Estimating sharka dispersal function by stochastic spatiotemporal modelling

Plant viral diseases, and especially the ones transmitted by aerial vectors, can cause considerable yield losses. A good knowledge of the distances of spread is key to the understanding of disease dynamics. Exploratory approaches aiming at characterizing the spatiotemporal distribution of diseased plants are often used to get an insight into the distances of spread. A more powerful approach is based on stochastic spatiotemporal modelling in order to estimate the dispersal function of the disease (probability density function describing the probability for an infectious plant to infect a healthy plant at distance d). In this study, we implemented a method for estimating the dispersal function of the sharka disease. Sharka is one of the most serious diseases of stone fruit trees (Prunus sp.). It is caused by Plum pox virus (PPV, genus Potyvirus), transmitted by at least twenty different aphid species in a non persistent manner. Due to the inefficiency of insecticides and the very rare sources of resistance against the virus available in the host species, prophylactic disease control is based on the removal of the diseased trees in the orchards. Thus, a very good knowledge of the dispersal function of sharka is crucial for building epidemiological models and optimizing the strategies of surveillance and control. We adapted the methodology published by Gibson (1997) based on a Markov chain Monte Carlo (MCMC) algorithm in order to estimate sharka dispersal function from the maps of 157 contiguous peach orchards reporting the exact location and the sanitary status (asymptomatic/symptomatic) of each of the trees during six consecutive years. An estimation method based on the Gibbs sampling algorithm was developed taking into account the specificities of the dataset (more than two dates of observation, annual removal of diseased trees). This estimation algorithm was validated on simulated data and was proved to be more powerful and better adapted to large datasets than the one proposed by Gibson. Moreover, the influence of latency on the estimation of the dispersal function was quantified. This methodology was then used to estimate the dispersal function of the disease from a subset of the real dataset. The methods developed in this study are generic enough to be used and adapted for the estimation of dispersal functions of any disease transmitted in a non persistent manner, and even for diseases with similar characteristics. (Texte intégral

Combining experimental assays with epidemiological surveys to assess indicators of Plum pox virus epidemicity

The huge increase in sequence data those last decades has allowed defining better demarcation criteria for viral taxonomic assignments. For the epidemiologists, such demarcation based on molecular properties, especially at the strain level, is particularly meaningful if one can link the different strains to specific phenotypes (host range, pathogenicity,...) and can thus identify specific epidemic risks for a given host or for a given agro-ecological context. Plum pox virus (PPV, genus Potyvirus, family Potyviridae) is responsible for the sharka disease, the most serious disease of stone fruit trees (Prunus species). In the framework of a collaborative European research program, an important effort has been made to increase the knowledge of PPV genetic diversity (www sharco.eu). Based on molecular criteria (genetic distances and successful recombinant genomes), eight different strains have been distinguished but very little is known about their specific biological and epidemiological properties. Such a situation is due to different reasons: (i) the quarantine pest status of PPV does not allow experiments unless carried out under a strict confinement; (ii) the perennial nature of the Prunus hosts makes the experiments generally long and complicated; and (iii) the epidemiological behaviour of a given strain (or even isolate) can be influenced by specific agro-ecological conditions occurring at a given location. In this study, we combined biological experiments with epidemiological surveys to gain a better knowledge on PPV epidemic properties. A first approach was thus developed for the three most prevalent PPV strains (M, D and Rec) in Europe, which have different geographical distributions. The experimental assays were designed to allow measuring indicators of the key steps of the infection cycle on three Prunus species (apricot, peach and plum): (i) ability for a given strain to infect the host after aphid-mediated (using a clone of Myzus persicae) inoculation, (ii) dynamic of infection in each Prunus host, and (iii) efficiency of the infected Prunus as virus sources (acquisition-transmission assays carried out with M. persicae as vector). In parallel to these experimental assays, surveys have been carried out in Serbia in order to assess (i) the relative prevalence of these three PPV strains known to spread in this country, and (ii) their Prunus host preference. These two approaches bring different but complementary information. The experimental assays did not evidence strict host specificity (pathotype) but rather several cumulative advantages (shorter latency in apricot, better generalization in peach, higher overall aphid transmission rates) that should confer a higher epidemicity to the PPV-M strain. The results from surveys evidenced a strong host specificity (PPV-M on peach), frequent coinfections and independence between infections by the three PPV strains in plum. (Texte intégral

