[{"page":"E11751-E11760","date_created":"2018-12-20T21:09:37Z","date_published":"2018-12-11T00:00:00Z","doi":"10.1073/pnas.1811580115","year":"2018","isi":1,"publication":"Proceedings of the National Academy of Sciences","day":"11","oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","article_processing_charge":"No","external_id":{"pmid":["30478053"],"isi":["000452866000022"]},"author":[{"last_name":"Qu","full_name":"Qu, Kun","first_name":"Kun"},{"full_name":"Glass, Bärbel","last_name":"Glass","first_name":"Bärbel"},{"full_name":"Doležal, Michal","last_name":"Doležal","first_name":"Michal"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Brice","full_name":"Murciano, Brice","last_name":"Murciano"},{"full_name":"Rein, Alan","last_name":"Rein","first_name":"Alan"},{"full_name":"Rumlová, Michaela","last_name":"Rumlová","first_name":"Michaela"},{"last_name":"Ruml","full_name":"Ruml, Tomáš","first_name":"Tomáš"},{"first_name":"Hans-Georg","full_name":"Kräusslich, Hans-Georg","last_name":"Kräusslich"},{"first_name":"John A. G.","last_name":"Briggs","full_name":"Briggs, John A. G."}],"title":"Structure and architecture of immature and mature murine leukemia virus capsids","citation":{"short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences 115 (2018) E11751–E11760.","ieee":"K. Qu et al., “Structure and architecture of immature and mature murine leukemia virus capsids,” Proceedings of the National Academy of Sciences, vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760, 2018.","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1811580115","ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 2018;115(50):E11751-E11760. doi:10.1073/pnas.1811580115","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:10.1073/pnas.1811580115.","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 115(50), E11751–E11760.","chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1811580115."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"50","volume":115,"publication_status":"published","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053"}],"scopus_import":"1","intvolume":" 115","month":"12","abstract":[{"text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","department":[{"_id":"FlSc"}],"date_updated":"2023-09-19T09:57:45Z","type":"journal_article","status":"public","_id":"5770"},{"year":"2018","isi":1,"publication":"Theoretical Computer Science","day":"15","page":"50 - 72","date_created":"2018-12-11T11:47:28Z","date_published":"2018-02-15T00:00:00Z","doi":"10.1016/j.tcs.2017.11.001","oa":1,"publisher":"Elsevier","quality_controlled":"1","citation":{"apa":"Avni, G., & Kupferman, O. (2018). Synthesis from component libraries with costs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2017.11.001","ama":"Avni G, Kupferman O. Synthesis from component libraries with costs. Theoretical Computer Science. 2018;712:50-72. doi:10.1016/j.tcs.2017.11.001","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.","short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72.","mla":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science, vol. 712, Elsevier, 2018, pp. 50–72, doi:10.1016/j.tcs.2017.11.001.","ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72.","chicago":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science. Elsevier, 2018. https://doi.org/10.1016/j.tcs.2017.11.001."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000424959200003"]},"publist_id":"7197","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"title":"Synthesis from component libraries with costs","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":712,"abstract":[{"text":"Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529","open_access":"1"}],"scopus_import":"1","intvolume":" 712","month":"02","date_updated":"2023-09-19T10:00:21Z","department":[{"_id":"ToHe"}],"_id":"608","type":"journal_article","article_type":"original","status":"public"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell. Cell Press, 2018. https://doi.org/10.1016/j.cell.2018.06.033.","ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24.","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:10.1016/j.cell.2018.06.033.","ieee":"T. Nishiyama et al., “The Chara genome: Secondary complexity and implications for plant