Addressing ambiguity in probabilistic assessments of future marine flooding using possibility distributions

International audienceToday, decision making in the area of coastal adaptation is facing a major challenge due to the deep uncertainties of sea level projections. These deep uncertainties (aka ambiguity or epistemic uncertainties), reflect the intrinsically imprecise nature of global sea level rise (GSLR) due to the lack of knowledge regarding the melting of ice, particularly in Antarctica. Possibility distributions are one of the mathematical tools enabling to overcome the ambiguity in the selection a unique probability laws by bounding all the plausible ones. By adopting this new mathematical tool, we aim at evaluating how GSLR uncertainties accumulate with other sources of uncertainties, namely: the choice in Representative Concentration Pathway (RCP) scenario, the ranking of high-end scenarios, the regional bias, the contributions of extremes and wave effects. The case study corresponds to a local low-lying coastal urban area exposed to storm surge and waves in the north-western Mediterranean coast. We focus on the probability of future flooding by 2100 defined as the probability of exceeding a critical threshold corresponding to the height of coastal defences. The joint sensitivity analysis of the probabilistic, possibilistic and scenario-like sources of uncertainty enables to highlight the key role of deep uncertainties of GSLR, of the statistical uncertainty related to extremes and to a lesser extent of the choice in the RCP scenario. These results heavily depend on the decision maker’s attitude to risk (neutral, averse), which suggests the importance of entering into a loop of interactions with users, in order to collect their requirements and feedbacks, and involves research at the interface between behavioural and decision analytics, climate and coastal science as well as applied statistics

AN INSIGHT IN SOME POPULATION FEATURES OF XANTHOMONAS ARBORICOLA pv. JUGLANDIS

Xanthomonas arboricola pv. juglandis (Xaj) is the causal agent of bacterial blight of walnut, an emerging disease, which has the potential to severely affect walnut orchards. An Italian strain collection of Xaj, obtained during the past 3 years from affected orchards in Romagna, was first assayed with conventional PCR with XajF/XajR primer pair developed to confirm strain identity. The population structure of the collection of Xaj isolates, confirms the presence of different genetic groups identified by rep-PCR (using Italian collection are currently being analysed by MLSA (multi locus sequence analysis), using 7 primers for 7 different housekeeping genes, with the purpose to better characterise the Italian isolates for phylotyping. The study of copper resistance on a wide collection of over 150 Xaj strains frequently showed high resistance (up to 500 ppm Cu++): two strains have been further studied confirming the presence of chromosomal genes copA and copB involved in the general copABCD copper resistance structure, as described for Pseudomonas syringae. Sequencing and comparing with other Xanthomonads were done. The elucidation of Xaj population structure may help to deeper investigate some additional aspects of the molecular epidemiology of the disease, thus allowing a better control strategy in the field. the REP, BOX and ERIC primers) and by multilocus sequence typing (MLST) and multilocus variable number analysis of tandem repeat (MLVA). Xaj and Xaj-like bacterial isolates from th

Management of uncertainties on parameters elicited by experts – Applications to sea-level rise and to CO 2 storage operations risk assessment

