--- _id: '5770' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Kun full_name: Qu, Kun last_name: Qu - first_name: Bärbel full_name: Glass, Bärbel last_name: Glass - first_name: Michal full_name: Doležal, Michal last_name: Doležal - first_name: Florian full_name: Schur, Florian id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Brice full_name: Murciano, Brice last_name: Murciano - first_name: Alan full_name: Rein, Alan last_name: Rein - first_name: Michaela full_name: Rumlová, Michaela last_name: Rumlová - first_name: Tomáš full_name: Ruml, Tomáš last_name: Ruml - first_name: Hans-Georg full_name: Kräusslich, Hans-Georg last_name: Kräusslich - first_name: John A. G. full_name: Briggs, John A. G. last_name: Briggs citation: 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 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 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. 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. 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. 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. 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. date_created: 2018-12-20T21:09:37Z date_published: 2018-12-11T00:00:00Z date_updated: 2023-09-19T09:57:45Z day: '11' department: - _id: FlSc doi: 10.1073/pnas.1811580115 external_id: isi: - '000452866000022' pmid: - '30478053' intvolume: ' 115' isi: 1 issue: '50' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30478053 month: '12' oa: 1 oa_version: Submitted Version page: E11751-E11760 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - '00278424' publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Structure and architecture of immature and mature murine leukemia virus capsids type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '608' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman citation: 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 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 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. ieee: G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018. ista: Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 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. short: G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72. date_created: 2018-12-11T11:47:28Z date_published: 2018-02-15T00:00:00Z date_updated: 2023-09-19T10:00:21Z day: '15' department: - _id: ToHe doi: 10.1016/j.tcs.2017.11.001 ec_funded: 1 external_id: isi: - '000424959200003' intvolume: ' 712' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529 month: '02' oa: 1 oa_version: Published Version page: 50 - 72 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '7197' quality_controlled: '1' scopus_import: '1' status: public title: Synthesis from component libraries with costs type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 712 year: '2018' ... --- _id: '705' abstract: - lang: eng text: Although dopamine receptors D1 and D2 play key roles in hippocampal function, their synaptic localization within the hippocampus has not been fully elucidated. In order to understand precise functions of pre- or postsynaptic dopamine receptors (DRs), the development of protocols to differentiate pre- and postsynaptic DRs is essential. So far, most studies on determination and quantification of DRs did not discriminate between subsynaptic localization. Therefore, the aim of the study was to generate a robust workflow for the localization of DRs. This work provides the basis for future work on hippocampal DRs, in light that DRs may have different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi isolated by a sucrose gradient protocol were prepared for super-resolution direct stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594 enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites. D1R immunoreactivity clusters were observed within the presynaptic active zone as well as at perisynaptic sites at the edge of the presynaptic active zone. The results may be useful for the interpretation of previous studies and the design of future work on DRs in the hippocampus. Moreover, the reduction of the complexity of brain tissue by the use of synaptosomal preparations and dSTORM technology may represent a useful tool for synaptic localization of brain proteins. article_processing_charge: No author: - first_name: Andras full_name: Miklosi, Andras last_name: Miklosi - first_name: Giorgia full_name: Del Favero, Giorgia last_name: Del Favero - first_name: Tanja full_name: Bulat, Tanja last_name: Bulat - first_name: Harald full_name: Höger, Harald last_name: Höger - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Doris full_name: Marko, Doris last_name: Marko - first_name: Gert full_name: Lubec, Gert last_name: Lubec citation: ama: Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 2018;55(6):4857 – 4869. doi:10.1007/s12035-017-0688-y apa: Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D., & Lubec, G. (2018). Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. Springer. https://doi.org/10.1007/s12035-017-0688-y chicago: Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology. Springer, 2018. https://doi.org/10.1007/s12035-017-0688-y. ieee: A. Miklosi et al., “Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” Molecular Neurobiology, vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018. ista: Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G. 2018. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869. mla: Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology, vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:10.1007/s12035-017-0688-y. short: A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G. Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869. date_created: 2018-12-11T11:48:02Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-19T09:58:11Z day: '01' department: - _id: RySh doi: 10.1007/s12035-017-0688-y external_id: isi: - '000431991500025' intvolume: ' 55' isi: 1 issue: '6' language: - iso: eng month: '06' oa_version: None page: 4857 – 4869 publication: Molecular Neurobiology publication_status: published publisher: Springer publist_id: '6991' quality_controlled: '1' scopus_import: '1' status: public title: Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 55 year: '2018' ... --- _id: '148' abstract: - lang: eng 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.' acknowledgement: In-Data-Review article_processing_charge: No author: - first_name: Tomoaki full_name: Nishiyama, Tomoaki last_name: Nishiyama - first_name: Hidetoshi full_name: Sakayama, Hidetoshi last_name: Sakayama - first_name: Jan full_name: De Vries, Jan last_name: De Vries - first_name: Henrik full_name: Buschmann, Henrik last_name: Buschmann - first_name: Denis full_name: Saint Marcoux, Denis last_name: Saint Marcoux - first_name: Kristian full_name: Ullrich, Kristian last_name: Ullrich - first_name: Fabian full_name: Haas, Fabian last_name: Haas - first_name: Lisa full_name: Vanderstraeten, Lisa last_name: Vanderstraeten - first_name: Dirk full_name: Becker, Dirk last_name: Becker - first_name: Daniel full_name: Lang, Daniel last_name: Lang - first_name: Stanislav full_name: Vosolsobě, Stanislav last_name: Vosolsobě - first_name: Stephane full_name: Rombauts, Stephane last_name: Rombauts - first_name: Per full_name: Wilhelmsson, Per last_name: Wilhelmsson - first_name: Philipp full_name: Janitza, Philipp last_name: Janitza - first_name: Ramona full_name: Kern, Ramona last_name: Kern - first_name: Alexander full_name: Heyl, Alexander last_name: Heyl - first_name: Florian full_name: Rümpler, Florian last_name: Rümpler - first_name: Luz full_name: Calderón Villalobos, Luz last_name: Calderón Villalobos - first_name: John full_name: Clay, John last_name: Clay - first_name: Roman full_name: Skokan, Roman last_name: Skokan - first_name: Atsushi full_name: Toyoda, Atsushi last_name: Toyoda - first_name: Yutaka full_name: Suzuki, Yutaka last_name: Suzuki - first_name: Hiroshi full_name: Kagoshima, Hiroshi last_name: Kagoshima - first_name: Elio full_name: Schijlen, Elio last_name: Schijlen - first_name: Navindra full_name: Tajeshwar, Navindra last_name: Tajeshwar - first_name: Bruno full_name: Catarino, Bruno last_name: Catarino - first_name: Alexander full_name: Hetherington, Alexander last_name: Hetherington - first_name: Assia full_name: Saltykova, Assia last_name: Saltykova - first_name: Clemence full_name: Bonnot, Clemence last_name: Bonnot - first_name: Holger full_name: Breuninger, Holger last_name: Breuninger - first_name: Aikaterini full_name: Symeonidi, Aikaterini last_name: Symeonidi - first_name: Guru full_name: Radhakrishnan, Guru last_name: Radhakrishnan - first_name: Filip full_name: Van Nieuwerburgh, Filip last_name: Van Nieuwerburgh - first_name: Dieter full_name: Deforce, Dieter last_name: Deforce - first_name: Caren full_name: Chang, Caren last_name: Chang - first_name: Kenneth full_name: Karol, Kenneth last_name: Karol - first_name: Rainer full_name: Hedrich, Rainer last_name: Hedrich - first_name: Peter full_name: Ulvskov, Peter last_name: Ulvskov - first_name: Gernot full_name: Glöckner, Gernot last_name: Glöckner - first_name: Charles full_name: Delwiche, Charles last_name: Delwiche - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Yves full_name: Van De Peer, Yves last_name: Van De Peer - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Mary full_name: Beilby, Mary last_name: Beilby - first_name: Liam full_name: Dolan, Liam last_name: Dolan - first_name: Yuji full_name: Kohara, Yuji last_name: Kohara - first_name: Sumio full_name: Sugano, Sumio last_name: Sugano - first_name: Asao full_name: Fujiyama, Asao last_name: Fujiyama - first_name: Pierre Marc full_name: Delaux, Pierre Marc last_name: Delaux - first_name: Marcel full_name: Quint, Marcel last_name: Quint - first_name: Gunter full_name: Theissen, Gunter last_name: Theissen - first_name: Martin full_name: Hagemann, Martin last_name: Hagemann - first_name: Jesper full_name: Harholt, Jesper last_name: Harholt - first_name: Christophe full_name: Dunand, Christophe last_name: Dunand - first_name: Sabine full_name: Zachgo, Sabine last_name: Zachgo - first_name: Jane full_name: Langdale, Jane last_name: Langdale - first_name: Florian full_name: Maumus, Florian last_name: Maumus - first_name: Dominique full_name: Van Der Straeten, Dominique last_name: Van Der Straeten - first_name: Sven B full_name: Gould, Sven B last_name: Gould - first_name: Stefan full_name: Rensing, Stefan last_name: Rensing citation: 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' 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' 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.' 