terrestrialization,” Cell, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. Cell Press. https://doi.org/10.1016/j.cell.2018.06.033","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 2018;174(2):448-464.e24. doi:10.1016/j.cell.2018.06.033"},"title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","author":[{"first_name":"Tomoaki","full_name":"Nishiyama, Tomoaki","last_name":"Nishiyama"},{"full_name":"Sakayama, Hidetoshi","last_name":"Sakayama","first_name":"Hidetoshi"},{"first_name":"Jan","full_name":"De Vries, Jan","last_name":"De Vries"},{"first_name":"Henrik","last_name":"Buschmann","full_name":"Buschmann, Henrik"},{"full_name":"Saint Marcoux, Denis","last_name":"Saint Marcoux","first_name":"Denis"},{"full_name":"Ullrich, Kristian","last_name":"Ullrich","first_name":"Kristian"},{"first_name":"Fabian","last_name":"Haas","full_name":"Haas, Fabian"},{"first_name":"Lisa","full_name":"Vanderstraeten, Lisa","last_name":"Vanderstraeten"},{"first_name":"Dirk","full_name":"Becker, Dirk","last_name":"Becker"},{"first_name":"Daniel","last_name":"Lang","full_name":"Lang, Daniel"},{"full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě","first_name":"Stanislav"},{"first_name":"Stephane","last_name":"Rombauts","full_name":"Rombauts, Stephane"},{"first_name":"Per","last_name":"Wilhelmsson","full_name":"Wilhelmsson, Per"},{"first_name":"Philipp","full_name":"Janitza, Philipp","last_name":"Janitza"},{"first_name":"Ramona","full_name":"Kern, Ramona","last_name":"Kern"},{"full_name":"Heyl, Alexander","last_name":"Heyl","first_name":"Alexander"},{"full_name":"Rümpler, Florian","last_name":"Rümpler","first_name":"Florian"},{"first_name":"Luz","full_name":"Calderón Villalobos, Luz","last_name":"Calderón Villalobos"},{"first_name":"John","full_name":"Clay, John","last_name":"Clay"},{"full_name":"Skokan, Roman","last_name":"Skokan","first_name":"Roman"},{"last_name":"Toyoda","full_name":"Toyoda, Atsushi","first_name":"Atsushi"},{"first_name":"Yutaka","full_name":"Suzuki, Yutaka","last_name":"Suzuki"},{"first_name":"Hiroshi","last_name":"Kagoshima","full_name":"Kagoshima, Hiroshi"},{"last_name":"Schijlen","full_name":"Schijlen, Elio","first_name":"Elio"},{"full_name":"Tajeshwar, Navindra","last_name":"Tajeshwar","first_name":"Navindra"},{"first_name":"Bruno","last_name":"Catarino","full_name":"Catarino, Bruno"},{"first_name":"Alexander","last_name":"Hetherington","full_name":"Hetherington, Alexander"},{"first_name":"Assia","last_name":"Saltykova","full_name":"Saltykova, Assia"},{"first_name":"Clemence","last_name":"Bonnot","full_name":"Bonnot, Clemence"},{"first_name":"Holger","last_name":"Breuninger","full_name":"Breuninger, Holger"},{"last_name":"Symeonidi","full_name":"Symeonidi, Aikaterini","first_name":"Aikaterini"},{"full_name":"Radhakrishnan, Guru","last_name":"Radhakrishnan","first_name":"Guru"},{"first_name":"Filip","full_name":"Van Nieuwerburgh, Filip","last_name":"Van Nieuwerburgh"},{"full_name":"Deforce, Dieter","last_name":"Deforce","first_name":"Dieter"},{"full_name":"Chang, Caren","last_name":"Chang","first_name":"Caren"},{"last_name":"Karol","full_name":"Karol, Kenneth","first_name":"Kenneth"},{"first_name":"Rainer","last_name":"Hedrich","full_name":"Hedrich, Rainer"},{"first_name":"Peter","full_name":"Ulvskov, Peter","last_name":"Ulvskov"},{"first_name":"Gernot","last_name":"Glöckner","full_name":"Glöckner, Gernot"},{"full_name":"Delwiche, Charles","last_name":"Delwiche","first_name":"Charles"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"full_name":"Van De Peer, Yves","last_name":"Van De Peer","first_name":"Yves"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Beilby, Mary","last_name":"Beilby","first_name":"Mary"},{"first_name":"Liam","last_name":"Dolan","full_name":"Dolan, Liam"},{"last_name":"Kohara","full_name":"Kohara, Yuji","first_name":"Yuji"},{"first_name":"Sumio","last_name":"Sugano","full_name":"Sugano, Sumio"},{"last_name":"Fujiyama","full_name":"Fujiyama, Asao","first_name":"Asao"},{"first_name":"Pierre Marc","last_name":"Delaux","full_name":"Delaux, Pierre