[{"oa_version":"Published Version","author":[{"full_name":"Cavallari, Nicola","first_name":"Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nibau","full_name":"Nibau, Candida","first_name":"Candida"},{"first_name":"Armin","full_name":"Fuchs, Armin","last_name":"Fuchs"},{"first_name":"Despoina","full_name":"Dadarou, Despoina","last_name":"Dadarou"},{"last_name":"Barta","full_name":"Barta, Andrea","first_name":"Andrea"},{"full_name":"Doonan, John","first_name":"John","last_name":"Doonan"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.1111/tpj.13914","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:17Z","volume":94,"external_id":{"isi":["000434365500008"]},"day":"01","date_published":"2018-06-01T00:00:00Z","article_processing_charge":"No","title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","date_updated":"2023-09-19T10:07:08Z","_id":"403","acknowledgement":"CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1). NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. AB and AF were supported by the Austrian Science Fund (FWF) [DK W1207; SFB RNAreg F43-P10]","year":"2018","has_accepted_license":"1","oa":1,"quality_controlled":"1","citation":{"ama":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 2018;94(6):1010-1022. doi:10.1111/tpj.13914","apa":"Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., & Doonan, J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.13914","chicago":"Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal. Wiley, 2018. https://doi.org/10.1111/tpj.13914.","ista":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022.","ieee":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A,” The Plant Journal, vol. 94, no. 6. Wiley, pp. 1010–1022, 2018.","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","mla":"Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:10.1111/tpj.13914."},"publication_status":"published","abstract":[{"text":"The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved.","lang":"eng"}],"department":[{"_id":"EvBe"}],"language":[{"iso":"eng"}],"publist_id":"7426","publisher":"Wiley","publication":"The Plant Journal","file":[{"date_updated":"2020-07-14T12:46:22Z","file_name":"2018_PlantJourn_Cavallari.pdf","date_created":"2019-02-06T11:40:54Z","file_size":1543354,"relation":"main_file","file_id":"5934","access_level":"open_access","creator":"dernst","checksum":"d9d3ad3215ac0e581731443fca312266","content_type":"application/pdf"}],"file_date_updated":"2020-07-14T12:46:22Z","scopus_import":"1","ddc":["580"],"type":"journal_article","intvolume":" 94","month":"06","isi":1,"page":"1010 - 1022","issue":"6"},{"intvolume":" 50","month":"01","isi":1,"page":"411 - 455","issue":"1","ddc":["510"],"type":"journal_article","abstract":[{"text":"We construct martingale solutions to stochastic thin-film equations by introducing a (spatial) semidiscretization and establishing convergence. The discrete scheme allows for variants of the energy and entropy estimates in the continuous setting as long as the discrete energy does not exceed certain threshold values depending on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy paths constant in time, arbitrary moments of coupled energy/entropy functionals can be controlled. Having established Hölder regularity of approximate solutions, the convergence proof is then based on compactness arguments---in particular on Jakubowski's generalization of Skorokhod's theorem---weak convergence methods, and recent tools on martingale convergence.\r\n\r\n","lang":"eng"}],"department":[{"_id":"JuFi"}],"publist_id":"7425","language":[{"iso":"eng"}],"publisher":"Society for Industrial and Applied Mathematics ","file":[{"file_id":"6992","access_level":"open_access","creator":"dernst","checksum":"89a8eae7c52bb356c04f52b44bff4b5a","content_type":"application/pdf","date_updated":"2020-07-14T12:46:22Z","file_name":"2018_SIAM_Fischer.pdf","file_size":557338,"date_created":"2019-11-07T12:20:25Z","relation":"main_file"}],"publication":"SIAM Journal on Mathematical Analysis","file_date_updated":"2020-07-14T12:46:22Z","scopus_import":"1","quality_controlled":"1","citation":{"mla":"Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 411–55, doi:10.1137/16M1098796.","short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455.","ista":"Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.","ieee":"J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic thin-film equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 1. Society for Industrial and Applied Mathematics , pp. 411–455, 2018.","apa":"Fischer, J. L., & Grün, G. (2018). Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1098796","chicago":"Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1098796.","ama":"Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 2018;50(1):411-455. doi:10.1137/16M1098796"},"article_type":"original","publication_status":"published","year":"2018","has_accepted_license":"1","oa":1,"title":"Existence of positive solutions to stochastic thin-film equations","article_processing_charge":"No","date_updated":"2023-09-11T13:59:22Z","_id":"404","external_id":{"isi":["000426630900015"]},"day":"30","date_published":"2018-01-30T00:00:00Z","oa_version":"Published Version","status":"public","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","full_name":"Fischer, Julian L","first_name":"Julian L","orcid":"0000-0002-0479-558X"},{"full_name":"Grün, Günther","first_name":"Günther","last_name":"Grün"}],"doi":"10.1137/16M1098796","date_created":"2018-12-11T11:46:17Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":50},{"type":"journal_article","ddc":["530","571"],"issue":"3","isi":1,"month":"03","pubrep_id":"995","intvolume":" 13","publication_status":"published","citation":{"chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049","mla":"Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018).","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018."},"quality_controlled":"1","publication":"PLoS One","file":[{"file_size":6887358,"date_created":"2018-12-12T10:15:43Z","date_updated":"2020-07-14T12:46:22Z","file_name":"IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf","relation":"main_file","file_id":"5165","content_type":"application/pdf","checksum":"684229493db75b43e98a46cd922da497","access_level":"open_access","creator":"system"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:46:22Z","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publist_id":"7423","language":[{"iso":"eng"}],"abstract":[{"text":"Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. ","lang":"eng"}],"related_material":{"record":[{"relation":"research_data","id":"9831","status":"public"}]},"_id":"406","date_updated":"2023-09-15T12:06:19Z","title":"Probabilistic models of individual and collective animal behavior","article_processing_charge":"Yes","oa":1,"has_accepted_license":"1","acknowledgement":"This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES).","year":"2018","project":[{"grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"volume":13,"date_created":"2018-12-11T11:46:18Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1371/journal.pone.0193049","author":[{"last_name":"Bod’Ová","full_name":"Bod’Ová, Katarína","first_name":"Katarína"},{"id":"315BCD80-F248-11E8-B48F-1D18A9856A87","last_name":"Mitchell","full_name":"Mitchell, Gabriel","first_name":"Gabriel"},{"full_name":"Harpaz, Roy","first_name":"Roy","last_name":"Harpaz"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Submitted Version","date_published":"2018-03-07T00:00:00Z","day":"07","external_id":{"isi":["000426896800032"]}},{"abstract":[{"lang":"eng","text":"Isoprenoid cytokinins play a number of crucial roles in the regulation of plant growth and development. To study cytokinin receptor properties in plants, we designed and prepared fluorescent derivatives of 6-[(3-methylbut-2-en-1-yl)amino]purine (N6-isopentenyladenine, iP) with several fluorescent labels attached to the C2 or N9 atom of the purine moiety via a 2- or 6-carbon linker. The fluorescent labels included dansyl (DS), fluorescein (FC), 7-nitrobenzofurazan (NBD), rhodamine B (RhoB), coumarin (Cou), 7-(diethylamino)coumarin (DEAC) and cyanine 5 dye (Cy5). All prepared compounds were screened for affinity for the Arabidopsis thaliana cytokinin receptor (CRE1/AHK4). Although the attachment of the fluorescent labels to iP via the linkers mostly disrupted binding to the receptor, several fluorescent derivatives interacted well. For this reason, three derivatives, two rhodamine B and one 4-chloro-7-nitrobenzofurazan labeled iP were tested for their interaction with CRE1/AHK4 and Zea mays cytokinin receptors in detail. We further showed that the three derivatives were able to activate transcription of cytokinin response regulator ARR5 in Arabidopsis seedlings. The activity of fluorescently labeled cytokinins was compared with corresponding 6-dimethylaminopurine fluorescently labeled negative controls. Selected rhodamine B C2-labeled compounds 17, 18 and 4-chloro-7-nitrobenzofurazan N9-labeled compound 28 and their respective negative controls (19, 20 and 29, respectively) were used for in planta staining experiments in Arabidopsis thaliana cell suspension culture using live cell confocal microscopy."}],"language":[{"iso":"eng"}],"department":[{"_id":"EvBe"}],"publist_id":"7422","publisher":"Elsevier","scopus_import":"1","publication":"Phytochemistry","citation":{"mla":"Kubiasová, Karolina, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry, vol. 150, Elsevier, 2018, pp. 1–11, doi:10.1016/j.phytochem.2018.02.015.","short":"K. Kubiasová, V. Mik, J. Nisler, M. Hönig, A. Husičková, L. Spíchal, Z. Pěkná, O. Šamajová, K. Doležal, O. Plíhal, E. Benková, M. Strnad, L. Plíhalová, Phytochemistry 150 (2018) 1–11.","ieee":"K. Kubiasová et al., “Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins,” Phytochemistry, vol. 150. Elsevier, pp. 1–11, 2018.","ista":"Kubiasová K, Mik V, Nisler J, Hönig M, Husičková A, Spíchal L, Pěkná Z, Šamajová O, Doležal K, Plíhal O, Benková E, Strnad M, Plíhalová L. 2018. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 150, 1–11.","chicago":"Kubiasová, Karolina, Václav Mik, Jaroslav Nisler, Martin Hönig, Alexandra Husičková, Lukáš Spíchal, Zuzana Pěkná, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry. Elsevier, 2018. https://doi.org/10.1016/j.phytochem.2018.02.015.","apa":"Kubiasová, K., Mik, V., Nisler, J., Hönig, M., Husičková, A., Spíchal, L., … Plíhalová, L. (2018). Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. Elsevier. https://doi.org/10.1016/j.phytochem.2018.02.015","ama":"Kubiasová K, Mik V, Nisler J, et al. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 2018;150:1-11. doi:10.1016/j.phytochem.2018.02.015"},"quality_controlled":"1","publication_status":"published","intvolume":" 150","month":"06","isi":1,"page":"1-11","type":"journal_article","external_id":{"isi":["000435623400001"]},"day":"01","date_published":"2018-06-01T00:00:00Z","oa_version":"None","author":[{"last_name":"Kubiasová","full_name":"Kubiasová, Karolina","first_name":"Karolina"},{"last_name":"Mik","full_name":"Mik, Václav","first_name":"Václav"},{"first_name":"Jaroslav","full_name":"Nisler, Jaroslav","last_name":"Nisler"},{"first_name":"Martin","full_name":"Hönig, Martin","last_name":"Hönig"},{"full_name":"Husičková, Alexandra","first_name":"Alexandra","last_name":"Husičková"},{"first_name":"Lukáš","full_name":"Spíchal, Lukáš","last_name":"Spíchal"},{"last_name":"Pěkná","first_name":"Zuzana","full_name":"Pěkná, Zuzana"},{"last_name":"Šamajová","full_name":"Šamajová, Olga","first_name":"Olga"},{"last_name":"Doležal","first_name":"Karel","full_name":"Doležal, Karel"},{"full_name":"Plíhal, Ondřej","first_name":"Ondřej","last_name":"Plíhal"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","orcid":"0000-0002-8510-9739"},{"full_name":"Strnad, Miroslav","first_name":"Miroslav","last_name":"Strnad"},{"last_name":"Plíhalová","first_name":"Lucie","full_name":"Plíhalová, Lucie"}],"status":"public","doi":"10.1016/j.phytochem.2018.02.015","volume":150,"date_created":"2018-12-11T11:46:18Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","acknowledgement":"This work was supported by the Ministry of Education Youth and Sports, Czech Republic (grant LO1204 from the National Program of Sustainability I and Agricultural Research ) and by Czech Science Foundation grants 16-04184S , 501/10/1450 and 13-39982S and by IGA projects IGA_PrF_2018_033 and IGA_PrF_2018_023 . We would like to thank Jarmila Balonová, Olga Hustáková and Miroslava Šubová for their skillful technical assistance and Mgr. Tomáš Pospíšil, Ph.D. for his measurement of 1 H NMR and analysis of some 2D NMR spectral data. \r\n","article_processing_charge":"No","title":"Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins","_id":"407","date_updated":"2023-09-11T12:53:11Z"},{"day":"01","date_published":"2018-03-01T00:00:00Z","external_id":{"pmid":["29525951"]},"pmid":1,"doi":"10.1007/978-1-4939-7747-5_7","volume":1761,"date_created":"2018-12-11T11:46:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","status":"public","author":[{"last_name":"Trinh","full_name":"Trinh, Hoang","first_name":"Hoang"},{"full_name":"Verstraeten, Inge","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten"},{"full_name":"Geelen, Danny","first_name":"Danny","last_name":"Geelen"}],"publication_identifier":{"issn":["1064-3745"]},"year":"2018","_id":"408","date_updated":"2021-01-12T07:54:21Z","article_processing_charge":"No","title":"In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls","publisher":"Springer Nature","publication":"Root Development ","scopus_import":"1","abstract":[{"lang":"eng","text":"Adventitious roots (AR) are de novo formed roots that emerge from any part of the plant or from callus in tissue culture, except root tissue. The plant tissue origin and the method by which they are induced determine the physiological properties of emerged ARs. Hence, a standard method encompassing all types of AR does not exist. Here we describe a method for the induction and analysis of AR that emerge from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis and shows a determined developmental pattern which usually does not involve AR formation. However, the hypocotyl shows propensity to form de novo roots under specific circumstances such as removal of the root system, high humidity or flooding, or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer surrounding the vascular tissue of the central cylinder, which is reminiscent to the developmental program of lateral roots. Here we propose an easy protocol for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings."}],"department":[{"_id":"JiFr"}],"publist_id":"7421","language":[{"iso":"eng"}],"publication_status":"published","citation":{"ama":"Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . Vol 1761. Springer Nature; 2018:95-102. doi:10.1007/978-1-4939-7747-5_7","apa":"Trinh, H., Verstraeten, I., & Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In Root Development (Vol. 1761, pp. 95–102). Springer Nature. https://doi.org/10.1007/978-1-4939-7747-5_7","chicago":"Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In Root Development , 1761:95–102. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-7747-5_7.","ieee":"H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102.","ista":"Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761, 95–102.","mla":"Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102, doi:10.1007/978-1-4939-7747-5_7.","short":"H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102."