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.' 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.' 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. date_created: 2018-12-11T11:44:53Z date_published: 2018-07-12T00:00:00Z date_updated: 2023-09-19T10:02:47Z day: '12' department: - _id: JiFr doi: 10.1016/j.cell.2018.06.033 ec_funded: 1 external_id: isi: - '000438482800019' pmid: - '30007417' intvolume: ' 174' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30007417 month: '07' oa: 1 oa_version: Published Version page: 448 - 464.e24 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Cell publication_status: published publisher: Cell Press publist_id: '7774' quality_controlled: '1' scopus_import: '1' status: public title: 'The Chara genome: Secondary complexity and implications for plant terrestrialization' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 174 year: '2018' ... --- _id: '403' 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. 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] article_processing_charge: No author: - first_name: Nicola full_name: Cavallari, Nicola id: 457160E6-F248-11E8-B48F-1D18A9856A87 last_name: Cavallari - first_name: Candida full_name: Nibau, Candida last_name: Nibau - first_name: Armin full_name: Fuchs, Armin last_name: Fuchs - first_name: Despoina full_name: Dadarou, Despoina last_name: Dadarou - first_name: Andrea full_name: Barta, Andrea last_name: Barta - first_name: John full_name: Doonan, John last_name: Doonan 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. 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. 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. 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. date_created: 2018-12-11T11:46:17Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-19T10:07:08Z day: '01' ddc: - '580' department: - _id: EvBe doi: 10.1111/tpj.13914 external_id: isi: - '000434365500008' file: - access_level: open_access checksum: d9d3ad3215ac0e581731443fca312266 content_type: application/pdf creator: dernst date_created: 2019-02-06T11:40:54Z date_updated: 2020-07-14T12:46:22Z file_id: '5934' file_name: 2018_PlantJourn_Cavallari.pdf file_size: 1543354 relation: main_file file_date_updated: 2020-07-14T12:46:22Z has_accepted_license: '1' intvolume: ' 94' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1010 - 1022 publication: The Plant Journal publication_status: published publisher: Wiley publist_id: '7426' quality_controlled: '1' scopus_import: '1' status: public title: The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 94 year: '2018' ... --- _id: '156' 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.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 citation: 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' 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. 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.' ista: 'Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.' 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. conference: end_date: 2018-07-17 location: Oxford, UK name: 'FM: International Symposium on Formal Methods' start_date: 2018-07-15 date_created: 2018-12-11T11:44:55Z date_published: 2018-07-12T00:00:00Z date_updated: 2023-09-19T10:05:37Z day: '12' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-95582-7_9 external_id: isi: - '000489765800009' file: - access_level: open_access checksum: a045c213c42c445f1889326f8db82a0a content_type: application/pdf creator: dernst date_created: 2020-10-09T06:22:41Z date_updated: 2020-10-09T06:22:41Z file_id: '8637' file_name: 2018_LNCS_Ferrere.pdf file_size: 485576 relation: main_file success: 1 file_date_updated: 2020-10-09T06:22:41Z has_accepted_license: '1' intvolume: ' 10951' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 147 - 164 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '7765' quality_controlled: '1' scopus_import: '1' status: public title: The compound interest in relaxing punctuality type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10951 year: '2018' ... --- _id: '104' abstract: - lang: eng text: The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host. acknowledgement: 'the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).' article_processing_charge: No author: - first_name: Denise full_name: Seitner, Denise last_name: Seitner - first_name: Simon full_name: Uhse, Simon last_name: Uhse - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Armin full_name: Djamei, Armin last_name: Djamei citation: ama: Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 2018;19(10):2277-2287. doi:10.1111/mpp.12698 apa: Seitner, D., Uhse, S., Gallei, M. C., & Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. Wiley. https://doi.org/10.1111/mpp.12698 chicago: Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology. Wiley, 2018. https://doi.org/10.1111/mpp.12698. ieee: D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” Molecular Plant Pathology, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018. ista: Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287. mla: Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:10.1111/mpp.12698. short: D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287. date_created: 2018-12-11T11:44:39Z date_published: 2018-10-01T00:00:00Z date_updated: 2023-09-19T10:06:42Z day: '01' ddc: - '580' department: - _id: GradSch doi: 10.1111/mpp.12698 external_id: isi: - '000445624100006' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2018-12-18T09:46:00Z date_updated: 2018-12-18T09:46:00Z file_id: '5740' file_name: 2018_MolecPlantPath_Seitner.pdf file_size: 682335 relation: main_file success: 1 file_date_updated: 2018-12-18T09:46:00Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 2277 - 2287 publication: Molecular Plant Pathology publication_status: published publisher: Wiley publist_id: '7950' quality_controlled: '1' scopus_import: '1' status: public title: The core effector Cce1 is required for early infection of maize by Ustilago maydis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '40' abstract: - lang: eng 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. article_processing_charge: Yes (via OA deal) article_type: letter_note author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950 apa: Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/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. ieee: N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018. ista: Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 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. short: N.H. Barton, Molecular Ecology 27 (2018) 4973–4975. date_created: 2018-12-11T11:44:18Z date_published: 2018-12-31T00:00:00Z date_updated: 2023-09-19T10:06:08Z day: '31' ddc: - '576' department: - _id: NiBa doi: 10.1111/mec.14950 external_id: isi: - '000454600500001' pmid: - '30599087' file: - access_level: open_access content_type: application/pdf creator: apreinsp date_created: 2019-07-19T06:54:46Z date_updated: 2020-07-14T12:46:22Z file_id: '6652' file_name: 2018_MolecularEcology_BartonNick.pdf file_size: 295452 relation: main_file file_date_updated: 2020-07-14T12:46:22Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '24' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 4973-4975 pmid: 1 publication: Molecular Ecology publication_identifier: issn: - 1365294X publication_status: published publisher: Wiley publist_id: '8014' quality_controlled: '1' related_material: record: - id: '9805' relation: research_data status: public scopus_import: '1' status: public title: The consequences of an introgression event tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 27 year: '2018' ... --- _id: '5861' abstract: - lang: eng text: In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal. article_number: e37888 article_processing_charge: No article_type: original author: - first_name: Jonna H full_name: Alanko, Jonna H id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87 last_name: Alanko orcid: 0000-0002-7698-3061 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 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 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. 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. 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. short: J.H. Alanko, M.K. Sixt, ELife 7 (2018). date_created: 2019-01-20T22:59:19Z date_published: 2018-06-06T00:00:00Z date_updated: 2023-09-19T10:01:39Z day: '06' ddc: - '570' department: - _id: MiSi doi: 10.7554/eLife.37888 external_id: isi: - '000434375000001' file: - access_level: open_access checksum: f1c7ec2a809408d763c4b529a98f9a3b content_type: application/pdf creator: dernst date_created: 2019-02-13T10:52:11Z date_updated: 2020-07-14T12:47:13Z file_id: '5973' file_name: 2018_eLife_Alanko.pdf file_size: 358141 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: The cell sets the tone tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7 year: '2018' ... --- _id: '147' abstract: - lang: eng 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. 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.). article_processing_charge: No article_type: original author: - first_name: Urszula full_name: Kania, Urszula id: 4AE5C486-F248-11E8-B48F-1D18A9856A87 last_name: Kania - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Qing full_name: Lu, Qing last_name: Lu - first_name: Glenn R full_name: Hicks, Glenn R last_name: Hicks - first_name: Wim full_name: Nerinckx, Wim last_name: Nerinckx - first_name: Kiril full_name: Mishev, Kiril last_name: Mishev - first_name: Francois full_name: Peurois, Francois last_name: Peurois - first_name: Jacqueline full_name: Cherfils, Jacqueline last_name: Cherfils - first_name: Rycke Riet Maria full_name: De, Rycke Riet Maria last_name: De - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:44:52Z date_published: 2018-11-12T00:00:00Z date_updated: 2023-09-19T10:09:12Z day: '12' department: - _id: JiFr doi: 10.1105/tpc.18.00127 ec_funded: 1 external_id: isi: - '000450000500023' pmid: - '30018156' intvolume: ' 30' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1105/tpc.18.00127 month: '11' oa: 1 oa_version: Published Version page: 2553 - 2572 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: The Plant Cell publication_identifier: issn: - 1040-4651 publication_status: published publisher: Oxford University Press publist_id: '7776' quality_controlled: '1' scopus_import: '1' status: public title: The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 30 year: '2018' ... --- _id: '146' 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. article_processing_charge: No article_type: original author: - first_name: Chun Lin full_name: Shi, Chun Lin last_name: Shi - first_name: Daniel full_name: Von Wangenheim, Daniel id: 49E91952-F248-11E8-B48F-1D18A9856A87 last_name: Von Wangenheim orcid: 0000-0002-6862-1247 - first_name: Ullrich full_name: Herrmann, Ullrich last_name: Herrmann - first_name: Mari full_name: Wildhagen, Mari last_name: Wildhagen - first_name: Ivan full_name: Kulik, Ivan id: F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB last_name: Kulik - first_name: Andreas full_name: Kopf, Andreas last_name: Kopf - first_name: Takashi full_name: Ishida, Takashi last_name: Ishida - first_name: Vilde full_name: Olsson, Vilde last_name: Olsson - first_name: Mari Kristine full_name: Anker, Mari Kristine last_name: Anker - first_name: Markus full_name: Albert, Markus last_name: Albert - first_name: Melinka A full_name: Butenko, Melinka A last_name: Butenko - first_name: Georg full_name: Felix, Georg last_name: Felix - first_name: Shinichiro full_name: Sawa, Shinichiro last_name: Sawa - first_name: Manfred full_name: Claassen, Manfred last_name: Claassen - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Reidunn B full_name: Aalen, Reidunn B last_name: Aalen citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:44:52Z date_published: 2018-07-30T00:00:00Z date_updated: 2023-09-19T10:08:45Z day: '30' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41477-018-0212-z external_id: isi: - '000443861300016' pmid: - '30061750' file: - access_level: open_access checksum: da33101c76ee1b2dc5ab28fd2ccba9d0 content_type: application/pdf creator: dernst date_created: 2019-11-18T16:24:07Z date_updated: 2020-07-14T12:44:56Z file_id: '7043' file_name: 2018_NaturePlants_Shi.pdf file_size: 226829 relation: main_file file_date_updated: 2020-07-14T12:44:56Z has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '8' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 596 - 604 pmid: 1 publication: Nature Plants publication_status: published publisher: Nature Publishing Group publist_id: '7777' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-process-in-root-development-discovered/ scopus_import: '1' status: public title: The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 4 year: '2018' ... --- _id: '293' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Moshe full_name: Hoffman, Moshe last_name: Hoffman - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:45:39Z date_published: 2018-05-28T00:00:00Z date_updated: 2023-09-19T10:12:03Z day: '28' ddc: - '000' department: - _id: KrCh doi: 10.1038/s41562-018-0354-z ec_funded: 1 external_id: isi: - '000435551300009' file: - access_level: open_access checksum: 32efaf06a597495c184df91b3fbb19c0 content_type: application/pdf creator: dernst date_created: 2019-11-19T08:17:23Z date_updated: 2020-07-14T12:45:54Z file_id: '7051' file_name: 2018_NatureHumanBeh_Hoffman.pdf file_size: 194734 relation: main_file file_date_updated: 2020-07-14T12:45:54Z has_accepted_license: '1' intvolume: ' 2' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 397 - 404 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Human Behaviour publication_status: published publisher: Nature Publishing Group publist_id: '7588' quality_controlled: '1' 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/ scopus_import: '1' status: public title: The signal-burying game can explain why we obscure positive traits and good deeds type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2 year: '2018' ... --- _id: '455' 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 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. alternative_title: - Annales Henri Poincare article_processing_charge: No author: - first_name: Niels P full_name: Benedikter, Niels P id: 3DE6C32A-F248-11E8-B48F-1D18A9856A87 last_name: Benedikter orcid: 0000-0002-1071-6091 - first_name: Jérémy full_name: Sok, Jérémy last_name: Sok - first_name: Jan full_name: Solovej, Jan last_name: Solovej citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:46:34Z date_published: 2018-04-01T00:00:00Z date_updated: 2023-09-19T10:07:41Z day: '01' ddc: - '510' - '539' department: - _id: RoSe doi: 10.1007/s00023-018-0644-z external_id: isi: - '000427578900006' file: - access_level: open_access checksum: 883eeccba8384ad7fcaa28761d99a0fa content_type: application/pdf creator: system date_created: 2018-12-12T10:11:57Z date_updated: 2020-07-14T12:46:31Z file_id: '4914' file_name: IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf file_size: 923252 relation: main_file file_date_updated: 2020-07-14T12:46:31Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1167 - 1214 publication: Annales Henri Poincare publication_status: published publisher: Birkhäuser publist_id: '7367' pubrep_id: '993' quality_controlled: '1' scopus_import: '1' status: public title: The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '314' 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. article_processing_charge: No article_type: letter_note author: - first_name: Guntram full_name: Bauer, Guntram last_name: Bauer - first_name: Nikta full_name: Fakhri, Nikta