International audienceIn a context of high degree of uncertainty, when very few data are available, experts are commonly requested to provide their opinions on input parameters of risk assessment models. Not only might each expert express a certain degree of uncertainty on his/her own statements, but the set of information collected from the pool of experts introduces an additional level of uncertainty. It is indeed very unlikely that all experts agree on exactly the same data, especially regarding parameters needed for natural risk assessments. In some cases, their opinions may differ only slightly (e.g. the most plausible value for a parameter is similar for different experts, and they only disagree on the level of uncertainties that taint the said value) while on other cases they may express incompatible opinions for a same parameter. Dealing with these different kinds of uncertainties remains a challenge for assessing geological hazards or/and risks. Extra-probabilistic approaches (such as the Dempster-Shafer theory or the possibility theory) have shown to offer promising solutions for representing parameters on which the knowledge is limited. It is the case for instance when the available information prevents an expert from identifying a unique probability law to picture the total uncertainty. Moreover, such approaches are known to be particularly flexible when it comes to aggregating several and potentially conflicting opinions. We therefore propose to discuss the opportunity of applying these new theories for managing the uncertainties on parameters elicited by experts, by a comparison with the application of more classical probability approaches. The discussion is based on two different examples. The first example deals with the estimation of the injected CO 2 plume extent in a reservoir in the context of CO 2 geological storage. This estimation requires information on the effective porosity of the reservoir, which has been estimated by 14 different experts. The Dempster-Shafer theory has been used to represent and aggregate these pieces of information. The results of different aggregation rules as well as those of a classical probabilistic approach are compared with the purpose of highlighting the elements each of them could provide to the decision-maker (Manceau et al., 2016). The second example focuses on projections of future sea-level rise. Based on IPCC's constraints on the projection quantiles, and on the scientific community consensus level on the physical limits to future sea-level rise, a possibility distribution of the projections by 2100 under the RCP 8.5 scenario has been established. This possibility distribution has been confronted with a set of previously published probabilistic sea-level projections, with a focus on their ability to explore high ranges of sea-level rise (Le Cozannet et al., 2016). These two examples are complementary in the sense that they allow to address various aspects of the problem (e.g. representation of different types of information, conflict among experts, sources dependence). Moreover, we believe that the issues faced during these two experiences can be generalized to many risks/hazards assessment situations. References Manceau, JC., Loschetter, A., Rohmer, J., de Lary, L., Le Guénan, T., Hnottavange-Telleen, K. (2016). Dealing with uncertainty on parameters elicited from a pool of experts for CCS risk assessment. Congrès λµ 20 (St-Malo, France). Le Cozannet G., Manceau JC., Rohmer, J. (2016). Bounding probabilistic sea-level rise projections within the framework of the possibility theory. Accepted in Environmental Research Letters

Homogénéisation de l'écoulement dans une cellule de Hele-Shaw et caractérisation par µPIV en champ large

Dans les capteurs biologiques basés sur la microfluidique, l'analyte d'intérêt est en général amené en contact avec une surface fonctionnalisée où il est capturé. Cette surface est ensuite analysée par mesure optique (SPR...) ou acoustique (QCM...), permettant ainsi de quantifier précisément les analytes présents dans le liquide. Notre groupe développe des capteurs acoustiques à base de membranes résonantes couplées qui sont agencées en matrice pour augmenter la sensibilité du capteur. Cette architecture nécessite l'utilisation d'une grande chambre d'analyse, de l'ordre de 1cmx1cm, où les écoulements doivent être contrôlés pour garantir une bonne homogénéité des débits sur l'ensemble de la surface du capteur lors de l'insertion ou du renouvellement des fluides dans la cavité. On limite ainsi les écarts de traitement lors des réactions de fonctionnalisation, de capture, d'inactivation ou encore lors des étapes de nettoyage de la surface de capture. Il est dès lors nécessaire de concevoir des puces microfluidiques où la géométrie et les caractéristiques des fluides permettent un écoulement homogène sans zone morte ou zone de recirculation au sein de la chambre. Ainsi nous avons étudié différentes géométries de canaux d'entrée et de sortie dans une chambre microfluidique de grande surface et de faible profondeur, à travers des simulations par éléments finis en 2D et par le développement d'un banc expérimental de caractérisation d'écoulements. Pour minimiser le volume de l'échantillon à analyser et pour faciliter la diffusion des bio-analytes vers la surface d'interaction, nous avons fixé la hauteur de la chambre à 80µm. Dans ces conditions, nous nous plaçons dans un régime d'écoulement laminaire et la cavité microfluidique peut être assimilée à une cellule de Hele-Shaw de 1cm x 1cm de côté. La simulation des écoulements par éléments finis de ces structures a été faite sous COMSOL en utilisant le modèle laminaire 2D avec approximation de faible profondeur, qui correspond bien à l'écoulement de Hele-Shaw. Nous avons étudié 5 configurations différentes en faisant varier le nombre et l'espacement des canaux d'alimentation (1 entrée/1 sortie, 16 entrées/1 sortie, 16 entrées/16 sorties) et la géométrie de la chambre (carrée, losange, bézier). L'objectif de vitesse moyenne dans la chambre était de 200µm/s et l'uniformité de l'écoulement a été évaluée en observant le profil de vitesse dans différentes sections. Pour l'étude expérimentale, les dispositifs microfluidiques ont été réalisés par microfabrication en salle blanche. Les canaux fluidiques et la chambre sont structurés dans un substrat de silicium par gravure chimique KOH puis la chambre est refermée par collage anodique d'un substrat de verre autorisant l'observation optique.  La mesure expérimentale des vitesses d'écoulement a demandé de concevoir un nouveau banc de µPIV permettant l'observation sur un champ d'un cm², tout en visualisant, en lumière blanche, des particules de faible taille. Ces particules en mélamine ont un diamètre de 920 nm pour répondre aux contraintes de sédimentation et de non modification des écoulements. La mesure locale du champ de vitesse est obtenue par corrélation entre des paires d'images espacées de 50ms, puis en faisant une moyenne sur 100 paires d'image. Nous présenterons dans l'exposé la comparaison entre les résultats expérimentaux et numériques pour les différentes chambres étudiées, qui montrent que l'on peut améliorer, en fonction de la configuration de la chambre, l'homogénéité des écoulements d'un facteur d'environ 5 sur 80% de la section

