[{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","page":"1010 - 1022","publication":"The Plant Journal","citation":{"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.","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.","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","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.","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","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.","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"},"date_published":"2018-06-01T00:00:00Z","type":"journal_article","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"}],"issue":"6","title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","status":"public","ddc":["580"],"intvolume":" 94","_id":"403","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"open_access","file_name":"2018_PlantJourn_Cavallari.pdf","creator":"dernst","file_size":1543354,"content_type":"application/pdf","file_id":"5934","relation":"main_file","checksum":"d9d3ad3215ac0e581731443fca312266","date_updated":"2020-07-14T12:46:22Z","date_created":"2019-02-06T11:40:54Z"}],"oa_version":"Published Version","month":"06","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000434365500008"]},"language":[{"iso":"eng"}],"doi":"10.1111/tpj.13914","file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7426","publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Wiley","year":"2018","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]","date_created":"2018-12-11T11:46:17Z","date_updated":"2023-09-19T10:07:08Z","volume":94,"author":[{"full_name":"Cavallari, Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari"},{"first_name":"Candida","last_name":"Nibau","full_name":"Nibau, Candida"},{"first_name":"Armin","last_name":"Fuchs","full_name":"Fuchs, Armin"},{"full_name":"Dadarou, Despoina","first_name":"Despoina","last_name":"Dadarou"},{"full_name":"Barta, Andrea","last_name":"Barta","first_name":"Andrea"},{"first_name":"John","last_name":"Doonan","full_name":"Doonan, John"}]},{"publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"year":"2018","date_created":"2018-12-11T11:44:55Z","date_updated":"2023-09-19T10:05:37Z","volume":10951,"author":[{"full_name":"Ferrere, Thomas","first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143"}],"file_date_updated":"2020-10-09T06:22:41Z","publist_id":"7765","quality_controlled":"1","isi":1,"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"external_id":{"isi":["000489765800009"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"FM: International Symposium on Formal Methods","end_date":"2018-07-17","start_date":"2018-07-15","location":"Oxford, UK"},"doi":"10.1007/978-3-319-95582-7_9","month":"07","status":"public","ddc":["000"],"title":"The compound interest in relaxing punctuality","intvolume":" 10951","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"156","file":[{"creator":"dernst","content_type":"application/pdf","file_size":485576,"access_level":"open_access","file_name":"2018_LNCS_Ferrere.pdf","success":1,"checksum":"a045c213c42c445f1889326f8db82a0a","date_updated":"2020-10-09T06:22:41Z","date_created":"2020-10-09T06:22:41Z","file_id":"8637","relation":"main_file"}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost."}],"page":"147 - 164","citation":{"chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. https://doi.org/10.1007/978-3-319-95582-7_9.","mla":"Ferrere, Thomas. The Compound Interest in Relaxing Punctuality. Vol. 10951, Springer, 2018, pp. 147–64, doi:10.1007/978-3-319-95582-7_9.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: International Symposium on Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: International Symposium on Formal Methods, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-95582-7_9","ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:10.1007/978-3-319-95582-7_9"},"date_published":"2018-07-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No","has_accepted_license":"1"},{"publist_id":"8014","file_date_updated":"2020-07-14T12:46:22Z","pmid":1,"year":"2018","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"9805"}]},"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"volume":27,"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-19T10:06:08Z","publication_identifier":{"issn":["1365294X"]},"month":"12","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["30599087"],"isi":["000454600500001"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1111/mec.14950","language":[{"iso":"eng"}],"type":"journal_article","issue":"24","abstract":[{"text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance.","lang":"eng"}],"_id":"40","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 27","ddc":["576"],"status":"public","title":"The consequences of an introgression event","file":[{"content_type":"application/pdf","file_size":295452,"creator":"apreinsp","file_name":"2018_MolecularEcology_BartonNick.