuni.2017.04.006.","ama":"Assen FP, Sixt MK. The dynamic cytokine niche. Immunity. 2017;46(4):519-520. doi:10.1016/j.immuni.2017.04.006","ieee":"F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” Immunity, vol. 46, no. 4. Cell Press, pp. 519–520, 2017.","chicago":"Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” Immunity. Cell Press, 2017. https://doi.org/10.1016/j.immuni.2017.04.006."},"intvolume":" 46","month":"04","language":[{"iso":"eng"}],"publisher":"Cell Press","article_processing_charge":"No","quality_controlled":"1","publication":"Immunity"},{"external_id":{"isi":["000404486700001"]},"author":[{"first_name":"Andi H","last_name":"Hansen","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian F","last_name":"Düllberg","orcid":"0000-0001-6335-9748","full_name":"Düllberg, Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mieck","first_name":"Christine","id":"34CAE85C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1919-7416","full_name":"Mieck, Christine"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon"}],"abstract":[{"lang":"eng","text":"The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context."}],"department":[{"_id":"SiHi"},{"_id":"MaLo"}],"ec_funded":1,"_id":"960","project":[{"call_identifier":"FP7","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"The biochemical basis of PAR polarization","call_identifier":"FWF","grant_number":"T00817-B21","_id":"25985A36-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","oa":1,"related_material":{"record":[{"id":"9962","relation":"dissertation_contains","status":"public"}]},"file":[{"access_level":"open_access","checksum":"dc1f5a475b918d09a0f9f587400b1626","date_created":"2018-12-12T10:09:40Z","creator":"system","file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf","relation":"main_file","file_id":"4764","content_type":"application/pdf","file_size":2153858,"date_updated":"2020-07-14T12:48:16Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"volume":11,"year":"2017","publication_status":"published","pubrep_id":"830","date_updated":"2026-06-22T22:30:34Z","file_date_updated":"2020-07-14T12:48:16Z","publication":"Frontiers in Cellular Neuroscience","quality_controlled":"1","article_processing_charge":"Yes","publisher":"Frontiers Research Foundation","language":[{"iso":"eng"}],"month":"06","article_number":"176","intvolume":" 11","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Hansen, Andi H, Christian F Düllberg, Christine Mieck, Martin Loose, and Simon Hippenmeyer. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fncel.2017.00176.","ieee":"A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks,” Frontiers in Cellular Neuroscience, vol. 11. Frontiers Research Foundation, 2017.","ama":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 2017;11. doi:10.3389/fncel.2017.00176","mla":"Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience, vol. 11, 176, Frontiers Research Foundation, 2017, doi:10.3389/fncel.2017.00176.","apa":"Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., & Hippenmeyer, S. (2017). Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncel.2017.00176","ista":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 11, 176.","short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (2017)."},"date_published":"2017-06-28T00:00:00Z","has_accepted_license":"1","status":"public","date_created":"2018-12-11T11:49:25Z","doi":"10.3389/fncel.2017.00176","day":"28","type":"journal_article","title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks","publication_identifier":{"issn":["1662-5102"]},"scopus_import":"1","publist_id":"6445","ddc":["570"]},{"related_material":{"record":[{"id":"51","status":"public","relation":"dissertation_contains"}]},"file":[{"creator":"system","date_created":"2018-12-12T10:12:16Z","checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8","access_level":"open_access","file_size":5798454,"date_updated":"2020-07-14T12:47:40Z","file_id":"4934","content_type":"application/pdf","relation":"main_file","file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2017","volume":12,"pubrep_id":"897","publication_status":"published","date_updated":"2026-06-22T22:30:37Z","file_date_updated":"2020-07-14T12:47:40Z","external_id":{"isi":["000402923200125"]},"author":[{"full_name":"Ukai, Hikari","first_name":"Hikari","last_name":"Ukai"},{"full_name":"Kawahara, Aiko","first_name":"Aiko","last_name":"Kawahara"},{"last_name":"Hirayama","first_name":"Keiko","full_name":"Hirayama, Keiko"},{"full_name":"Case, Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","last_name":"Case"},{"first_name":"Shotaro","last_name":"Aino","full_name":"Aino, Shotaro"},{"full_name":"Miyabe, Masahiro","first_name":"Masahiro","last_name":"Miyabe"},{"full_name":"Wakita, Ken","last_name":"Wakita","first_name":"Ken"},{"full_name":"Oogi, Ryohei","first_name":"Ryohei","last_name":"Oogi"},{"first_name":"Michiyo","last_name":"Kasayuki","full_name":"Kasayuki, Michiyo"},{"last_name":"Kawashima","first_name":"Shihomi","full_name":"Kawashima, Shihomi"},{"full_name":"Sugimoto, Shunichi","last_name":"Sugimoto","first_name":"Shunichi"},{"full_name":"Chikamatsu, Kanako","first_name":"Kanako","last_name":"Chikamatsu"},{"full_name":"Nitta, Noritaka","first_name":"Noritaka","last_name":"Nitta"},{"last_name":"Koga","first_name":"Tsuneyuki","full_name":"Koga, Tsuneyuki"},{"first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Takai, Toshiyuki","first_name":"Toshiyuki","last_name":"Takai"},{"full_name":"Ito, Isao","last_name":"Ito","first_name":"Isao"}],"abstract":[{"text":"Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry.","lang":"eng"}],"department":[{"_id":"RySh"}],"_id":"682","oa_version":"Published