Marc"},{"first_name":"Marcel","full_name":"Quint, Marcel","last_name":"Quint"},{"first_name":"Gunter","last_name":"Theissen","full_name":"Theissen, Gunter"},{"last_name":"Hagemann","full_name":"Hagemann, Martin","first_name":"Martin"},{"first_name":"Jesper","full_name":"Harholt, Jesper","last_name":"Harholt"},{"first_name":"Christophe","last_name":"Dunand","full_name":"Dunand, Christophe"},{"first_name":"Sabine","last_name":"Zachgo","full_name":"Zachgo, Sabine"},{"full_name":"Langdale, Jane","last_name":"Langdale","first_name":"Jane"},{"full_name":"Maumus, Florian","last_name":"Maumus","first_name":"Florian"},{"first_name":"Dominique","full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten"},{"first_name":"Sven B","last_name":"Gould","full_name":"Gould, Sven B"},{"full_name":"Rensing, Stefan","last_name":"Rensing","first_name":"Stefan"}],"publist_id":"7774","external_id":{"isi":["000438482800019"],"pmid":["30007417"]},"article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"day":"12","publication":"Cell","isi":1,"year":"2018","doi":"10.1016/j.cell.2018.06.033","date_published":"2018-07-12T00:00:00Z","date_created":"2018-12-11T11:44:53Z","page":"448 - 464.e24","acknowledgement":"In-Data-Review","publisher":"Cell Press","quality_controlled":"1","oa":1,"date_updated":"2023-09-19T10:02:47Z","department":[{"_id":"JiFr"}],"_id":"148","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":174,"issue":"2","ec_funded":1,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.","lang":"eng"}],"month":"07","intvolume":" 174","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}]},{"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]","quality_controlled":"1","publisher":"Wiley","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"The Plant Journal","page":"1010 - 1022","doi":"10.1111/tpj.13914","date_published":"2018-06-01T00:00:00Z","date_created":"2018-12-11T11:46:17Z","citation":{"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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"first_name":"Candida","full_name":"Nibau, Candida","last_name":"Nibau"},{"first_name":"Armin","last_name":"Fuchs","full_name":"Fuchs, Armin"},{"full_name":"Dadarou, Despoina","last_name":"Dadarou","first_name":"Despoina"},{"first_name":"Andrea","full_name":"Barta, Andrea","last_name":"Barta"},{"first_name":"John","full_name":"Doonan, John","last_name":"Doonan"}],"publist_id":"7426","article_processing_charge":"No","external_id":{"isi":["000434365500008"]},"title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 94","publication_status":"published","file":[{"date_created":"2019-02-06T11:40:54Z","file_name":"2018_PlantJourn_Cavallari.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:22Z","file_size":1543354,"file_id":"5934","checksum":"d9d3ad3215ac0e581731443fca312266","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":94,"issue":"6","_id":"403","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-19T10:07:08Z","ddc":["580"],"department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:46:22Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","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.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","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.","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164."},"title":"The compound interest in relaxing punctuality","publist_id":"7765","author":[{"last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000489765800009"]},"article_processing_charge":"No","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"day":"12","has_accepted_license":"1","isi":1,"year":"2018","doi":"10.1007/978-3-319-95582-7_9","date_published":"2018-07-12T00:00:00Z","date_created":"2018-12-11T11:44:55Z","page":"147 - 164","quality_controlled":"1","publisher":"Springer","oa":1,"ddc":["000"],"date_updated":"2023-09-19T10:05:37Z","file_date_updated":"2020-10-09T06:22:41Z","department":[{"_id":"ToHe"}],"_id":"156","status":"public","type":"conference","conference":{"location":"Oxford, UK","end_date":"2018-07-17","start_date":"2018-07-15","name":"FM: International Symposium on Formal Methods"},"file":[{"file_name":"2018_LNCS_Ferrere.pdf","date_created":"2020-10-09T06:22:41Z","file_size":485576,"date_updated":"2020-10-09T06:22:41Z","creator":"dernst","success":1,"file_id":"8637","checksum":"a045c213c42c445f1889326f8db82a0a","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":10951,"oa_version":"Submitted Version","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."}],"month":"07","intvolume":" 10951","scopus_import":"1","alternative_title":["LNCS"]}]