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:22Z","date_created":"2019-07-19T06:54:46Z","relation":"main_file","file_id":"6652"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"31","citation":{"ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950."},"publication":"Molecular Ecology","page":"4973-4975","article_type":"letter_note","date_published":"2018-12-31T00:00:00Z"},{"file_date_updated":"2020-07-14T12:47:13Z","article_number":"e37888","date_created":"2019-01-20T22:59:19Z","date_updated":"2023-09-19T10:01:39Z","volume":7,"author":[{"orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","first_name":"Jonna H","full_name":"Alanko, Jonna H"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"eLife Sciences Publications","year":"2018","month":"06","publication_identifier":{"issn":["2050084X"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.37888","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000434375000001"]},"abstract":[{"lang":"eng","text":"In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2018_eLife_Alanko.pdf","content_type":"application/pdf","file_size":358141,"creator":"dernst","relation":"main_file","file_id":"5973","checksum":"f1c7ec2a809408d763c4b529a98f9a3b","date_created":"2019-02-13T10:52:11Z","date_updated":"2020-07-14T12:47:13Z"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"The cell sets the tone","intvolume":" 7","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5861","day":"06","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-06T00:00:00Z","article_type":"original","publication":"eLife","citation":{"ama":"Alanko JH, Sixt MK. The cell sets the tone. eLife. 2018;7. doi:10.7554/eLife.37888","apa":"Alanko, J. H., & Sixt, M. K. (2018). The cell sets the tone. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.37888","ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” eLife, vol. 7. eLife Sciences Publications, 2018.","ista":"Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018).","mla":"Alanko, Jonna H., and Michael K. Sixt. “The Cell Sets the Tone.” ELife, vol. 7, e37888, eLife Sciences Publications, 2018, doi:10.7554/eLife.37888.","chicago":"Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.37888."}},{"author":[{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","last_name":"Kania","first_name":"Urszula","full_name":"Kania, Urszula"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"last_name":"Lu","first_name":"Qing","full_name":"Lu, Qing"},{"last_name":"Hicks","first_name":"Glenn R","full_name":"Hicks, Glenn R"},{"last_name":"Nerinckx","first_name":"Wim","full_name":"Nerinckx, Wim"},{"full_name":"Mishev, Kiril","last_name":"Mishev","first_name":"Kiril"},{"last_name":"Peurois","first_name":"Francois","full_name":"Peurois, Francois"},{"full_name":"Cherfils, Jacqueline","first_name":"Jacqueline","last_name":"Cherfils"},{"full_name":"De, Rycke Riet Maria","first_name":"Rycke Riet Maria","last_name":"De"},{"full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"date_updated":"2023-09-19T10:09:12Z","date_created":"2018-12-11T11:44:52Z","volume":30,"year":"2018","acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","pmid":1,"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"publist_id":"7776","ec_funded":1,"doi":"10.1105/tpc.18.00127","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.18.00127"}],"oa":1,"external_id":{"isi":["000450000500023"],"pmid":["30018156"]},"quality_controlled":"1","isi":1,"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"month":"11","publication_identifier":{"issn":["1040-4651"]},"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"147","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","status":"public","intvolume":" 30","abstract":[{"text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development.","lang":"eng"}],"issue":"10","type":"journal_article","date_published":"2018-11-12T00:00:00Z","publication":"The Plant Cell","citation":{"chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell. Oxford University Press, 2018. https://doi.org/10.1105/tpc.18.00127.","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:10.1105/tpc.18.00127.","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.","apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. Oxford University Press. https://doi.org/10.1105/tpc.18.00127","ieee":"U. Kania et al., “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” The Plant Cell, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 2018;30(10):2553-2572. doi:10.1105/tpc.18.00127"},"article_type":"original","page":"2553 - 2572","day":"12","article_processing_charge":"No","scopus_import":"1"},{"publist_id":"7777","file_date_updated":"2020-07-14T12:44:56Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/"}]},"author":[{"full_name":"Shi, Chun