Version","article_type":"original","oa":1,"has_accepted_license":"1","status":"public","date_created":"2018-12-11T11:47:54Z","doi":"10.1371/journal.pone.0179377","day":"01","type":"journal_article","title":"PirB regulates asymmetries in hippocampal circuitry","issue":"6","scopus_import":"1","publist_id":"7034","publication_identifier":{"issn":["1932-6203"]},"ddc":["571"],"publication":"PLoS One","quality_controlled":"1","article_processing_charge":"No","publisher":"Public Library of Science","language":[{"iso":"eng"}],"month":"06","article_number":"e0179377","intvolume":" 12","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Ukai H, Kawahara A, Hirayama K, Case MJ, Aino S, Miyabe M, Wakita K, Oogi R, Kasayuki M, Kawashima S, Sugimoto S, Chikamatsu K, Nitta N, Koga T, Shigemoto R, Takai T, Ito I. 2017. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 12(6), e0179377.","apa":"Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., … Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0179377","short":"H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita, R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga, R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017).","chicago":"Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino, Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0179377.","ieee":"H. Ukai et al., “PirB regulates asymmetries in hippocampal circuitry,” PLoS One, vol. 12, no. 6. Public Library of Science, 2017.","ama":"Ukai H, Kawahara A, Hirayama K, et al. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 2017;12(6). doi:10.1371/journal.pone.0179377","mla":"Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:10.1371/journal.pone.0179377."},"date_published":"2017-06-01T00:00:00Z"},{"abstract":[{"lang":"eng","text":"The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation."}],"external_id":{"pmid":["28512197"],"isi":["000402275900007"]},"author":[{"last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"full_name":"Veldhuis, Jim","last_name":"Veldhuis","first_name":"Jim"},{"last_name":"Barone","first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367"},{"id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel","last_name":"Capek","first_name":"Daniel"},{"orcid":"0000-0002-3688-1474","full_name":"Maître, Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon","last_name":"Maître"},{"full_name":"Brodland, Wayne","last_name":"Brodland","first_name":"Wayne"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"department":[{"_id":"Bio"},{"_id":"CaHe"}],"oa_version":"Published Version","_id":"676","oa":1,"article_type":"original","page":"1798 - 1806","isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"id":"50","relation":"dissertation_contains","status":"public"}]},"file":[{"file_name":"2017_Development_Krens.pdf","file_id":"6905","content_type":"application/pdf","relation":"main_file","file_size":8194516,"date_updated":"2020-07-14T12:47:39Z","access_level":"open_access","date_created":"2019-09-24T06:56:22Z","checksum":"bc25125fb664706cdf180e061429f91d","creator":"dernst"}],"publication_status":"published","year":"2017","volume":144,"date_updated":"2026-06-22T22:30:36Z","file_date_updated":"2020-07-14T12:47:39Z","quality_controlled":"1","article_processing_charge":"No","publication":"Development","month":"05","pmid":1,"publisher":"Company of Biologists","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 144","citation":{"ista":"Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 144(10), 1798–1806.","apa":"Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W., & Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.144964","short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806.","ama":"Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 2017;144(10):1798-1806. doi:10.1242/dev.144964","ieee":"G. Krens et al., “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation,” Development, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017.","chicago":"Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître, Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144964.","mla":"Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806, doi:10.1242/dev.144964."