last_name: Fakhri - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Jané full_name: Kondev, Jané last_name: Kondev - first_name: Karsten full_name: Kruse, Karsten last_name: Kruse - first_name: Hiroyuki full_name: Noji, Hiroyuki last_name: Noji - first_name: Daniel full_name: Riveline, Daniel last_name: Riveline - first_name: Timothy full_name: Saunders, Timothy last_name: Saunders - first_name: Mukund full_name: Thatta, Mukund last_name: Thatta - first_name: Eric full_name: Wieschaus, Eric last_name: Wieschaus citation: 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 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 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. ieee: G. Bauer et al., “The science of living matter for tomorrow,” Cell Systems, vol. 6, no. 4. Cell Press, pp. 400–402, 2018. 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. 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. date_created: 2018-12-11T11:45:46Z date_published: 2018-04-25T00:00:00Z date_updated: 2023-09-19T10:11:25Z day: '25' department: - _id: AnKi doi: 10.1016/j.cels.2018.04.003 external_id: isi: - '000432192100003' pmid: - '29698645' intvolume: ' 6' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cels.2018.04.003 month: '04' oa: 1 oa_version: Published Version page: 400 - 402 pmid: 1 publication: Cell Systems publication_identifier: eissn: - 2405-4712 publication_status: published publisher: Cell Press publist_id: '7551' quality_controlled: '1' scopus_import: '1' status: public title: The science of living matter for tomorrow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 6 year: '2018' ... --- _id: '565' 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. ' article_processing_charge: No article_type: original author: - first_name: Brian full_name: Charlesworth, Brian last_name: Charlesworth - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 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 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. 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. 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. short: B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382. date_created: 2018-12-11T11:47:12Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-09-19T10:12:31Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.117.300426 external_id: isi: - '000419356300025' pmid: - '29158424' intvolume: ' 208' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/ month: '01' oa: 1 oa_version: Published Version page: 377 - 382 pmid: 1 publication: Genetics publication_status: published publisher: 'Genetics ' publist_id: '7249' quality_controlled: '1' scopus_import: '1' status: public title: The spread of an inversion with migration and selection type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 208 year: '2018' ... --- _id: '446' abstract: - lang: eng text: We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z > 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential. acknowledgement: "We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n" article_processing_charge: No article_type: original author: - first_name: Rupert full_name: Frank, Rupert last_name: Frank - first_name: Nam full_name: Phan Thanh, Nam id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Phan Thanh - first_name: Hanne full_name: Van Den Bosch, Hanne last_name: Van Den Bosch citation: ama: Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 2018;71(3):577-614. doi:10.1002/cpa.21717 apa: Frank, R., Nam, P., & Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21717 chicago: Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2018. https://doi.org/10.1002/cpa.21717. ieee: R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” Communications on Pure and Applied Mathematics, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018. ista: Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614. mla: Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:10.1002/cpa.21717. short: R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614. date_created: 2018-12-11T11:46:31Z date_published: 2018-03-01T00:00:00Z date_updated: 2023-09-19T10:09:40Z day: '01' department: - _id: RoSe doi: 10.1002/cpa.21717 external_id: arxiv: - '1606.07355' isi: - '000422675800004' intvolume: ' 71' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.07355 month: '03' oa: 1 oa_version: Preprint page: 577 - 614 publication: Communications on Pure and Applied Mathematics publication_status: published publisher: Wiley-Blackwell publist_id: '7377' quality_controlled: '1' status: public title: The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 71 year: '2018' ... --- _id: '430' abstract: - lang: eng text: In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly. article_processing_charge: No author: - first_name: John full_name: Novembre, John last_name: Novembre - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786 apa: Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786 chicago: Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786. ieee: J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018. ista: Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355. mla: Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786. short: J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355. date_created: 