The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae

<p>Abstract</p> <p>Background</p> <p>The <it>Xanthomonadaceae </it>family contains two xylem-limited plant pathogenic bacterial species, <it>Xanthomonas albilineans </it>and <it>Xylella fastidiosa</it>. <it>X. fastidiosa </it>was the first completely sequenced plant pathogen. It is insect-vectored, has a reduced genome and does not possess <it>hrp </it>genes which encode a Type III secretion system found in most plant pathogenic bacteria. <it>X. fastidiosa </it>was excluded from the <it>Xanthomonas </it>group based on phylogenetic analyses with rRNA sequences.</p> <p>Results</p> <p>The complete genome of <it>X. albilineans </it>was sequenced and annotated. <it>X. albilineans</it>, which is not known to be insect-vectored, also has a reduced genome and does not possess <it>hrp </it>genes. Phylogenetic analysis using <it>X. albilineans </it>genomic sequences showed that <it>X. fastidiosa </it>belongs to the <it>Xanthomonas </it>group. Order of divergence of the <it>Xanthomonadaceae </it>revealed that <it>X. albilineans </it>and <it>X. fastidiosa </it>experienced a convergent reductive genome evolution during their descent from the progenitor of the <it>Xanthomonas </it>genus. Reductive genome evolutions of the two xylem-limited <it>Xanthomonadaceae </it>were compared in light of their genome characteristics and those of obligate animal symbionts and pathogens.</p> <p>Conclusion</p> <p>The two xylem-limited <it>Xanthomonadaceae</it>, during their descent from a common ancestral parent, experienced a convergent reductive genome evolution. Adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. However, genome characteristics of <it>X. albilineans </it>differ from those of <it>X. fastidiosa </it>and obligate animal symbionts and pathogens, indicating that a distinctive process was responsible for the reductive genome evolution in this pathogen. The possible role in genome reduction of the unique toxin albicidin, produced by <it>X. albilineans</it>, is discussed.</p