},"alternative_title":["MIMB"],"quality_controlled":"1","page":"95 - 102","intvolume":" 1761","month":"03","type":"book_chapter"},{"date_updated":"2023-09-13T09:34:12Z","_id":"409","article_processing_charge":"No","title":"On the number of non-hexagons in a planar tiling","publication_identifier":{"issn":["1631073X"]},"oa":1,"year":"2018","date_created":"2018-12-11T11:46:19Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":356,"doi":"10.1016/j.crma.2018.03.005","author":[{"last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","first_name":"Arseniy"}],"status":"public","oa_version":"Preprint","date_published":"2018-04-01T00:00:00Z","day":"01","external_id":{"arxiv":["1805.01652"],"isi":["000430402700009"]},"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1805.01652","open_access":"1"}],"arxiv":1,"issue":"4","page":"412-414","isi":1,"month":"04","intvolume":" 356","publication_status":"published","article_type":"original","quality_controlled":"1","citation":{"ama":"Akopyan A. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 2018;356(4):412-414. doi:10.1016/j.crma.2018.03.005","apa":"Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. Elsevier. https://doi.org/10.1016/j.crma.2018.03.005","chicago":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique. Elsevier, 2018. https://doi.org/10.1016/j.crma.2018.03.005.","ieee":"A. Akopyan, “On the number of non-hexagons in a planar tiling,” Comptes Rendus Mathematique, vol. 356, no. 4. Elsevier, pp. 412–414, 2018.","ista":"Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 356(4), 412–414.","short":"A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414.","mla":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:10.1016/j.crma.2018.03.005."},"publication":"Comptes Rendus Mathematique","scopus_import":"1","publisher":"Elsevier","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"publist_id":"7420","abstract":[{"lang":"eng","text":"We give a simple proof of T. Stehling's result [4], whereby in any normal tiling of the plane with convex polygons with number of sides not less than six, all tiles except a finite number are hexagons."}]},{"date_published":"2018-09-19T00:00:00Z","day":"19","external_id":{"isi":["000445090100002"]},"date_created":"2018-12-11T11:44:19Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":12,"doi":"10.3389/fncel.2018.00311","author":[{"first_name":"Rafæl","full_name":"Luján, Rafæl","last_name":"Luján"},{"last_name":"Aguado","full_name":"Aguado, Carolina","first_name":"Carolina"},{"last_name":"Ciruela","full_name":"Ciruela, Francisco","first_name":"Francisco"},{"last_name":"Arus","first_name":"Xavier","full_name":"Arus, Xavier"},{"full_name":"Martín Belmonte, Alejandro","first_name":"Alejandro","last_name":"Martín Belmonte"},{"last_name":"Alfaro Ruiz","first_name":"Rocío","full_name":"Alfaro Ruiz, Rocío"},{"full_name":"Martinez Gomez, Jesus","first_name":"Jesus","last_name":"Martinez Gomez"},{"full_name":"De La Ossa, Luis","first_name":"Luis","last_name":"De La Ossa"},{"last_name":"Watanabe","full_name":"Watanabe, Masahiko","first_name":"Masahiko"},{"first_name":"John","full_name":"Adelman, John","last_name":"Adelman"},{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Published Version","publication_identifier":{"issn":["16625102"]},"oa":1,"has_accepted_license":"1","project":[{"call_identifier":"H2020","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)"}],"year":"2018","date_updated":"2023-09-18T09:31:18Z","_id":"41","title":"Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells","article_processing_charge":"No","publication":"Frontiers in Cellular Neuroscience","file":[{"date_created":"2018-12-17T08:49:03Z","file_size":6834251,"date_updated":"2020-07-14T12:46:23Z","file_name":"fncel-12-00311.pdf","relation":"main_file","file_id":"5684","content_type":"application/pdf","checksum":"0bcaec8d596162af0b7fe3f31325d480","access_level":"open_access","creator":"dernst"}],"file_date_updated":"2020-07-14T12:46:23Z","scopus_import":"1","publisher":"Frontiers Media","language":[{"iso":"eng"}],"publist_id":"8013","department":[{"_id":"RySh"}],"abstract":[{"text":"The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells (PCs). To understand the molecular basis by which SK2 channels mediate these functions, we analyzed the exact location and densities of SK2 channels along the neuronal surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold particles for SK2 were observed on post- and pre-synaptic compartments showing both scattered and clustered distribution patterns. We found an axo-somato-dendritic gradient of the SK2 particle density increasing 12-fold from soma to dendritic spines. Using two different immunogold approaches, we also found that SK2 immunoparticles were frequently adjacent to, but never overlap with, the postsynaptic density of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated that SK2 channels form macromolecular complexes with two types of proteins that mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture replica double-labeling showed significant co-clustering of particles for SK2 with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are close to CaV2.1 channels, though they are not significantly co-clustered. These data demonstrate that SK2 channels located in different neuronal compartments can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures voltage (excitability) regulation by distinct intracellular Ca2+ transients in PCs.","lang":"eng"}],"publication_status":"published","article_type":"original","quality_controlled":"1","citation":{"ista":"Luján R, Aguado C, Ciruela F, Arus X, Martín Belmonte A, Alfaro Ruiz R, Martinez Gomez J, De La Ossa L, Watanabe M, Adelman J, Shigemoto R, Fukazawa Y. 2018. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 12, 311.","ieee":"R. Luján et al., “Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells,” Frontiers in Cellular Neuroscience, vol. 12. Frontiers Media, 2018.","short":"R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz, J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa, Frontiers in Cellular Neuroscience 12 (2018).","mla":"Luján, Rafæl, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience, vol. 12, 311, Frontiers Media, 2018, doi:10.3389/fncel.2018.00311.","ama":"Luján R, Aguado C, Ciruela F, et al. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 2018;12. doi:10.3389/fncel.2018.00311","apa":"Luján, R., Aguado, C., Ciruela, F., Arus, X., Martín Belmonte, A., Alfaro Ruiz, R., … Fukazawa, Y. (2018). Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2018.00311","chicago":"Luján, Rafæl, Carolina Aguado, Francisco Ciruela, Xavier Arus, Alejandro Martín Belmonte, Rocío Alfaro Ruiz, Jesus Martinez Gomez, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience. Frontiers Media, 2018. https://doi.org/10.3389/fncel.2018.00311."},"ec_funded":1,"month":"09","isi":1,"intvolume":" 12","article_number":"311","ddc":["570"],"type":"journal_article"},{"publication_status":"published","quality_controlled":"1","citation":{"ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 8(1), 5184.","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for quantitative brain lesion characterization and electrode localization,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports, vol. 8, no. 1, 5184, Nature Publishing Group, 2018, doi:10.1038/s41598-018-23247-z.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Scientific Reports 8 (2018).","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-23247-z","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-23247-z","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-23247-z."