2018-12-11T11:46:26Z date_published: 2018-04-01T00:00:00Z date_updated: 2023-09-19T10:17:30Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1534/genetics.118.300786 external_id: isi: - '000429094400005' file: - access_level: open_access checksum: 3d838dc285df394376555b794b6a5ad1 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:40Z date_updated: 2020-07-14T12:46:26Z file_id: '4958' file_name: IST-2018-1012-v1+1_2018_Barton_Tread.pdf file_size: 500129 relation: main_file file_date_updated: 2020-07-14T12:46:26Z has_accepted_license: '1' intvolume: ' 208' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1351 - 1355 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '7393' pubrep_id: '1012' quality_controlled: '1' scopus_import: '1' status: public title: Tread lightly interpreting polygenic tests of selection tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 208 year: '2018' ... --- _id: '199' abstract: - lang: eng text: Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes. article_number: '294' article_processing_charge: No author: - first_name: Wen full_name: Ma, Wen last_name: Ma - first_name: Paris full_name: Veltsos, Paris last_name: Veltsos - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Nicolas full_name: Rodrigues, Nicolas last_name: Rodrigues - first_name: Roberto full_name: Sermier, Roberto last_name: Sermier - first_name: Daniel full_name: Jeffries, Daniel last_name: Jeffries - first_name: Nicolas full_name: Perrin, Nicolas last_name: Perrin citation: ama: Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294 apa: Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI AG. https://doi.org/10.3390/genes9060294 chicago: Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294. ieee: W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI AG, 2018. ista: Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294. mla: Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294. short: W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018). date_created: 2018-12-11T11:45:09Z date_published: 2018-06-12T00:00:00Z date_updated: 2023-09-19T10:15:31Z day: '12' ddc: - '570' department: - _id: BeVi doi: 10.3390/genes9060294 external_id: isi: - '000436494200026' file: - access_level: open_access checksum: 423069beb1cd3cdd25bf3f464b38f1d7 content_type: application/pdf creator: dernst date_created: 2019-02-01T07:52:28Z date_updated: 2020-07-14T12:45:22Z file_id: '5905' file_name: 2018_Genes_Ma.pdf file_size: 3985796 relation: main_file file_date_updated: 2020-07-14T12:45:22Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Genes publication_status: published publisher: MDPI AG publist_id: '7714' quality_controlled: '1' scopus_import: '1' status: public title: Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 9 year: '2018' ... --- _id: '543' abstract: - lang: eng text: A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits. article_processing_charge: No author: - first_name: Matthew J full_name: Chalk, Matthew J id: 2BAAC544-F248-11E8-B48F-1D18A9856A87 last_name: Chalk orcid: 0000-0001-7782-4436 - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115 apa: Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1711114115 chicago: Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1711114115. ieee: M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018. ista: Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191. mla: Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115. short: M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191. date_created: 2018-12-11T11:47:04Z date_published: 2018-01-02T00:00:00Z date_updated: 2023-09-19T10:16:35Z day: '02' department: - _id: GaTk doi: 10.1073/pnas.1711114115 external_id: isi: - '000419128700049' intvolume: ' 115' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/152660 ' month: '01' oa: 1 oa_version: Submitted Version page: 186 - 191 project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '7273' quality_controlled: '1' scopus_import: '1' status: public title: Toward a unified theory of efficient, predictive, and sparse coding type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '421' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Kinjal full_name: Dasbiswas, Kinjal last_name: Dasbiswas - first_name: Claude-Edouard B full_name: Hannezo, Claude-Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Nir full_name: Gov, Nir last_name: Gov citation: 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 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. 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. 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. short: K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977. date_created: 2018-12-11T11:46:23Z date_published: 2018-02-27T00:00:00Z date_updated: 2023-09-19T10:13:55Z day: '27' department: - _id: EdHa doi: 10.1016/j.bpj.2017.12.022 external_id: arxiv: - '1709.01486' isi: - '000428016700021' intvolume: ' 114' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.01486 month: '02' oa: 1 oa_version: Submitted Version page: 968 - 977 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '7403' quality_controlled: '1' scopus_import: '1' status: public title: Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 114 year: '2018' ...