Lin","last_name":"Shi","first_name":"Chun Lin"},{"full_name":"Von Wangenheim, Daniel","first_name":"Daniel","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247"},{"full_name":"Herrmann, Ullrich","first_name":"Ullrich","last_name":"Herrmann"},{"full_name":"Wildhagen, Mari","last_name":"Wildhagen","first_name":"Mari"},{"full_name":"Kulik, Ivan","last_name":"Kulik","first_name":"Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB"},{"full_name":"Kopf, Andreas","last_name":"Kopf","first_name":"Andreas"},{"first_name":"Takashi","last_name":"Ishida","full_name":"Ishida, Takashi"},{"last_name":"Olsson","first_name":"Vilde","full_name":"Olsson, Vilde"},{"full_name":"Anker, Mari Kristine","last_name":"Anker","first_name":"Mari Kristine"},{"last_name":"Albert","first_name":"Markus","full_name":"Albert, Markus"},{"full_name":"Butenko, Melinka A","last_name":"Butenko","first_name":"Melinka A"},{"full_name":"Felix, Georg","last_name":"Felix","first_name":"Georg"},{"full_name":"Sawa, Shinichiro","first_name":"Shinichiro","last_name":"Sawa"},{"first_name":"Manfred","last_name":"Claassen","full_name":"Claassen, Manfred"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"full_name":"Aalen, Reidunn B","last_name":"Aalen","first_name":"Reidunn B"}],"volume":4,"date_updated":"2023-09-19T10:08:45Z","date_created":"2018-12-11T11:44:52Z","pmid":1,"year":"2018","publisher":"Nature Publishing Group","department":[{"_id":"JiFr"}],"publication_status":"published","month":"07","doi":"10.1038/s41477-018-0212-z","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000443861300016"],"pmid":["30061750"]},"quality_controlled":"1","isi":1,"issue":"8","abstract":[{"lang":"eng","text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"7043","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","date_created":"2019-11-18T16:24:07Z","date_updated":"2020-07-14T12:44:56Z","access_level":"open_access","file_name":"2018_NaturePlants_Shi.pdf","file_size":226829,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Submitted Version","_id":"146","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 4","ddc":["580"],"title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"30","scopus_import":"1","date_published":"2018-07-30T00:00:00Z","citation":{"ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604.","ieee":"C. L. Shi et al., “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0212-z","ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 2018;4(8):596-604. doi:10.1038/s41477-018-0212-z","chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0212-z.","mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:10.1038/s41477-018-0212-z.","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604."},"publication":"Nature Plants","page":"596 - 604","article_type":"original"},{"file_date_updated":"2020-07-14T12:45:54Z","publist_id":"7588","ec_funded":1,"date_created":"2018-12-11T11:45:39Z","date_updated":"2023-09-19T10:12:03Z","volume":2,"author":[{"full_name":"Hoffman, Moshe","first_name":"Moshe","last_name":"Hoffman"},{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/the-logic-of-modesty-why-it-pays-to-be-humble/"}]},"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"year":"2018","acknowledgement":"This work was supported by a grant from the John Templeton Foundation and by the Office of Naval Research Grant N00014-16-1-2914 (M.A.N.). C.H. acknowledges generous support from the ISTFELLOW programme and by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","month":"05","language":[{"iso":"eng"}],"doi":"10.1038/s41562-018-0354-z","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000435551300009"]},"abstract":[{"text":"People sometimes make their admirable deeds and accomplishments hard to spot, such as by giving anonymously or avoiding bragging. Such ‘buried’ signals are hard to reconcile with standard models of signalling or indirect reciprocity, which motivate costly pro-social behaviour by reputational gains. To explain these phenomena, we design a simple game theory model, which we call the signal-burying game. This game has the feature that senders can bury their signal by deliberately reducing the probability of the signal being observed. If the signal is observed, however, it is identified as having been buried. We show under which conditions buried signals can be maintained, using static equilibrium concepts and calculations of the evolutionary dynamics. We apply our analysis to shed light on a number of otherwise puzzling social phenomena, including modesty, anonymous donations, subtlety in art and fashion, and overeagerness.