},"date_published":"2017-05-15T00:00:00Z","doi":"10.1242/dev.144964","date_created":"2018-12-11T11:47:52Z","status":"public","has_accepted_license":"1","type":"journal_article","day":"15","issue":"10","title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","publication_identifier":{"issn":["0950-1991"]},"publist_id":"7047","scopus_import":"1","ddc":["570"],"corr_author":"1"},{"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8350"},{"id":"50","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","year":"2017","volume":19,"date_updated":"2026-06-22T22:30:36Z","abstract":[{"lang":"eng","text":"During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo."}],"acknowledged_ssus":[{"_id":"SSU"}],"author":[{"full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Smutny"},{"full_name":"Ákos, Zsuzsa","first_name":"Zsuzsa","last_name":"Ákos"},{"last_name":"Grigolon","first_name":"Silvia","full_name":"Grigolon, Silvia"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","last_name":"Shamipour","first_name":"Shayan"},{"full_name":"Ruprecht, Verena","first_name":"Verena","last_name":"Ruprecht"},{"first_name":"Daniel","last_name":"Capek","orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Behrndt"},{"first_name":"Ekaterina","last_name":"Papusheva","full_name":"Papusheva, Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tada, Masazumi","first_name":"Masazumi","last_name":"Tada"},{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicsek, Tamás","first_name":"Tamás","last_name":"Vicsek"},{"full_name":"Salbreux, Guillaume","first_name":"Guillaume","last_name":"Salbreux"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000397917000009"],"pmid":["28346437"]},"department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}],"oa_version":"Submitted Version","ec_funded":1,"_id":"661","project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"},{"call_identifier":"FWF","grant_number":"I930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","name":"Control of Epithelial Cell Layer Spreading in Zebrafish"}],"oa":1,"page":"306 - 317","main_file_link":[{"url":"https://europepmc.org/articles/pmc5635970","open_access":"1"}],"date_created":"2018-12-11T11:47:46Z","doi":"10.1038/ncb3492","status":"public","type":"journal_article","day":"27","title":"Friction forces position the neural anlage","corr_author":"1","publist_id":"7074","publication_identifier":{"issn":["1465-7392"]},"scopus_import":"1","article_processing_charge":"No","quality_controlled":"1","publication":"Nature Cell Biology","pmid":1,"month":"03","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","intvolume":" 19","date_published":"2017-03-27T00:00:00Z","citation":{"short":"M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M. Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 306–317.","ista":"Smutny M, Ákos Z, Grigolon S, Shamipour S, Ruprecht V, Capek D, Behrndt M, Papusheva E, Tada M, Hof B, Vicsek T, Salbreux G, Heisenberg C-PJ. 2017. Friction forces position the neural anlage. Nature Cell Biology. 19, 306–317.","apa":"Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D., … Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3492","mla":"Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” Nature Cell Biology, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:10.1038/ncb3492.","ieee":"M. Smutny et al., “Friction forces position the neural anlage,” Nature Cell Biology, vol. 19. Nature Publishing Group, pp. 306–317, 2017.","chicago":"Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural Anlage.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3492.","ama":"Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage. Nature Cell Biology. 2017;19:306-317. doi:10.1038/ncb3492"}},{"department":[{"_id":"EvBe"}],"abstract":[{"lang":"eng","text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges."}],"author":[{"last_name":"Hurny","first_name":"Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"}],"oa":1,"page":"1 - 29","oa_version":"Submitted Version","_id":"1024","project":[{"call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development"}],"pubrep_id":"1019","publication_status":"published","year":"2017","volume":1569,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","date_created":"2018-12-12T10:14:18Z","creator":"system","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","relation":"main_file","file_id":"5068","content_type":"application/pdf","date_updated":"2019-10-15T07:47:05Z","file_size":840646}],"related_material":{"record":[{"id":"539","relation":"dissertation_contains","status":"public"}]},"file_date_updated":"2019-10-15T07:47:05Z","alternative_title":["Methods in Molecular Biology"],"date_updated":"2026-06-22T22:30:37Z","month":"03","language":[{"iso":"eng"}],"publisher":"Springer","article_processing_charge":"No","quality_controlled":"1","publication":"Auxins and Cytokinins in Plant Biology","date_published":"2017-03-17T00:00:00Z","citation":{"short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","apa":"Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29.","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer, 2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.","ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1","ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29, 2017.","chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1."