Scientific Opinion on the pest categorisation of Strawberry vein banding virus

The Panel on Plant Health performed a pest categorisation of Strawberry vein banding virus (SVBV) for the European Union (EU) territory. SVBV is a well-defined virus species of the genus Caulimovirus for which the entire genome sequence is known and molecular detection assays are available. SVBV is transmitted by vegetative multiplication of infected hosts and through the activity of aphid vectors, the most efficient being Chaetosiphon spp. The virus is reported from all continents and is present in three EU Member States: the Czech Republic, Italy and Slovakia. The host range of SVBV is restricted to cultivated and wild strawberries. It is listed in Annex IAI of Directive 2000/29/EC. SVBV is not expected to be affected by ecoclimatic conditions wherever its hosts are present and has the potential to establish in large parts of the EU territory, and to subsequently spread through the action of its Chaetosiphon fragaefolii vector, which is present in many Member States. SVBV does not cause severe symptoms, and modern cultivars are mostly symptomless if infected with SVBV alone. SVBV can, however, contribute to more severe symptoms when it occurs in mixed infections with other strawberry viruses. Despite this, SVBV is considered a minor problem in strawberry production as a consequence of modern practices including the systematic use of certified planting materials and the use of short crop cycles, which have greatly reduced the impact of strawberry viruses. Overall, SVBV does not have the potential to be a quarantine pest as, given current agricultural practices, it does not fulfil the pest categorisation criteria defined in the International Standards for Phytosanitary Measures No 11 of having a severe impact. However, SVBV has the potential to be a regulated non-quarantine pest because it fulfils all pest categorisation criteria defined in the International Standards for Phytosanitary Measures No 21

Scientific Opinion on the pest categorisation of Eotetranychus lewisi

The Panel on Plant Health performed a pest categorisation of the Lewis spider mite, Eotetranychus lewisi, for the European Union (EU). The Lewis spider mite is a well-defined and distinguishable pest species that has been reported from a wide range of hosts, including cultivated species. Its distribution in the EU territory is restricted to (i) Madeira in Portugal; and to (ii) Poland where few occurrences were reported in glasshouses only. The pest is listed in Annex IIAI of Council Directive 2000/29/EC. A potential pathway of introduction and spread is plants traded from outside Europe and between Member States. The Lewis spider mite has the potential to establish in most part of the EU territory based on climate similarities with the distribution area outside the EU and the widespread availability of hosts present both in open fields and in protected cultivations. With regards to the potential consequences, one study is providing quantitative data on impact showing that the pest can reduce yield and affect quality of peaches and poinsettias, and only few studies describe the general impact of the pest on cultivated hosts. Although chemical treatments are reported to be effective in controlling the Lewis spider mite, it is mentioned as a growing concern for peaches, strawberries, raspberries and vines in the Americas. Overall, Eotetranychus lewisi meets the pest categorisation criteria defined in the International Standards for Phytosanitary Measures No 11 for a quarantine pest and in No 21 for a regulated non-quarantine pest

Scientific Opinion on the pest categorisation of Paysandisia archon (Burmeister)

The Panel on Plant Health performed a pest categorisation of Paysandisia archon for the European Union territory. P. archon is a well-defined pest species attacking many palm species. It is currently present in several southern European Member States (Croatia, Cyprus, France, Greece, Italy, Slovenia and Spain). Malta and Portugal are considered to be very important areas for further spread of the pest. The pest is listed in Annex IIAII of Council Directive 2000/29/EC and special requirements for host plants with respect to P. archon are formulated in Annexes IVAI and IVAII of Council Directive 2000/29/EC. This moth is a strong flier, but its main pathway of spread is via ornamental palms traded from outside the European Union and between Member States. Wherever its hosts are present outdoors in southern Europe, P. archon has the potential to establish. Although P. archon can complete its development in protected cultivation and in private/public indoor plant collections, there is no evidence of establishment. The damage produced by the larvae can cause the death of the plant with consequences for cultivated and native palm trees, and therefore on ecosystem services and biodiversity. At the moment no fully effective chemical or biological control methods are available against spread and impact of P. archon, while the use of glues on the stipe of the palm can be effective but affects the ornamental value of the plant. P. archon meets all pest categorisation criteria for both quarantine pests and regulated non-quarantine pests