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","file":[{"date_created":"2019-11-19T08:17:23Z","date_updated":"2020-07-14T12:45:54Z","checksum":"32efaf06a597495c184df91b3fbb19c0","relation":"main_file","file_id":"7051","file_size":194734,"content_type":"application/pdf","creator":"dernst","file_name":"2018_NatureHumanBeh_Hoffman.pdf","access_level":"open_access"}],"ddc":["000"],"title":"The signal-burying game can explain why we obscure positive traits and good deeds","status":"public","intvolume":" 2","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"293","day":"28","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-05-28T00:00:00Z","article_type":"original","page":"397 - 404","publication":"Nature Human Behaviour","citation":{"mla":"Hoffman, Moshe, et al. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 397–404, doi:10.1038/s41562-018-0354-z.","short":"M. Hoffman, C. Hilbe, M. Nowak, Nature Human Behaviour 2 (2018) 397–404.","chicago":"Hoffman, Moshe, Christian Hilbe, and Martin Nowak. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0354-z.","ama":"Hoffman M, Hilbe C, Nowak M. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2018;2:397-404. doi:10.1038/s41562-018-0354-z","ista":"Hoffman M, Hilbe C, Nowak M. 2018. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2, 397–404.","ieee":"M. Hoffman, C. Hilbe, and M. Nowak, “The signal-burying game can explain why we obscure positive traits and good deeds,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 397–404, 2018.","apa":"Hoffman, M., Hilbe, C., & Nowak, M. (2018). The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0354-z"}},{"abstract":[{"lang":"eng","text":"The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities"}],"issue":"4","alternative_title":["Annales Henri Poincare"],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":923252,"creator":"system","access_level":"open_access","file_name":"IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf","checksum":"883eeccba8384ad7fcaa28761d99a0fa","date_updated":"2020-07-14T12:46:31Z","date_created":"2018-12-12T10:11:57Z","relation":"main_file","file_id":"4914"}],"oa_version":"Published Version","pubrep_id":"993","title":"The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations","ddc":["510","539"],"status":"public","intvolume":" 19","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"455","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-04-01T00:00:00Z","page":"1167 - 1214","publication":"Annales Henri Poincare","citation":{"ista":"Benedikter NP, Sok J, Solovej J. 2018. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 19(4), 1167–1214.","ieee":"N. P. Benedikter, J. Sok, and J. Solovej, “The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations,” Annales Henri Poincare, vol. 19, no. 4. Birkhäuser, pp. 1167–1214, 2018.","apa":"Benedikter, N. P., Sok, J., & Solovej, J. (2018). The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-018-0644-z","ama":"Benedikter NP, Sok J, Solovej J. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 2018;19(4):1167-1214. doi:10.1007/s00023-018-0644-z","chicago":"Benedikter, Niels P, Jérémy Sok, and Jan Solovej. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare. Birkhäuser, 2018. https://doi.org/10.1007/s00023-018-0644-z.","mla":"Benedikter, Niels P., et al. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare, vol. 19, no. 4, Birkhäuser, 2018, pp. 1167–214, doi:10.1007/s00023-018-0644-z.","short":"N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214."},"file_date_updated":"2020-07-14T12:46:31Z","publist_id":"7367","date_updated":"2023-09-19T10:07:41Z","date_created":"2018-12-11T11:46:34Z","volume":19,"author":[{"orcid":"0000-0002-1071-6091","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","last_name":"Benedikter","first_name":"Niels P","full_name":"Benedikter, Niels P"},{"last_name":"Sok","first_name":"Jérémy","full_name":"Sok, Jérémy"},{"last_name":"Solovej","first_name":"Jan","full_name":"Solovej, Jan"}],"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Birkhäuser","year":"2018","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors acknowledge support by ERC Advanced Grant 321029 and by VILLUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059). The authors would like to thank Sébastien Breteaux, Enno Lenzmann, Mathieu Lewin and Jochen Schmid for comments and discussions about well-posedness of the Bogoliubov–de Gennes equations.","month":"04","language":[{"iso":"eng"}],"doi":"10.1007/s00023-018-0644-z","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000427578900006"]},"oa":1},{"publication_identifier":{"eissn":["2405-4712"]},"month":"04","main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2018.04.003","open_access":"1"}],"external_id":{"pmid":["29698645"],"isi":["000432192100003"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1016/j.cels.2018.04.003","language":[{"iso":"eng"}],"publist_id":"7551","pmid":1,"year":"2018","department":[{"_id":"AnKi"}],"publisher":"Cell