},"intvolume":" 1569","day":"17","type":"journal_article","doi":"10.1007/978-1-4939-6831-2_1","date_created":"2018-12-11T11:49:45Z","has_accepted_license":"1","status":"public","corr_author":"1","ddc":["575"],"publist_id":"6369","publication_identifier":{"issn":["1064-3745"]},"scopus_import":"1","title":"Methodological advances in auxin and cytokinin biology"},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 6","article_number":"e25100","date_published":"2017-07-25T00:00:00Z","citation":{"short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","apa":"Steinrück, M., & Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25100","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.” ELife, vol. 6, e25100, eLife Sciences Publications, 2017, doi:10.7554/eLife.25100.","ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 2017;6. doi:10.7554/eLife.25100","chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25100.","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” eLife, vol. 6. eLife Sciences Publications, 2017."},"article_processing_charge":"No","quality_controlled":"1","publication":"eLife","month":"07","language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","corr_author":"1","ddc":["576"],"publication_identifier":{"issn":["2050-084X"]},"publist_id":"6990","scopus_import":"1","doi":"10.7554/eLife.25100","date_created":"2018-12-11T11:48:01Z","has_accepted_license":"1","status":"public","day":"25","type":"journal_article","oa_version":"Published Version","_id":"704","oa":1,"abstract":[{"lang":"eng","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."}],"author":[{"last_name":"Steinrück","first_name":"Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1229-9719","full_name":"Steinrück, Magdalena"},{"last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"external_id":{"isi":["000406183700001"]},"department":[{"_id":"CaGu"}],"date_updated":"2026-06-22T22:30:38Z","file_date_updated":"2020-07-14T12:47:48Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"access_level":"open_access","date_created":"2018-12-12T10:12:54Z","checksum":"6b908b5db9f61f6820ebd7f8fa815571","creator":"system","file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","content_type":"application/pdf","file_id":"4975","relation":"main_file","file_size":2092088,"date_updated":"2020-07-14T12:47:48Z"},{"date_updated":"2020-07-14T12:47:48Z","file_size":3428681,"relation":"main_file","content_type":"application/pdf","file_id":"4976","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","creator":"system","checksum":"ca21530389b720243552678125fdba35","date_created":"2018-12-12T10:12:55Z","access_level":"open_access"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5564"},{"relation":"dissertation_contains","status":"public","id":"26"}]},"publication_status":"published","pubrep_id":"890","year":"2017","volume":6},{"oa_version":"Submitted Version","_id":"679","project":[{"name":"The biochemical basis of PAR polarization","call_identifier":"FWF","_id":"25985A36-B435-11E9-9278-68D0E5697425","grant_number":"T00817-B21"},{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"}],"oa":1,"page":"2051 - 2065","abstract":[{"text":"Protective responses against pathogens require a rapid mobilization of resting neutrophils and the timely removal of activated ones. Neutrophils are exceptionally short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged neutrophils is regulated differently from that in the circulating steady-state pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection site. In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP. The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates that posttranscriptional gene regulation by TTP schedules the termination of the antimicrobial engagement of neutrophils. The balancing role of TTP comes at the cost of an increased risk of bacterial infections.","lang":"eng"}],"external_id":{"pmid":["28504646"],"isi":["000402620800008"]},"author":[{"last_name":"Ebner","first_name":"Florian","full_name":"Ebner, Florian"},{"first_name":"Vitaly","last_name":"Sedlyarov","full_name":"Sedlyarov, Vitaly"},{"full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","last_name":"Tasciyan"},{"first_name":"Masa","last_name":"Ivin","full_name":"Ivin, Masa"},{"full_name":"Kratochvill, Franz","first_name":"Franz","last_name":"Kratochvill"},{"last_name":"Gratz","first_name":"Nina","full_name":"Gratz, Nina"},{"full_name":"Kenner, Lukas","first_name":"Lukas","last_name":"Kenner"},{"full_name":"Villunger, Andreas","last_name":"Villunger","first_name":"Andreas"},{"last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"last_name":"Kovarik","first_name":"Pavel","full_name":"Kovarik, Pavel"}],"department":[{"_id":"MiSi"}],"date_updated":"2026-06-22T22:31:06Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"related_material":{"record":[{"id":"12401","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","volume":127,"year":"2017","intvolume":" 127","citation":{"short":"F. Ebner, V. Sedlyarov, S. Tasciyan, M. Ivin, F. Kratochvill, N. Gratz, L. Kenner, A. Villunger, M.K. Sixt, P. Kovarik, The Journal of Clinical Investigation 127 (2017) 2051–2065.","ista":"Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L, Villunger A, Sixt MK, Kovarik P. 2017. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 127(6), 2051–2065.","apa":"Ebner, F., Sedlyarov, V., Tasciyan, S., Ivin, M., Kratochvill, F., Gratz, N., … Kovarik, P. (2017). The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI80631","mla":"Ebner, Florian, et al. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation, vol. 127, no. 6, American Society for Clinical Investigation, 2017, pp. 2051–65, doi:10.1172/JCI80631.","ieee":"F. Ebner et al., “The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection,” The Journal of Clinical Investigation, vol. 127, no. 6. American Society for Clinical Investigation, pp. 2051–2065, 2017.","chicago":"Ebner, Florian, Vitaly Sedlyarov, Saren Tasciyan, Masa Ivin, Franz Kratochvill, Nina Gratz, Lukas Kenner, Andreas Villunger, Michael K Sixt, and Pavel Kovarik. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation. American Society for Clinical Investigation, 2017. https://doi.org/10.1172/JCI80631.","ama":"Ebner F, Sedlyarov V, Tasciyan S, et al. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 2017;127(6):2051-2065. doi:10.1172/JCI80631"},"date_published":"2017-06-01T00:00:00Z","quality_controlled":"1","article_processing_charge":"No","publication":"The Journal of Clinical Investigation","pmid":1,"month":"06","publisher":"American Society for Clinical Investigation","language":[{"iso":"eng"}],"title":"The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection","issue":"6","publist_id":"7038","publication_identifier":{"issn":["0021-9738"]},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/"}],"doi":"10.1172/JCI80631","date_created":"2018-12-11T11:47:53Z","status":"public","type":"journal_article","day":"01","acknowledgement":"This work was supported by grants from the Austrian Science Fund (FWF) (P27538-B21, I1621-B22, and SFB 43, to PK); by funding from the European Union Seventh Framework Programme Marie Curie Initial Training Networks (FP7-PEOPLE-2012-ITN) for the project INBIONET (INfection BIOlogy Training NETwork under grant agreement PITN-GA-2012-316682; and by a joint research cluster initiative of the University of Vienna and the Medical University of Vienna."},{"author":[{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias"},{"full_name":"Voutyras, Orfefs","last_name":"Voutyras","first_name":"Orfefs"},{"first_name":"Theodora","last_name":"Varvarigou","full_name":"Varvarigou, Theodora"}],"publication":"2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation","abstract":[{"text":"The integration of social networking concepts into Internet of Things systems is a burgeoning topic of research that promises to support novel and more powerful applications. In this paper we focus on the design and implementation of a highly scalable Trust and Reputation Model for the Internet of Things based on the social approach that the COSMOS project introduces, as part of its final results. We create our model by combining popular solutions proposed for Peer-to-Peer and mobile ad-hoc networks and adapting them on the Internet of Things concept. Each Thing can compute the Trust index of another Thing based on its own experiences, while it has the capability of determining its Reputation Index either by consulting its other “friends” (Followees) or referring to the Platform, a management system used in COSMOS. The model is tested through simulations of the proposed social system, demonstrating the ability of TRM-SIoT to achieve the Social Exclusion of malicious nodes and collectives from the network, with low computational overhead and high scalability. Furthermore, due to the adaptive nature of the system, Social Reintegration of these nodes is also possible.","lang":"eng"}],"article_processing_charge":"No","extern":"1","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"IEEE","month":"09","article_number":"7733612","_id":"8300","oa_version":"None","conference":{"end_date":"2016-09-09","name":"ETFA: Conference on Emerging Technologies and Factory Automation","start_date":"2016-09-06","location":"Berlin, Germany"},"date_published":"2016-09-09T00:00:00Z","citation":{"ieee":"E. Kokoris Kogias, O. Voutyras, and T. Varvarigou, “TRM-SIoT: A scalable hybrid trust & reputation model for the social Internet of Things,” in 2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation, Berlin, Germany, 2016.","chicago":"Kokoris Kogias, Eleftherios, Orfefs Voutyras, and Theodora Varvarigou. “TRM-SIoT: A Scalable Hybrid Trust & Reputation Model for the Social Internet of Things.” In 2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation. IEEE, 2016. https://doi.org/10.1109/etfa.2016.7733612.","ama":"Kokoris Kogias E, Voutyras O, Varvarigou T. TRM-SIoT: A scalable hybrid trust & reputation model for the social Internet of Things. In: 2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation. IEEE; 2016. doi:10.1109/etfa.2016.7733612","mla":"Kokoris Kogias, Eleftherios, et al. “TRM-SIoT: A Scalable Hybrid Trust & Reputation Model for the Social Internet of Things.” 