Tooth wear as a means to quantify intra-specific variations in diet and chewing movements

9 pagesInternational audienceIn mammals, tooth function, and its efficiency, depends both on the mechanical properties of the foodand on chewing dynamics. These aspects have rarely been studied in combination and/or at the intraspecificlevel. Here we applied 3D dental surface texture analysis to a sample of field voles (Microtusagrestis) trapped from Finnish Lapland at different seasons and localities to test for inter-populationvariations. We also explored intra-individual variation in chewing dynamics by analysing two facetson the second upper molars. Our results confirm that the two localities have similar environments andthat the voles feed on the same items there. On the other hand, the texture data suggest that diets areseasonally variable, probably due to varying concentrations of abrasives. Lastly, the textures on thebuccal facets are more isotropic and their direction deviates more from the mesial chewing directionthan the lingual facets. We interpret these results as reflecting food, rather than chewing, movements,where food particles are more guided on the lingual side of the molars. This has implications for theapplication of dental microwear analysis to fossils: only homologous facets can be compared, evenwhen the molar row seems to constitute a functional unit

Expression of osterix Is Regulated by FGF and Wnt/β-Catenin Signalling during Osteoblast Differentiation

Osteoblast differentiation from mesenchymal cells is regulated by multiple signalling pathways. Here we have analysed the roles of Fibroblast Growth Factor (FGF) and canonical Wingless-type MMTV integration site (Wnt/β-Catenin) signalling pathways on zebrafish osteogenesis. We have used transgenic and chemical interference approaches to manipulate these pathways and have found that both pathways are required for osteoblast differentiation in vivo. Our analysis of bone markers suggests that these pathways act at the same stage of differentiation to initiate expression of the osteoblast master regulatory gene osterix (osx). We use two independent approaches that suggest that osx is a direct target of these pathways. Firstly, we manipulate signalling and show that osx gene expression responds with similar kinetics to that of known transcriptional targets of the FGF and Wnt pathways. Secondly, we have performed ChIP with transcription factors for both pathways and our data suggest that a genomic region in the first intron of osx mediates transcriptional activation. Based upon these data, we propose that FGF and Wnt/β-Catenin pathways act in part by directing transcription of osx to promote osteoblast differentiation at sites of bone formation

Production and characterization of monoclonal antibodies to Xenopus proteins

Monoclonal antibodies are powerful and versatile tools that enable the study of proteins in diverse contexts. They are often utilized to assist with identification of subcellular localization and characterization of the function of target proteins of interest. However, because there can be considerable sequence diversity between orthologous proteins in Xenopus and mammals, antibodies produced against mouse or human proteins often do not recognize Xenopus counterparts. To address this issue, we refined existing mouse monoclonal antibody production protocols to generate antibodies against Xenopus proteins of interest. Here, we describe several approaches for the generation of useful mouse anti-Xenopus antibodies to multiple Xenopus proteins and their validation in various experimental approaches. These novel antibodies are now available to the research community through the Developmental Study Hybridoma Bank (DSHB)

