@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}, }