2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation, 7733612, IEEE, 2016, doi:10.1109/etfa.2016.7733612.","apa":"Kokoris Kogias, E., Voutyras, O., & Varvarigou, T. (2016). TRM-SIoT: A scalable hybrid trust & reputation model for the social Internet of Things. In 2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation. Berlin, Germany: IEEE. https://doi.org/10.1109/etfa.2016.7733612","ista":"Kokoris Kogias E, Voutyras O, Varvarigou T. 2016. TRM-SIoT: A scalable hybrid trust & reputation model for the social Internet of Things. 2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation. ETFA: Conference on Emerging Technologies and Factory Automation, 7733612.","short":"E. Kokoris Kogias, O. Voutyras, T. Varvarigou, in:, 2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation, IEEE, 2016."},"status":"public","date_created":"2020-08-26T11:48:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1109/etfa.2016.7733612","year":"2016","type":"conference","day":"09","publication_status":"published","date_updated":"2021-01-12T08:17:59Z","title":"TRM-SIoT: A scalable hybrid trust & reputation model for the social Internet of Things","publication_identifier":{"isbn":["9781509013142"]}},{"citation":{"chicago":"Kokoris Kogias, Eleftherios, Philipp Jovanovic, Nicolas Gailly, Ismail Khoffi, Linus Gasser, and Bryan Ford. “Enhancing Bitcoin Security and Performance with Strong Consistency via Collective Signing.” In Proceedings of the 25th USENIX Conference on Security Symposium, 279–296. USENIX Association, 2016.","ieee":"E. Kokoris Kogias, P. Jovanovic, N. Gailly, I. Khoffi, L. Gasser, and B. Ford, “Enhancing bitcoin security and performance with strong consistency via collective signing,” in Proceedings of the 25th USENIX Conference on Security Symposium, Austin, TX, United States, 2016, pp. 279–296.","ama":"Kokoris Kogias E, Jovanovic P, Gailly N, Khoffi I, Gasser L, Ford B. Enhancing bitcoin security and performance with strong consistency via collective signing. In: Proceedings of the 25th USENIX Conference on Security Symposium. USENIX Association; 2016:279–296.","mla":"Kokoris Kogias, Eleftherios, et al. “Enhancing Bitcoin Security and Performance with Strong Consistency via Collective Signing.” Proceedings of the 25th USENIX Conference on Security Symposium, USENIX Association, 2016, pp. 279–296.","apa":"Kokoris Kogias, E., Jovanovic, P., Gailly, N., Khoffi, I., Gasser, L., & Ford, B. (2016). Enhancing bitcoin security and performance with strong consistency via collective signing. In Proceedings of the 25th USENIX Conference on Security Symposium (pp. 279–296). Austin, TX, United States: USENIX Association.","ista":"Kokoris Kogias E, Jovanovic P, Gailly N, Khoffi I, Gasser L, Ford B. 2016. Enhancing bitcoin security and performance with strong consistency via collective signing. Proceedings of the 25th USENIX Conference on Security Symposium. SEC: Security Symposium, 279–296.","short":"E. Kokoris Kogias, P. Jovanovic, N. Gailly, I. Khoffi, L. Gasser, B. Ford, in:, Proceedings of the 25th USENIX Conference on Security Symposium, USENIX Association, 2016, pp. 279–296."},"oa":1,"date_published":"2016-09-01T00:00:00Z","page":"279–296","conference":{"location":"Austin, TX, United States","start_date":"2016-08-10","name":"SEC: Security Symposium","end_date":"2016-08-12"},"oa_version":"Published Version","_id":"8302","month":"09","publisher":"USENIX Association","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","abstract":[{"lang":"eng","text":"While showing great promise, Bitcoin requires users to wait tens of minutes for transactions to commit, and even then, offering only probabilistic guarantees. This paper introduces ByzCoin, a novel Byzantine consensus protocol that leverages scalable collective signing to commit Bitcoin transactions irreversibly within seconds. ByzCoin achieves Byzantine consensus while preserving Bitcoin’s open membership by dynamically forming hash power-proportionate consensus groups that represent recently-successful block miners. ByzCoin employs communication trees to optimize transaction commitment and verification under normal operation while guaranteeing safety and liveness under Byzantine faults, up to a near-optimal tolerance of f faulty group members among 3f + 2 total. ByzCoin mitigates double spending and selfish mining attacks by producing collectively signed transaction blocks within one minute of transaction submission. Tree-structured communication further reduces this latency to less than 30 seconds. Due to these optimizations, ByzCoin achieves a throughput higher than Paypal currently handles, with a confirmation latency of 15-20 seconds."