@article{5770, abstract = {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.}, author = {Qu, Kun and Glass, Bärbel and Doležal, Michal and Schur, Florian and Murciano, Brice and Rein, Alan and Rumlová, Michaela and Ruml, Tomáš and Kräusslich, Hans-Georg and Briggs, John A. G.}, issn = {00278424}, journal = {Proceedings of the National Academy of Sciences}, number = {50}, pages = {E11751--E11760}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Structure and architecture of immature and mature murine leukemia virus capsids}}, doi = {10.1073/pnas.1811580115}, volume = {115}, year = {2018}, } @article{608, abstract = {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.}, author = {Avni, Guy and Kupferman, Orna}, journal = {Theoretical Computer Science}, pages = {50 -- 72}, publisher = {Elsevier}, title = {{Synthesis from component libraries with costs}}, doi = {10.1016/j.tcs.2017.11.001}, volume = {712}, year = {2018}, } @article{705, abstract = {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.}, author = {Miklosi, Andras and Del Favero, Giorgia and Bulat, Tanja and Höger, Harald and Shigemoto, Ryuichi and Marko, Doris and Lubec, Gert}, journal = {Molecular Neurobiology}, number = {6}, pages = {4857 – 4869}, publisher = {Springer}, title = {{Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes}}, doi = {10.1007/s12035-017-0688-y}, volume = {55}, year = {2018}, } @article{148, abstract = {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.}, author = {Nishiyama, Tomoaki and Sakayama, Hidetoshi and De Vries, Jan and Buschmann, Henrik and Saint Marcoux, Denis and Ullrich, Kristian and Haas, Fabian and Vanderstraeten, Lisa and Becker, Dirk and Lang, Daniel and Vosolsobě, Stanislav and Rombauts, Stephane and Wilhelmsson, Per and Janitza, Philipp and Kern, Ramona and Heyl, Alexander and Rümpler, Florian and Calderón Villalobos, Luz and Clay, John and Skokan, Roman and Toyoda, Atsushi and Suzuki, Yutaka and Kagoshima, Hiroshi and Schijlen, Elio and Tajeshwar, Navindra and Catarino, Bruno and Hetherington, Alexander and Saltykova, Assia and Bonnot, Clemence and Breuninger, Holger and Symeonidi, Aikaterini and Radhakrishnan, Guru and Van Nieuwerburgh, Filip and Deforce, Dieter and Chang, Caren and Karol, Kenneth and Hedrich, Rainer and Ulvskov, Peter and Glöckner, Gernot and Delwiche, Charles and Petrášek, Jan and Van De Peer, Yves and Friml, Jirí and Beilby, Mary and Dolan, Liam and Kohara, Yuji and Sugano, Sumio and Fujiyama, Asao and Delaux, Pierre Marc and Quint, Marcel and Theissen, Gunter and Hagemann, Martin and Harholt, Jesper and Dunand, Christophe and Zachgo, Sabine and Langdale, Jane and Maumus, Florian and Van Der Straeten, Dominique and Gould, Sven B and Rensing, Stefan}, journal = {Cell}, number = {2}, pages = {448 -- 464.e24}, publisher = {Cell Press}, title = {{The Chara genome: Secondary complexity and implications for plant terrestrialization}}, doi = {10.1016/j.cell.2018.06.033}, volume = {174}, year = {2018}, } @article{403, abstract = {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.}, author = {Cavallari, Nicola and Nibau, Candida and Fuchs, Armin and Dadarou, Despoina and Barta, Andrea and Doonan, John}, journal = {The Plant Journal}, number = {6}, pages = {1010 -- 1022}, publisher = {Wiley}, title = {{The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A}}, doi = {10.1111/tpj.13914}, volume = {94}, year = {2018}, } @inproceedings{156, abstract = {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.}, author = {Ferrere, Thomas}, location = {Oxford, UK}, pages = {147 -- 164}, publisher = {Springer}, title = {{The compound interest in relaxing punctuality}}, doi = {10.1007/978-3-319-95582-7_9}, volume = {10951}, year = {2018}, } @article{104, abstract = {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.}, author = {Seitner, Denise and Uhse, Simon and Gallei, Michelle C and Djamei, Armin}, journal = {Molecular Plant Pathology}, number = {10}, pages = {2277 -- 2287}, publisher = {Wiley}, title = {{The core effector Cce1 is required for early infection of maize by Ustilago maydis}}, doi = {10.1111/mpp.12698}, volume = {19}, year = {2018}, } @article{40, abstract = {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.}, author = {Barton, Nicholas H}, issn = {1365294X}, journal = {Molecular Ecology}, number = {24}, pages = {4973--4975}, publisher = {Wiley}, title = {{The consequences of an introgression event}}, doi = {10.1111/mec.14950}, volume = {27}, year = {2018}, } @article{5861, abstract = {In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal.}, author = {Alanko, Jonna H and Sixt, Michael K}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{The cell sets the tone}}, doi = {10.7554/eLife.37888}, volume = {7}, year = {2018}, } @article{147, abstract = {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.}, author = {Kania, Urszula and Nodzyński, Tomasz and Lu, Qing and Hicks, Glenn R and Nerinckx, Wim and Mishev, Kiril and Peurois, Francois and Cherfils, Jacqueline and De, Rycke Riet Maria and Grones, Peter and Robert, Stéphanie and Russinova, Eugenia and Friml, Jirí}, issn = {1040-4651}, journal = {The Plant Cell}, number = {10}, pages = {2553 -- 2572}, publisher = {Oxford University Press}, title = {{The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes}}, doi = {10.1105/tpc.18.00127}, volume = {30}, year = {2018}, }