Press","publication_status":"published","author":[{"first_name":"Guntram","last_name":"Bauer","full_name":"Bauer, Guntram"},{"full_name":"Fakhri, Nikta","first_name":"Nikta","last_name":"Fakhri"},{"full_name":"Kicheva, Anna","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"},{"first_name":"Jané","last_name":"Kondev","full_name":"Kondev, Jané"},{"full_name":"Kruse, Karsten","last_name":"Kruse","first_name":"Karsten"},{"full_name":"Noji, Hiroyuki","first_name":"Hiroyuki","last_name":"Noji"},{"last_name":"Riveline","first_name":"Daniel","full_name":"Riveline, Daniel"},{"full_name":"Saunders, Timothy","last_name":"Saunders","first_name":"Timothy"},{"full_name":"Thatta, Mukund","first_name":"Mukund","last_name":"Thatta"},{"full_name":"Wieschaus, Eric","first_name":"Eric","last_name":"Wieschaus"}],"volume":6,"date_created":"2018-12-11T11:45:46Z","date_updated":"2023-09-19T10:11:25Z","scopus_import":"1","article_processing_charge":"No","day":"25","citation":{"chicago":"Bauer, Guntram, Nikta Fakhri, Anna Kicheva, Jané Kondev, Karsten Kruse, Hiroyuki Noji, Daniel Riveline, Timothy Saunders, Mukund Thatta, and Eric Wieschaus. “The Science of Living Matter for Tomorrow.” Cell Systems. Cell Press, 2018. https://doi.org/10.1016/j.cels.2018.04.003.","mla":"Bauer, Guntram, et al. “The Science of Living Matter for Tomorrow.” Cell Systems, vol. 6, no. 4, Cell Press, 2018, pp. 400–02, doi:10.1016/j.cels.2018.04.003.","short":"G. Bauer, N. Fakhri, A. Kicheva, J. Kondev, K. Kruse, H. Noji, D. Riveline, T. Saunders, M. Thatta, E. Wieschaus, Cell Systems 6 (2018) 400–402.","ista":"Bauer G, Fakhri N, Kicheva A, Kondev J, Kruse K, Noji H, Riveline D, Saunders T, Thatta M, Wieschaus E. 2018. The science of living matter for tomorrow. Cell Systems. 6(4), 400–402.","apa":"Bauer, G., Fakhri, N., Kicheva, A., Kondev, J., Kruse, K., Noji, H., … Wieschaus, E. (2018). The science of living matter for tomorrow. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2018.04.003","ieee":"G. Bauer et al., “The science of living matter for tomorrow,” Cell Systems, vol. 6, no. 4. Cell Press, pp. 400–402, 2018.","ama":"Bauer G, Fakhri N, Kicheva A, et al. The science of living matter for tomorrow. Cell Systems. 2018;6(4):400-402. doi:10.1016/j.cels.2018.04.003"},"publication":"Cell Systems","page":"400 - 402","article_type":"letter_note","date_published":"2018-04-25T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"The interface of physics and biology pro-vides a fruitful environment for generatingnew concepts and exciting ways forwardto understanding living matter. Examplesof successful studies include the estab-lishment and readout of morphogen gra-dients during development, signal pro-cessing in protein and genetic networks,the role of fluctuations in determining thefates of cells and tissues, and collectiveeffects in proteins and in tissues. It is nothard to envision that significant further ad-vances will translate to societal benefitsby initiating the development of new de-vices and strategies for curing disease.However, research at the interface posesvarious challenges, in particular for youngscientists, and current institutions arerarely designed to facilitate such scientificprograms. In this Letter, we propose aninternational initiative that addressesthese challenges through the establish-ment of a worldwide network of platformsfor cross-disciplinary training and incuba-tors for starting new collaborations."}],"_id":"314","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 6","status":"public","title":"The science of living matter for tomorrow","oa_version":"Published Version"},{"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"565","title":"The spread of an inversion with migration and selection","status":"public","intvolume":" 208","abstract":[{"lang":"eng","text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. "}],"issue":"1","type":"journal_article","date_published":"2018-01-01T00:00:00Z","publication":"Genetics","citation":{"ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426","apa":"Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:10.1534/genetics.117.300426.","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426."},"article_type":"original","page":"377 - 382","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Charlesworth","first_name":"Brian","full_name":"Charlesworth, Brian"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-19T10:12:31Z","date_created":"2018-12-11T11:47:12Z","volume":208,"year":"2018","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics ","publist_id":"7249","doi":"10.1534/genetics.117.300426","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/"}],"oa":1,"external_id":{"isi":["000419356300025"],"pmid":["29158424"]},"quality_controlled":"1","isi":1,"month":"01"}]