},"file":[{"content_type":"application/pdf","checksum":"653fcb852f899c75b00ceee2a670d738","creator":"system","access_level":"open_access","file_id":"4831","relation":"main_file","date_created":"2018-12-12T10:10:42Z","file_size":2359430,"file_name":"IST-2018-994-v1+1_2018_Joesch_A-micro-CT-based.pdf","date_updated":"2020-07-14T12:46:23Z"}],"publication":"Scientific Reports","file_date_updated":"2020-07-14T12:46:23Z","scopus_import":"1","publisher":"Nature Publishing Group","department":[{"_id":"MaJö"}],"language":[{"iso":"eng"}],"publist_id":"7419","abstract":[{"text":"Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.","lang":"eng"}],"ddc":["571","572"],"type":"journal_article","issue":"1","isi":1,"month":"03","intvolume":" 8","pubrep_id":"994","article_number":"5184","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:19Z","volume":8,"doi":"10.1038/s41598-018-23247-z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Masís, Javier","first_name":"Javier","last_name":"Masís"},{"last_name":"Mankus","full_name":"Mankus, David","first_name":"David"},{"full_name":"Wolff, Steffen","first_name":"Steffen","last_name":"Wolff"},{"full_name":"Guitchounts, Grigori","first_name":"Grigori","last_name":"Guitchounts"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330"},{"full_name":"Cox, David","first_name":"David","last_name":"Cox"}],"oa_version":"Published Version","date_published":"2018-03-26T00:00:00Z","day":"26","external_id":{"isi":["000428234100005"]},"date_updated":"2023-09-08T11:48:39Z","_id":"410","title":"A micro-CT-based method for quantitative brain lesion characterization and electrode localization","article_processing_charge":"No","oa":1,"has_accepted_license":"1","year":"2018"},{"page":"131 - 143","month":"03","intvolume":" 1761","year":"2018","_id":"411","type":"book_chapter","date_updated":"2021-01-12T07:54:34Z","title":"Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia","scopus_import":1,"publication":"Root Development. Methods and Protocols","date_published":"2018-03-11T00:00:00Z","day":"11","publisher":"Springer","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publist_id":"7418","abstract":[{"text":"Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins.","lang":"eng"}],"editor":[{"first_name":"Daniela","full_name":"Ristova, Daniela","last_name":"Ristova"},{"last_name":"Barbez","full_name":"Barbez, Elke","first_name":"Elke"}],"volume":1761,"date_created":"2018-12-11T11:46:20Z","publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-1-4939-7747-5_10","citation":{"ista":"Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology, vol. 1761, 131–143.","ieee":"M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia,” in Root Development. Methods and Protocols, vol. 1761, D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143.","mla":"Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, vol. 1761, Springer, 2018, pp. 131–43, doi:10.1007/978-1-4939-7747-5_10.","short":"M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez (Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143.","ama":"Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Ristova D, Barbez E, eds. Root Development. Methods and Protocols. Vol 1761. MIMB. Springer; 2018:131-143. doi:10.1007/978-1-4939-7747-5_10","apa":"Karampelias, M., Tejos, R., Friml, J., & Vanneste, S. (2018). Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In D. Ristova & E. Barbez (Eds.), Root Development. Methods and Protocols (Vol. 1761, pp. 131–143). Springer. https://doi.org/10.1007/978-1-4939-7747-5_10","chicago":"Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” In Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018. https://doi.org/10.1007/978-1-4939-7747-5_10."},"alternative_title":["Methods in Molecular Biology"],"series_title":"MIMB","quality_controlled":"1","author":[{"first_name":"Michael","full_name":"Karampelias, Michael","last_name":"Karampelias"},{"first_name":"Ricardo","full_name":"Tejos, Ricardo","last_name":"Tejos"},{"full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"}],"status":"public","oa_version":"None"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","last_name":"Kania","first_name":"Urszula","full_name":"Kania, Urszula"},{"orcid":"0000-0003-0619-7783","first_name":"Matous","full_name":"Glanc, Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","date_created":"2018-12-11T11:46:20Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":30,"doi":"10.1105/tpc.17.00785","pmid":1,"external_id":{"isi":["000429441400018"],"pmid":["29511054"]},"date_published":"2018-04-09T00:00:00Z","day":"09","title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6269"}]},"date_updated":"2025-05-07T11:12:27Z","_id":"412","has_accepted_license":"1","year":"2018","project":[{"grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"oa":1,"quality_controlled":"1","citation":{"ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018.","ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785.","ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785.","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785"},"publication_status":"published","article_type":"original","department":[{"_id":"JiFr"}],"publist_id":"7417","language":[{"iso":"eng"}],"abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana.","lang":"eng"}],"scopus_import":"1","file":[{"file_name":"2018_PlantCell_Adamowski.pdf","date_updated":"2022-05-23T09:12:38Z","file_size":4407538,"success":1,"date_created":"2022-05-23T09:12:38Z","relation":"main_file","file_id":"11406","creator":"dernst","access_level":"open_access","checksum":"4e165e653b67d3f0684697f21aace5a1","content_type":"application/pdf"}],"file_date_updated":"2022-05-23T09:12:38Z","publication":"The Plant Cell","publisher":"American Society of Plant Biologists","ddc":["580"],"type":"journal_article","month":"04","isi":1,"intvolume":" 30","issue":"3","page":"700 - 716","ec_funded":1},{"volume":115,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:20Z","pmid":1,"doi":"10.1073/pnas.1713501115","author":[{"full_name":"Konrad, Matthias","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad"},{"full_name":"Pull, Christopher","first_name":"Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull"},{"id":"48204546-F248-11E8-B48F-1D18A9856A87","last_name":"Metzler","first_name":"Sina","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494"},{"full_name":"Seif, Katharina","first_name":"Katharina","last_name":"Seif","id":"90F7894A-02CF-11E9-976E-E38CFE5CBC1D"},{"full_name":"Naderlinger, Elisabeth","first_name":"Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V","full_name":"Grasse, Anna V"},{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"status":"public","oa_version":"Published Version","date_published":"2018-03-13T00:00:00Z","day":"13","external_id":{"pmid":["29463746"],"isi":["000427245400069"]},"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/helping-in-spite-of-risk-ants-perform-risk-averse-sanitary-care-of-infectious-nest-mates/","description":"News on IST Homepage"}]},"_id":"413","date_updated":"2023-09-08T13:22:21Z","title":"Ants avoid superinfections by performing risk-adjusted sanitary care","article_processing_charge":"No","oa":1,"project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","call_identifier":"FP7"}],"year":"2018","publication_status":"published","citation":{"ama":"Konrad M, Pull C, Metzler S, et al. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 2018;115(11):2782-2787. doi:10.1073/pnas.1713501115","chicago":"Konrad, Matthias, Christopher Pull, Sina Metzler, Katharina Seif, Elisabeth Naderlinger, Anna V Grasse, and Sylvia Cremer. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713501115.","apa":"Konrad, M., Pull, C., Metzler, S., Seif, K., Naderlinger, E., Grasse, A. V., & Cremer, S. (2018). Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713501115","ista":"Konrad M, Pull C, Metzler S, Seif K, Naderlinger E, Grasse AV, Cremer S. 2018. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 115(11), 2782–2787.","ieee":"M. Konrad et al., “Ants avoid superinfections by performing risk-adjusted sanitary care,” PNAS, vol. 115, no. 11. National Academy of Sciences, pp. 2782–2787, 2018.","mla":"Konrad, Matthias, et al. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS, vol. 115, no. 11, National Academy of Sciences, 2018, pp. 2782–87, doi:10.1073/pnas.1713501115.","short":"M. Konrad, C. Pull, S. Metzler, K. Seif, E. Naderlinger, A.V. Grasse, S. Cremer, PNAS 115 (2018) 2782–2787."},"quality_controlled":"1","publication":"PNAS","scopus_import":"1","publisher":"National Academy of Sciences","department":[{"_id":"SyCr"}],"publist_id":"7416","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Being cared for when sick is a benefit of sociality that can reduce disease and improve survival of group members. However, individuals providing care risk contracting infectious diseases themselves. If they contract a low pathogen dose, they may develop low-level infections that do not cause disease but still affect host immunity by either decreasing or increasing the host’s vulnerability to subsequent infections. Caring for contagious individuals can thus significantly alter the future disease susceptibility of caregivers. Using ants and their fungal pathogens as a model system, we tested if the altered disease susceptibility of experienced caregivers, in turn, affects their expression of sanitary care behavior. We found that low-level infections contracted during sanitary care had protective or neutral effects on secondary exposure to the same (homologous) pathogen but consistently caused high mortality on superinfection with a different (heterologous) pathogen. In response to this risk, the ants selectively adjusted the expression of their sanitary care. Specifically, the ants performed less grooming and more antimicrobial disinfection when caring for nestmates contaminated with heterologous pathogens compared with homologous ones. By modulating the components of sanitary care in this way the ants acquired less infectious particles of the heterologous pathogens, resulting in reduced superinfection. The performance of risk-adjusted sanitary care reveals the remarkable capacity of ants to react to changes in their disease susceptibility, according to their own infection history and to flexibly adjust collective care to individual risk."}],"type":"journal_article","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29463746","open_access":"1"}],"issue":"11","ec_funded":1,"page":"2782 - 2787","month":"03","isi":1,"intvolume":" 115"},{"abstract":[{"lang":"eng","text":"Recently it was shown that a molecule rotating in a quantum solvent can be described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett. 118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules possessing an additional spin-1/2 degree of freedom and study the behavior of the system in the presence of a static magnetic field. We show that exchange of angular momentum between the molecule and the solvent can be altered by the field, even though the solvent itself is non-magnetic. In particular, we demonstrate a possibility to control resonant emission of phonons with a given angular momentum using a magnetic field."}],"language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"publist_id":"7408","publisher":"AIP Publishing","publication":"The Journal of Chemical Physics","scopus_import":"1","quality_controlled":"1","citation":{"short":"W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018).","mla":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics, vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:10.1063/1.5017591.","ieee":"W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent angular momentum transfer,” The Journal of Chemical Physics, vol. 148, no. 10. AIP Publishing, 2018.","ista":"Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307.","chicago":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics. AIP Publishing, 2018. https://doi.org/10.1063/1.5017591.","apa":"Rzadkowski, W., & Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5017591","ama":"Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 2018;148(10). doi:10.1063/1.5017591"},"article_type":"original","publication_status":"published","intvolume":" 148","article_number":"104307","month":"03","isi":1,"ec_funded":1,"issue":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.09904"}],"arxiv":1,"type":"journal_article","external_id":{"isi":["000427517200065"],"arxiv":["1711.09904"]},"day":"14","date_published":"2018-03-14T00:00:00Z","oa_version":"Preprint","status":"public","author":[{"orcid":"0000-0002-1106-4419","first_name":"Wojciech","full_name":"Rzadkowski, Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1063/1.5017591","date_created":"2018-12-11T11:46:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":148,"project":[{"name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","call_identifier":"FWF"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"acknowledgement":"We acknowledge insightful discussions with Giacomo Bighin, Igor Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","year":"2018","oa":1,"article_processing_charge":"No","title":"Effect of a magnetic field on molecule–solvent angular momentum transfer","date_updated":"2024-02-28T13:01:59Z","_id":"415","related_material":{"record":[{"status":"public","id":"10759","relation":"dissertation_contains"}]}},{"article_processing_charge":"No","title":"Diagrammatic Monte Carlo approach to rotating molecular impurities","_id":"417","date_updated":"2024-02-28T13:14:53Z","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902"}],"year":"2018","oa":1,"oa_version":"Preprint","author":[{"last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","first_name":"Giacomo"},{"last_name":"Tscherbul","first_name":"Timur","full_name":"Tscherbul, Timur"},{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"status":"public","doi":"10.1103/PhysRevLett.121.165301","volume":121,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:46:22Z","external_id":{"arxiv":["1803.07990"]},"day":"16","date_published":"2018-10-16T00:00:00Z","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.07990"}],"type":"journal_article","article_number":"165301","intvolume":" 121","month":"10","issue":"16","citation":{"mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to rotating molecular impurities,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 121(16), 165301.","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301"},"quality_controlled":"1","publication_status":"published","abstract":[{"text":"We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular impurities with rotational degrees of freedom interacting with a many-particle environment. The treatment is based on the diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach works at arbitrary coupling, is free of systematic errors and of finite size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model, however, the method is quite general and can be applied to a broad variety of quantum impurities possessing angular momentum degrees of freedom. ","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"8025","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","scopus_import":"1","publication":"Physical Review Letters"},{"type":"dissertation","ddc":["571","570"],"page":"107","degree_awarded":"PhD","pubrep_id":"913","month":"01","supervisor":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","full_name":"Janovjak, Harald L","first_name":"Harald L","orcid":"0000-0002-8023-9315"}],"publication_status":"published","citation":{"ista":"Gschaider-Reichhart E. 2018. Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria.","ieee":"E. Gschaider-Reichhart, “Optical and optogenetic control of proliferation and survival ,” Institute of Science and Technology Austria, 2018.","mla":"Gschaider-Reichhart, Eva. Optical and Optogenetic Control of Proliferation and Survival . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_913.","short":"E. Gschaider-Reichhart, Optical and Optogenetic Control of Proliferation and Survival , Institute of Science and Technology Austria, 2018.","ama":"Gschaider-Reichhart E. Optical and optogenetic control of proliferation and survival . 