}],"extern":"1","publication":"Proceedings of the 25th USENIX Conference on Security Symposium","external_id":{"arxiv":["1602.06997"]},"author":[{"first_name":"Eleftherios","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Jovanovic, Philipp","first_name":"Philipp","last_name":"Jovanovic"},{"full_name":"Gailly, Nicolas","first_name":"Nicolas","last_name":"Gailly"},{"full_name":"Khoffi, Ismail","last_name":"Khoffi","first_name":"Ismail"},{"last_name":"Gasser","first_name":"Linus","full_name":"Gasser, Linus"},{"last_name":"Ford","first_name":"Bryan","full_name":"Ford, Bryan"}],"publication_identifier":{"isbn":["9781931971324"]},"title":"Enhancing bitcoin security and performance with strong consistency via collective signing","date_updated":"2021-01-12T08:18:00Z","publication_status":"published","day":"01","type":"conference","year":"2016","date_created":"2020-08-26T12:08:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.06997"}],"arxiv":1,"status":"public"},{"oa_version":"None","_id":"8452","intvolume":" 113","date_published":"2016-09-28T00:00:00Z","citation":{"apa":"Rodrigues, C. D. A., Henry, X., Neumann, E., Kurauskas, V., Bellard, L., Fichou, Y., … Morlot, C. (2016). A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1609604113","ista":"Rodrigues CDA, Henry X, Neumann E, Kurauskas V, Bellard L, Fichou Y, Schanda P, Schoehn G, Rudner DZ, Morlot C. 2016. A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. Proceedings of the National Academy of Sciences. 113(41), 11585–11590.","short":"C.D.A. Rodrigues, X. Henry, E. Neumann, V. Kurauskas, L. Bellard, Y. Fichou, P. Schanda, G. Schoehn, D.Z. Rudner, C. Morlot, Proceedings of the National Academy of Sciences 113 (2016) 11585–11590.","ama":"Rodrigues CDA, Henry X, Neumann E, et al. A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. Proceedings of the National Academy of Sciences. 2016;113(41):11585-11590. doi:10.1073/pnas.1609604113","ieee":"C. D. A. Rodrigues et al., “A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis,” Proceedings of the National Academy of Sciences, vol. 113, no. 41. National Academy of Sciences, pp. 11585–11590, 2016.","chicago":"Rodrigues, Christopher D. A., Xavier Henry, Emmanuelle Neumann, Vilius Kurauskas, Laure Bellard, Yann Fichou, Paul Schanda, Guy Schoehn, David Z. Rudner, and Cecile Morlot. “A Ring-Shaped Conduit Connects the Mother Cell and Forespore during Sporulation in Bacillus Subtilis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1609604113.","mla":"Rodrigues, Christopher D. A., et al. “A Ring-Shaped Conduit Connects the Mother Cell and Forespore during Sporulation in Bacillus Subtilis.” Proceedings of the National Academy of Sciences, vol. 113, no. 41, National Academy of Sciences, 2016, pp. 11585–90, doi:10.1073/pnas.1609604113."},"page":"11585-11590","article_type":"original","abstract":[{"lang":"eng","text":"During spore formation in Bacillus subtilis a transenvelope complex is assembled across the double membrane that separates the mother cell and forespore. This complex (called the “A–Q complex”) is required to maintain forespore development and is composed of proteins with remote homology to components of type II, III, and IV secretion systems found in Gram-negative bacteria. Here, we show that one of these proteins, SpoIIIAG, which has remote homology to ring-forming proteins found in type III secretion systems, assembles into an oligomeric ring in the periplasmic-like space between the two membranes. Three-dimensional reconstruction of images generated by cryo-electron microscopy indicates that the SpoIIIAG ring has a cup-and-saucer architecture with a 6-nm central pore. Structural modeling of SpoIIIAG generated a 24-member ring with dimensions similar to those of the EM-derived saucer. Point mutations in the predicted oligomeric interface disrupted ring formation in vitro and impaired forespore gene expression and efficient spore formation in vivo. Taken together, our data provide strong support for the model in which the A–Q transenvelope complex contains a conduit that connects the mother cell and forespore. We propose that a set of stacked rings spans the intermembrane space, as has been found for type III secretion systems."}],"extern":"1","article_processing_charge":"No","quality_controlled":"1","author":[{"last_name":"Rodrigues","first_name":"Christopher D. A.","full_name":"Rodrigues, Christopher D. A."