Forêts de montagne et changement climatique : impacts et adaptation

This review identifies the main impacts of climate change on mountain forests, mainly in Europe, and the management practices proposed for forest adaption. The rise in temperatures, more frequent droughts and the multiplication of extreme events should lead, especially below 1000m in altitude, to the disappearance of highly drought-intolerant tree species (spruce, Scots pine) and their replacement by deciduous trees. In addition, recruitment of some species (fir, beech) is observed at higher altitudes and the duration of the growing season is increasing. Management recommendations for forest adaptation to climate change focus on reducing tree species' vulnerability to water stress and pests, as well as increasing their resilience and ability to respond to extreme weather events. They require genetic improvements and practices that encourage the establishment of suitable species, reduce water consumption and reduce the exposure of stands to risk.Les impacts du changement climatique sur les forêts de montagne sont déjà perceptibles et les prévisions nous montrent, par leurs contradictions, la complexité des phénomènes en jeu. L'objectif de cette étude bibliographique est d'abord de caractériser les principaux effets du changement climatique, principalement dans les forêts alpines, puis de présenter différentes options d'adaptation devant permettre de conserver les services actuellement fournis par la forêt. L'épicéa, le sapin et le hêtre, dominants dans les Alpes françaises, y sont privilégiés

Forêts de montagne et changement climatique : impacts et adaptations

This review identifies the main impacts of climate change on mountain forests, mainly in Europe, and the management practices proposed for forest adaption. The rise in temperatures, more frequent droughts and the multiplication of extreme events should lead, especially below 1000m in altitude, to the disappearance of highly drought-intolerant tree species (spruce, Scots pine) and their replacement by deciduous trees. In addition, recruitment of some species (fir, beech) is observed at higher altitudes and the duration of the growing season is increasing. Management recommendations for forest adaptation to climate change focus on reducing tree species' vulnerability to water stress and pests, as well as increasing their resilience and ability to respond to extreme weather events. They require genetic improvements and practices that encourage the establishment of suitable species, reduce water consumption and reduce the exposure of stands to risk.Cette étude bibliographique recense les principaux impacts du changement climatique sur les forêts de montagne, principalement européennes, ainsi que les pratiques de gestion proposées pour adapter les forêts à ces changements. La hausse des températures, les sécheresses plus fréquentes et la multiplication des évènements extrêmes devraient entrainer, surtout en-deçà de 1000m d'altitude, une réduction des essences les moins tolérantes à la sécheresse (épicéa, pin sylvestre) et leur remplacement par des feuillus. D'ores et déjà, le recrutement de certaines essences (sapin, hêtre) est observé à des altitudes plus élevées et la durée de la saison de végétation augmente. Les préconisations de gestion pour l'adaptation des forêts au changement climatique s'attachent à réduire la vulnérabilité des essences au stress hydrique et aux parasites, ainsi qu'à renforcer leur résilience et leur capacité de réponse aux évènements climatiques extrêmes. Elles passent par des améliorations génétiques et des pratiques qui favorisent l'installation d'espèces adaptées, réduisent la consommation d'eau et l'exposition des peuplements aux risques

Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene

Primula vulgaris (primrose) exhibits heterostyly: plants produce self-incompatible pin- or thrum-form flowers, with anthers and stigma at reciprocal heights. Darwin concluded that this arrangement promotes insect-mediated cross-pollination; later studies revealed control by a cluster of genes, or supergene, known as the S (Style length) locus. The P. vulgaris S locus is absent from pin plants and hemizygous in thrum plants (thrum-specific); mutation of S locus genes produces self-fertile homostyle flowers with anthers and stigma at equal heights. Here, we present a 411 Mb P. vulgaris genome assembly of a homozygous inbred long homostyle, representing ~87% of the genome. We annotate over 24,000 P. vulgaris genes, and reveal more genes up-regulated in thrum than pin flowers. We show reduced genomic read coverage across the S locus in other Primula species, including P. veris, where we define the conserved structure and expression of the S locus genes in thrum. Further analysis reveals the S locus has elevated repeat content (64%) compared to the wider genome (37%). Our studies suggest conservation of S locus genetic architecture in Primula, and provide a platform for identification and evolutionary analysis of the S locus and downstream targets that regulate heterostyly in diverse heterostylous species