2018. doi:10.15479/AT:ISTA:th_913","chicago":"Gschaider-Reichhart, Eva. “Optical and Optogenetic Control of Proliferation and Survival .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_913.","apa":"Gschaider-Reichhart, E. (2018). Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_913"},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:46:24Z","file":[{"creator":"dernst","access_level":"closed","checksum":"697fa72ca36fb1b8ceabc133d58a73e5","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6222","relation":"source_file","file_name":"2018_THESIS_Gschaider-Reichhart_source.docx","date_updated":"2020-07-14T12:46:24Z","date_created":"2019-04-05T09:28:03Z","file_size":7012495},{"relation":"main_file","date_updated":"2020-07-14T12:46:24Z","file_name":"2018_THESIS_Gschaider-Reichhart.pdf","date_created":"2019-04-05T09:28:03Z","file_size":6355280,"access_level":"open_access","creator":"dernst","checksum":"58d7d1e9e58aeb7f061ab686b1d8a48c","content_type":"application/pdf","file_id":"6223"}],"abstract":[{"lang":"eng","text":"The aim of this thesis was the development of new strategies for optical and optogenetic control of proliferative and pro-survival signaling, and characterizing them from the molecular mechanism up to cellular effects. These new light-based methods have unique features, such as red light as an activator, or the avoidance of gene delivery, which enable to overcome current limitations, such as light delivery to target tissues and feasibility as therapeutic approach. A special focus was placed on implementing these new light-based approaches in pancreatic β-cells, as β-cells are the key players in diabetes and especially their loss in number negatively affects disease progression. Currently no treatment options are available to compensate the lack of functional β-cells in diabetic patients.\r\nIn a first approach, red-light-activated growth factor receptors, in particular receptor tyrosine kinases were engineered and characterized. Receptor activation with light allows spatio-temporal control compared to ligand-based activation, and especially red light exhibits deeper tissue penetration than other wavelengths of the visible spectrum. Red-light-activated receptor tyrosine kinases robustly activated major growth factor related signaling pathways with a high temporal resolution. Moreover, the remote activation of the proliferative MAPK/Erk pathway by red-light-activated receptor tyrosine kinases in a pancreatic β-cell line was also achieved, through one centimeter thick mouse tissue. Although red-light-activated receptor tyrosine kinases are particularly attractive for applications in animal models due to the deep tissue penetration of red light, a drawback, especially with regard to translation into humans, is the requirement of gene therapy.\r\nIn a second approach an endogenous light-sensitive mechanism was identified and its potential to promote proliferative and pro-survival signals was explored, towards light-based tissue regeneration without the need for gene transfer. Blue-green light illumination was found to be sufficient for the activation of proliferation and survival promoting signaling pathways in primary pancreatic murine and human islets. Blue-green light also led to an increase in proliferation of primary islet cells, an effect which was shown to be mostly β-cell specific in human islets. Moreover, it was demonstrated that this approach of pancreatic β-cell expansion did not have any negative effect on the β-cell function, in particular on their insulin secretion capacity. In contrast, a trend for enhanced insulin secretion under high glucose conditions after illumination was detected. In order to unravel the detailed characteristics of this endogenous light-sensitive mechanism, the precise light requirements were determined. In addition, the expression of light sensing proteins, OPN3 and rhodopsin, was detected. The observed effects were found to be independent of handling effects such as temperature differences and cytochrome c oxidase dependent ATP increase, but they were found to be enhanced through the knockout of OPN3. The exact mechanism of how islets cells sense light and the identity of the photoreceptor remains unknown.\r\nSummarized two new light-based systems with unique features were established that enable the activation of proliferative and pro-survival signaling pathways. While red-light-activated receptor tyrosine kinases open a new avenue for optogenetics research, by allowing non-invasive control of signaling in vivo, the identified endogenous light-sensitive mechanism has the potential to be the basis of a gene therapy-free therapeutical approach for light-based β-cell expansion."}],"language":[{"iso":"eng"}],"department":[{"_id":"HaJa"}],"publist_id":"7405","_id":"418","date_updated":"2023-09-22T09:20:10Z","related_material":{"record":[{"status":"public","id":"1441","relation":"part_of_dissertation"},{"status":"public","id":"1678","relation":"part_of_dissertation"},{"id":"2084","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1028"}]},"article_processing_charge":"No","title":"Optical and optogenetic control of proliferation and survival ","oa":1,"publication_identifier":{"issn":["2663-337X"]},"year":"2018","has_accepted_license":"1","doi":"10.15479/AT:ISTA:th_913","date_created":"2018-12-11T11:46:22Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","first_name":"Eva"}],"status":"public","day":"08","date_published":"2018-01-08T00:00:00Z"},{"citation":{"ama":"Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2018;2:469–477. doi:10.1038/s41562-018-0320-9","apa":"Hilbe, C., Chatterjee, K., & Nowak, M. (2018). Partners and rivals in direct reciprocity. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0320-9","chicago":"Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0320-9.","ieee":"C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 469–477, 2018.","ista":"Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2, 469–477.","mla":"Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:10.1038/s41562-018-0320-9.","short":"C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477."},"quality_controlled":"1","publication_status":"published","article_type":"review","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publist_id":"7404","abstract":[{"text":"Reciprocity is a major factor in human social life and accounts for a large part of cooperation in our communities. Direct reciprocity arises when repeated interactions occur between the same individuals. The framework of iterated games formalizes this phenomenon. Despite being introduced more than five decades ago, the concept keeps offering beautiful surprises. Recent theoretical research driven by new mathematical tools has proposed a remarkable dichotomy among the crucial strategies: successful individuals either act as partners or as rivals. Rivals strive for unilateral advantages by applying selfish or extortionate strategies. Partners aim to share the payoff for mutual cooperation, but are ready to fight back when being exploited. Which of these behaviours evolves depends on the environment. Whereas small population sizes and a limited number of rounds favour rivalry, partner strategies are selected when populations are large and relationships stable. Only partners allow for evolution of cooperation, while the rivals’ attempt to put themselves first leads to defection. Hilbe et al. synthesize recent theoretical work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas. They describe the environments under which these contrasting selfish or cooperative strategies emerge in