},{"first_name":"Xavier","last_name":"Henry","full_name":"Henry, Xavier"},{"first_name":"Emmanuelle","last_name":"Neumann","full_name":"Neumann, Emmanuelle"},{"full_name":"Kurauskas, Vilius","last_name":"Kurauskas","first_name":"Vilius"},{"first_name":"Laure","last_name":"Bellard","full_name":"Bellard, Laure"},{"full_name":"Fichou, Yann","last_name":"Fichou","first_name":"Yann"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda"},{"full_name":"Schoehn, Guy","last_name":"Schoehn","first_name":"Guy"},{"full_name":"Rudner, David Z.","first_name":"David Z.","last_name":"Rudner"},{"last_name":"Morlot","first_name":"Cecile","full_name":"Morlot, Cecile"}],"publication":"Proceedings of the National Academy of Sciences","month":"09","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","title":"A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis","issue":"41","date_updated":"2021-01-12T08:19:22Z","publication_identifier":{"issn":["0027-8424","1091-6490"]},"date_created":"2020-09-18T10:06:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1073/pnas.1609604113","status":"public","type":"journal_article","day":"28","publication_status":"published","volume":113,"year":"2016"},{"publication_identifier":{"issn":["1520-6106","1520-5207"]},"title":"Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics measurements","issue":"34","keyword":["Physical and Theoretical Chemistry","Materials Chemistry","Surfaces","Coatings and Films"],"date_updated":"2021-01-12T08:19:22Z","publication_status":"published","type":"journal_article","day":"08","year":"2016","volume":120,"date_created":"2020-09-18T10:07:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1021/acs.jpcb.6b06129","status":"public","citation":{"short":"V. Kurauskas, E. Weber, A. Hessel, I. Ayala, D. Marion, P. Schanda, The Journal of Physical Chemistry B 120 (2016) 8905–8913.","ista":"Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. 2016. Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics measurements. The Journal of Physical Chemistry B. 120(34), 8905–8913.","apa":"Kurauskas, V., Weber, E., Hessel, A., Ayala, I., Marion, D., & Schanda, P. (2016). Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics measurements. The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.6b06129","mla":"Kurauskas, Vilius, et al. “Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application to Protein Backbone Dynamics Measurements.” The Journal of Physical Chemistry B, vol. 120, no. 34, American Chemical Society, 2016, pp. 8905–13, doi:10.1021/acs.jpcb.6b06129.","ama":"Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics measurements. The Journal of Physical Chemistry B. 2016;120(34):8905-8913. doi:10.1021/acs.jpcb.6b06129","ieee":"V. Kurauskas, E. Weber, A. Hessel, I. Ayala, D. Marion, and P. Schanda, “Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics measurements,” The Journal of Physical Chemistry B, vol. 120, no. 34. American Chemical Society, pp. 8905–8913, 2016.","chicago":"Kurauskas, Vilius, Emmanuelle Weber, Audrey Hessel, Isabel Ayala, Dominique Marion, and Paul Schanda. “Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application to Protein Backbone Dynamics Measurements.” The Journal of Physical Chemistry B. American Chemical Society, 2016. https://doi.org/10.1021/acs.jpcb.6b06129."},"date_published":"2016-08-08T00:00:00Z","article_type":"original","page":"8905-8913","oa_version":"None","intvolume":" 120","_id":"8453","month":"08","publisher":"American Chemical Society","language":[{"iso":"eng"}],"quality_controlled":"1","abstract":[{"text":"Transverse relaxation rate measurements in magic-angle spinning solid-state nuclear magnetic resonance provide information about molecular motions occurring on nanosecond-to-millisecond (ns–ms) time scales. The measurement of heteronuclear (13C, 15N) relaxation rate constants in the presence of a spin-lock radiofrequency field (R1ρ relaxation) provides access to such motions, and an increasing number of studies involving R1ρ relaxation in proteins have been reported. However, two factors that influence the observed relaxation rate constants have so far been neglected, namely, (1) the role of CSA/dipolar cross-correlated relaxation (CCR) and (2) the impact of fast proton spin flips (i.e., proton spin diffusion and relaxation). We show that CSA/D CCR in R1ρ experiments is measurable and that the CCR rate constant depends on ns–ms motions; it can thus provide insight into dynamics. We find that proton spin diffusion attenuates this CCR due to its decoupling effect on the doublet components. For measurements of dynamics, the use of R1ρ rate constants has practical advantages over the use of CCR rates, and this article reveals factors that have so far been disregarded and which are important for accurate measurements and interpretation.","lang":"eng"}],"extern":"1","article_processing_charge":"No","publication":"The Journal of Physical Chemistry B","author":[{"last_name":"Kurauskas","first_name":"Vilius","full_name":"Kurauskas, Vilius"},{"full_name":"Weber, Emmanuelle","last_name":"Weber","first_name":"Emmanuelle"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"full_name":"Marion, Dominique","first_name":"Dominique","last_name":"Marion"},{"last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}]}]