51 research outputs found

    Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors

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    BACKGROUND: Plant-pathogenic oomycetes are responsible for economically important losses in crops worldwide. Phytophthora palmivora, a tropical relative of the potato late blight pathogen, causes rotting diseases in many tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus. Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped in understanding how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce. RESULTS: We employed the model plant Nicotiana benthamiana to study the P. palmivora root infections at the cellular and molecular levels. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features. CONCLUSIONS: These results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection-relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.This work was supported by the Gatsby Charitable Foundation (RG62472), by the Royal Society (RG69135) and by the European Research Council (ERC-2014-STG, H2020, 637537)

    Anti-Unification for Unranked Terms and Hedges

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    We study anti-unification for unranked terms and hedges that may contain term and hedge variables. The anti-unification problem of two hedges S1 and S2 is concerned with finding their generalization, a hedge ǭ such that both S1 and S2 are instances of ǭ under some substitutions. Hedge variables help to fill in gaps in generalizations, while term variables abstract single (sub)terms with different top function symbols. First, we design a complete and minimal algorithm to compute least general generalizations. Then, we improve the efficiency of the algorithm by restrictingpossible alternatives permitted in the generalizations. The restrictions are imposed with the help of a rigidity function that is a parameter in the improved algorithm and selects certain common subsequences from the hedges to be generalized. Finally, we indicate a possible application of the algorithm in software engineeringThis research has been partially supported by the Spanish Ministerio de Economa y Competitividad under the projects HeLo (TIN2012-33042) and TASSAT (TIN2010-20967-C04-01), by the EC FP6 for Integrated Infrastructures Initiatives under the project SCIEnce (contract No. 026133), by the Austrian Science Fund (FWF)under the project SToUT (P 24087-N18), and by the Generalitat de Catalunya under the grant AGAUR 2009-SGR-143

    Anti-unification for unranked terms and hedges

    No full text
    We study anti-unification for unranked terms and hedges that may contain term and hedge variables. The anti-unification problem of two hedges -1 and -2 is concerned with finding their generalization, a hedge q such that both -1 and -2 are instances of q under some substitutions. Hedge variables help to fill in gaps in generalizations, while term variables abstract single (sub)terms with different top function symbols. First, we design a complete and minimal algorithm to compute least general generalizations. Then, we improve the efficiency of the algorithm by restricting possible alternatives permitted in the generalizations. The restrictions are imposed with the help of a rigidity function, which is a parameter in the improved algorithm and selects certain common subsequences from the hedges to be generalized. The obtained rigid anti-unification algorithm is further made more precise by permitting combination of hedge and term variables in generalizations. Finally, we indicate a possible application of the algorithm in software engineeringThis research has been partially supported by the Spanish Ministerio de Economía y Competitividad under the projects HeLo (TIN2012-33042) and TASSAT (TIN2010-20967-C04-01), by the EC FP6 for Integrated Infrastructures Initiatives under the project SCIEnce (contract No. 026133), by the Austrian Science Fund (FWF) under the project SToUT (P 24087-N18), and by the Generalitat de Catalunya under the grant AGAUR 2009-SGR-143

    Lipid peroxidation in follicular fluid of women with polycystic ovary syndrome during assisted reproduction cycles

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    OBJECTIVE: To investigate the ovarian lipid peroxidation pattern in polycystic ovary syndrome (PCOS). STUDY DESIGN: Twenty-six women with PCOS who underwent in vitro fertilization and embryo transfer (IVF-ET) cycles between January 1999 and November 2000 at the hospital IVF unit were included in the study. Seventeen regularly cycling women with male factors (oligospermia or azoospermia) were enrolled as the control group. Malondialde hyde (MDA) levels in preovulatory follicular fluid were measured. RESULTS: There was a significant difference in follicular fluid MDA levels among the control (median, 2.23 nmol/mL; range, 0.98-4.93) and PCOS group (median, 3.53 nmol/mL; range, 1.51-4.81). Follicular fluid MDA and plasma progesterone levels correlated positively in the subjects (r = 0.55, p= 0.041) and PCOS group (r=0.074, p = 0.0001). Plasma luteinizing hormone/follicle stimulating hormone (LH/FSH) levels correlated positively with follicular fluid MDA levels in the PCOS group (r=0.72, p= 0.0001). CONCLUSION: The specific ovarian lipid peroxidation profile of PCOS patients is probably related to insufficient progesterone production and higher FSH/LH lev els. © Journal of Reproductive Medicine®, Inc

    The first case of Horn Kolb Syndrome in Turkey, diagnosed prenatally at the 23rd week of a pregnancy: A very rare and unusual case far from the original geography

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    Background: The aim of this report was to evaluate and announce the first documented appearance of Horn Kolb syndrome in Turkey. Case Report: Acheiropodia (Horn Kolb Syndrome) is the bilateral congenital amputation of the distal parts of the 4 extremities. It is an autosomal recessive developmental disorder. The characteristic features are amputation of the upper and lower extremities with aplasia of the hands and feet. The disorder affects only the extremities without other systemic manifestations. In this report, we present the first known case of Horn Kolb syndrome in Turkey, along with the diagnostic features. Conclusions: Severe dysmorphic skeletal anomalies should be excluded as soon as the earlier gestational weeks in every pregnancy by visualizing all 4 limbs of the fetus in routine prenatal ultrasound screening. © Am J Case Rep

    A Variant of Higher-Order Anti-Unification

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    We present a rule-based Huet’s style anti-unification algorithm for simply-typed lambda-terms in ɳ long β normal form, which computes a least general higher-order pattern generalization. For a pair of arbitrary terms of the same type, such a generalization always exists and is unique modulo α equivalence and variable renaming. The algorithm computes it in cubic time within linear space. It has been implemented and the code is freely availabl
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