evolution.","lang":"eng"}],"file":[{"relation":"main_file","file_name":"2018_NatureHumanBeh_Hilbe.pdf","date_updated":"2020-07-14T12:46:25Z","file_size":598033,"date_created":"2019-11-19T08:19:51Z","creator":"dernst","access_level":"open_access","checksum":"571b8cc0ba14e8d5d8b18e439a9835eb","content_type":"application/pdf","file_id":"7052"}],"publication":"Nature Human Behaviour","file_date_updated":"2020-07-14T12:46:25Z","scopus_import":"1","publisher":"Nature Publishing Group","type":"journal_article","ddc":["000"],"isi":1,"month":"03","intvolume":" 2","ec_funded":1,"page":"469–477","status":"public","author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","full_name":"Hilbe, Christian","first_name":"Christian","orcid":"0000-0001-5116-955X"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"oa_version":"Submitted Version","volume":2,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:22Z","doi":"10.1038/s41562-018-0320-9","external_id":{"isi":["000446612000016"]},"date_published":"2018-03-19T00:00:00Z","day":"19","article_processing_charge":"No","title":"Partners and rivals in direct reciprocity","related_material":{"link":[{"url":"http://doi.org/10.1038/s41562-018-0342-3","relation":"erratum"}]},"_id":"419","date_updated":"2023-09-13T09:38:54Z","has_accepted_license":"1","year":"2018","project":[{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"oa":1},{"external_id":{"isi":["000448163900015"]},"date_published":"2018-07-26T00:00:00Z","day":"26","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Cucinotta, Mara","first_name":"Mara","last_name":"Cucinotta"},{"first_name":"Silvia","full_name":"Manrique, Silvia","last_name":"Manrique"},{"last_name":"Cuesta","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","first_name":"Candela","full_name":"Cuesta, Candela"},{"first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"last_name":"Colombo","full_name":"Colombo, Lucia","first_name":"Lucia"}],"oa_version":"Published Version","volume":69,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:19Z","doi":"10.1093/jxb/ery281","has_accepted_license":"1","year":"2018","acknowledgement":"This work was funded by the Ministry of Education, Youth and Sports of the Czech Republic through the National Program of Sustainability (grant no. LO1204).","oa":1,"title":"Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis","article_processing_charge":"No","_id":"42","date_updated":"2023-09-11T12:52:03Z","publist_id":"8012","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"}],"abstract":[{"lang":"eng","text":"Seeds derive from ovules upon fertilization and therefore the total number of ovules determines the final seed yield, a fundamental trait in crop plants. Among the factors that co-ordinate the process of ovule formation, the transcription factors CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 and the hormone cytokinin (CK) have a particularly prominent role. Indeed, the absence of both CUC1 and CUC2 causes a severe reduction in ovule number, a phenotype that can be rescued by CK treatment. In this study, we combined CK quantification with an integrative genome-wide target identification approach to select Arabidopsis genes regulated by CUCs that are also involved in CK metabolism. We focused our attention on the functional characterization of UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) and UGT73C1, which are up-regulated in the absence of CUC1 and CUC2 and encode enzymes able to catalyse CK inactivation by O-glucosylation. Our results demonstrate a role for these UGTs as a link between CUCs and CK homeostasis, and highlight the importance of CUCs and CKs in the determination of seed yield."}],"file_date_updated":"2020-07-14T12:46:25Z","file":[{"relation":"main_file","date_created":"2018-12-17T10:44:16Z","file_size":1292128,"date_updated":"2020-07-14T12:46:25Z","file_name":"2018_JournalExperimBotany_Cucinotta.pdf","checksum":"ca3b6711040b1662488aeb3d1f961f13","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_id":"5691"}],"publication":"Journal of Experimental Botany","scopus_import":"1","publisher":"Oxford University Press","citation":{"ieee":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, and L. Colombo, “Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis,” Journal of Experimental Botany, vol. 69, no. 21. Oxford University Press, pp. 5169–5176, 2018.","ista":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. 2018. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 69(21), 5169–5176.","short":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, L. Colombo, Journal of Experimental Botany 69 (2018) 5169–5176.","mla":"Cucinotta, Mara, et al. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany, vol. 69, no. 21, Oxford University Press, 2018, pp. 5169–76, doi:10.1093/jxb/ery281.","ama":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 2018;69(21):5169-5176. doi:10.1093/jxb/ery281","apa":"Cucinotta, M., Manrique, S., Cuesta, C., Benková, E., Novák, O., & Colombo, L. (2018). Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery281","chicago":"Cucinotta, Mara, Silvia Manrique, Candela Cuesta, Eva Benková, Ondřej Novák, and Lucia Colombo. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery281."},"quality_controlled":"1","publication_status":"published","month":"07","isi":1,"intvolume":" 69","issue":"21","page":"5169 - 5176","type":"journal_article","ddc":["575"]},{"department":[{"_id":"MiLe"}],"publist_id":"7402","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We analyze the theoretical derivation of the beyond-mean-field equation of state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer (BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature our theory — considering Gaussian fluctuations on top of the mean-field equation of state — is in very good agreement with experimental data. Subsequently, we investigate the superfluid density at finite temperature and its renormalization due to the proliferation of vortex–antivortex pairs. By doing so, we determine the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the renormalized superfluid density jumps to zero — as a function of the inter-atomic potential strength. We find that the Nelson–Kosterlitz criterion overestimates the BKT temperature with respect to the renormalization group equations, this effect being particularly relevant in the intermediate regime of the crossover."}],"publication":"International Journal of Modern Physics B","scopus_import":"1","publisher":"World Scientific Publishing","quality_controlled":"1","citation":{"ieee":"G. Bighin and L. Salasnich, “Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover,” International Journal of Modern Physics B, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018.","ista":"Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 32(17), 1840022.","short":"G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018) 1840022.","mla":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022, doi:10.1142/S0217979218400222.","ama":"Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 2018;32(17):1840022. doi:10.1142/S0217979218400222","chicago":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B. World Scientific Publishing, 2018. https://doi.org/10.1142/S0217979218400222.","apa":"Bighin, G., & Salasnich, L. (2018). Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. World Scientific Publishing. https://doi.org/10.1142/S0217979218400222"},"publication_status":"published","isi":1,"month":"07","intvolume":" 32","issue":"17","page":"1840022","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.11171"}],"type":"journal_article","external_id":{"isi":["000438217300007"]},"date_published":"2018-07-10T00:00:00Z","day":"10","status":"public","author":[{"orcid":"0000-0001-8823-9777","first_name":"Giacomo","full_name":"Bighin, Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Salasnich","full_name":"Salasnich, Luca","first_name":"Luca"}],"oa_version":"Preprint","date_created":"2018-12-11T11:46:22Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":32,"doi":"10.1142/S0217979218400222","year":"2018","oa":1,"article_processing_charge":"No","title":"Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover","date_updated":"2023-09-18T08:09:59Z","_id":"420"},{"issue":"4","page":"968 - 977","isi":1,"month":"02","intvolume":" 114","type":"journal_article","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.01486"}],"scopus_import":"1","publication":"Biophysical Journal","publisher":"Biophysical Society","publist_id":"7403","language":[{"iso":"eng"}],"department":[{"_id":"EdHa"}],"abstract":[{"text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients.","lang":"eng"}],"publication_status":"published","citation":{"apa":"Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022","chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977. doi:10.1016/j.bpj.2017.12.022","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022.","ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” Biophysical Journal, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.","ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977."},"quality_controlled":"1","oa":1,"year":"2018","_id":"421","date_updated":"2023-09-19T10:13:55Z","title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","article_processing_charge":"No","date_published":"2018-02-27T00:00:00Z","day":"27","external_id":{"isi":["000428016700021"],"arxiv":["1709.01486"]},"volume":114,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:23Z","doi":"10.1016/j.bpj.2017.12.022","status":"public","author":[{"first_name":"Kinjal","full_name":"Dasbiswas, Kinjal","last_name":"Dasbiswas"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Claude-Edouard B","first_name":"Claude-Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nir","full_name":"Gov, Nir","last_name":"Gov"}],"oa_version":"Submitted Version"},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7258"}]},"date_updated":"2024-03-25T23:30:20Z","_id":"422","title":"Relaminarization by steady modification of the streamwise velocity profile in a pipe","article_processing_charge":"Yes (via OA deal)","oa":1,"has_accepted_license":"1","project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589"}],"year":"2018","date_created":"2018-12-11T11:46:23Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":100,"doi":"10.1007/s10494-018-9896-4","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen","full_name":"Kühnen, Jakob","first_name":"Jakob","orcid":"0000-0003-4312-0179"},{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","full_name":"Scarselli, Davide","first_name":"Davide","orcid":"0000-0001-5227-4271"},{"full_name":"Schaner, Markus","first_name":"Markus","last_name":"Schaner","id":"316CE034-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"status":"public","oa_version":"Published Version","date_published":"2018-01-01T00:00:00Z","day":"01","external_id":{"isi":["000433113900004"]},"ddc":["530"],"type":"journal_article","issue":"4","page":"919 - 942","ec_funded":1,"isi":1,"month":"01","intvolume":" 100","publication_status":"published","quality_controlled":"1","citation":{"short":"J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion 100 (2018) 919–942.","mla":"Kühnen, Jakob, et al. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow Turbulence and Combustion, vol. 100, no. 4, Springer, 2018, pp. 919–42, doi:10.1007/s10494-018-9896-4.","ieee":"J. Kühnen, D. Scarselli, M. Schaner, and B. Hof, “Relaminarization by steady modification of the streamwise velocity profile in a pipe,” Flow Turbulence and Combustion, vol. 100, no. 4. Springer, pp. 919–942, 2018.","ista":"Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 100(4), 919–942.","apa":"Kühnen, J., Scarselli, D., Schaner, M., & Hof, B. (2018). Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. Springer. https://doi.org/10.1007/s10494-018-9896-4","chicago":"Kühnen, Jakob, Davide Scarselli, Markus Schaner, and Björn Hof. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow Turbulence and Combustion. Springer, 2018. https://doi.org/10.1007/s10494-018-9896-4.","ama":"Kühnen J, Scarselli D, Schaner M, Hof B. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 2018;100(4):919-942. doi:10.1007/s10494-018-9896-4"},"file_date_updated":"2020-07-14T12:46:25Z","publication":"Flow Turbulence and Combustion","scopus_import":"1","file":[{"relation":"main_file","date_updated":"2020-07-14T12:46:25Z","file_name":"2018_FlowTurbulenceCombust_Kuehnen.pdf","date_created":"2018-12-17T15:52:37Z","file_size":2210020,"access_level":"open_access","creator":"dernst","checksum":"d7c0bade150faabca150b0a9986e60ca","content_type":"application/pdf","file_id":"5717"}],"publisher":"Springer","language":[{"iso":"eng"}],"publist_id":"7401","department":[{"_id":"BjHo"}],"abstract":[{"lang":"eng","text":"We show that a rather simple, steady modification of the streamwise velocity profile in a pipe can lead to a complete collapse of turbulence and the flow fully relaminarizes. Two different devices, a stationary obstacle (inset) and a device which injects fluid through an annular gap close to the wall, are used to control the flow. Both devices modify the streamwise velocity profile such that the flow in the center of the pipe is decelerated and the flow in the near wall region is accelerated. We present measurements with stereoscopic particle image velocimetry to investigate and capture the development of the relaminarizing flow downstream these devices and the specific circumstances responsible for relaminarization. We find total relaminarization up to Reynolds numbers of 6000, where the skin friction in the far downstream distance is reduced by a factor of 3.4 due to relaminarization. In a smooth straight pipe the flow remains completely laminar downstream of the control. Furthermore, we show that transient (temporary) relaminarization in a spatially confined region right downstream the devices occurs also at much higher Reynolds numbers, accompanied by a significant local skin friction drag reduction. The underlying physical mechanism of relaminarization is attributed to a weakening of the near-wall turbulence production cycle."}]},{"external_id":{"isi":["000431035800001"]},"day":"09","date_published":"2018-03-09T00:00:00Z","oa_version":"Published Version","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel","first_name":"Pavel","last_name":"Payne","id":"35F78294-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Geyrhofer","first_name":"Lukas","full_name":"Geyrhofer, Lukas"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P"}],"doi":"10.7554/eLife.32035","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:23Z","volume":7,"acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","year":"2018","project":[{"name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020"}],"has_accepted_license":"1","oa":1,"title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","article_processing_charge":"No","date_updated":"2023-09-11T12:49:17Z","_id":"423","related_material":{"record":[{"relation":"research_data","id":"9840","status":"public"}]},"abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"language":[{"iso":"eng"}],"publist_id":"7400","publisher":"eLife Sciences Publications","publication":"eLife","file_date_updated":"2020-07-14T12:46:25Z","file":[{"relation":"main_file","file_size":3533881,"date_created":"2018-12-17T10:36:07Z","file_name":"2018_eLife_Payne.pdf","date_updated":"2020-07-14T12:46:25Z","content_type":"application/pdf","checksum":"447cf6e680bdc3c01062a8737d876569","creator":"dernst","access_level":"open_access","file_id":"5689"}],"scopus_import":"1","quality_controlled":"1","citation":{"ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035."},"publication_status":"published","intvolume":" 7","article_number":"e32035","isi":1,"month":"03","ec_funded":1,"ddc":["576"],"type":"journal_article"}]