Structure de l’écoulement tridimensionnel, turbulence et contrainte de cisaillement dans une boucle de méandre

Plusieurs facteurs contribuent à l’instabilité des berges dans les méandres, mais le rôle joué par la dynamique de l’écoulement complexe au sein de ces sites n’est pas clairement élucidé. L’objectif de cette recherche est d’examiner la dynamique de l’écoulement tridimensionnel (3D) d’une boucle de méandre en vue de déterminer les liens entre la structure de l’écoulement moyen et turbulent, la contrainte de cisaillement et l’érosion des berges. Des données de vitesse 3D ont été recueillies dans une boucle de méandre avec un vélocimètre acoustique Doppler (ADV) et un profileur acoustique Doppler conçu pour les rivières peu profondes (PC-ADP). Une comparaison entre ces deux appareils a révélé que le PC-ADP donne de bons estimés de vitesse moyenne dans un écoulement relativement simple (au centre du chenal), mais le problème de moyennage spatial le rend moins efficace dans un plan de mélange où l’écoulement est plus complexe. L’ADV est aussi supérieur au PC-ADP pour les estimés de contrainte de cisaillement et l’étude de la turbulence à petite échelle, mais ce dernier révèle mieux les patrons à grande échelle. Deux cellules d’écoulement secondaire dans le méandre ressortent nettement avec les mesures simultanées du PC-ADP. Les maxima de contrainte de cisaillement mesurée avec l’ADV par la méthode d’énergie turbulente cinétique sont situés à l’entrée du méandre lorsque le niveau est plus bas, et à la sortie du méandre lorsque le niveau augmente. Ces deux zones correspondent à des observations de décrochement de berge au site d’étude.Many factors contribute to bank instability in meanders, but the exact role played by the complex flow dynamics is not very well understood. The objective of this research is to examine the three-dimensional (3D) flow dynamics in a meander loop to determine the links between the mean and turbulent flow structure, and bank erosion. 3D velocity data were collected in a meander loop with an acoustic Doppler velocimeter (ADV) and a pulse-coherent acoustic Doppler profiler (PC-ADP). A comparison between these two devices revealed that the PC-ADP provides accurate estimates of mean velocity in a relatively simple flow (in the centre of the channel), but that it is less efficient in a complex flow field with a mixing zone due to spatial averaging problems. The ADV is also better than the PC-ADP for bed shear stress estimates and for small-scale turbulence studies, but the latter reveals large-scale structures efficiently. Two secondary cells in the meander loop are clearly seen from the simultaneous PC-ADP measurements. The maximum values of bed shear stress measured with the ADV with the turbulent kinetic energy method are located at the meander entrance when flow stage is low, and at the meander exit when flow stage increases. These two zones correspond to observations of bank failure events at the field site

The potential for reassortment between Oropouche and Schmallenberg Orthobunyaviruses

A number of viruses within the Peribunyaviridae family are naturally occurring reassortants, a common phenomenon for segmented viruses. Using a minigenome-reporter and virus-like particle (VLP) production assay, we have accessed the potential of Oropouche virus (OROV), Schmallenberg virus (SBV), and other orthobunyaviruses within the Simbu serogroup to reassort. We found that the untranslated region (UTR) in the medium segment is a potential contributing factor for reassortment by the tested viruses. We demonstrate that for promoter activity to occur it was essential that the viral RNA polymerase (L) and nucleocapsid (N) proteins were from the same virus, reinforcing the hypothesis that the large and small segments that encode these proteins segregate together during genome reassortment. Our results indicate that, given the right epidemiological setting, reassortment between SBV and OROV would potentially be feasible and could contribute to the emergence of a new Simbu virus

New flow relaxation mechanism explains scour fields at the end of submarine channels

Particle-laden gravity flows, called turbidity currents, flow through river-like channels across the ocean floor. These submarine channels funnel sediment, nutrients, pollutants and organic carbon into ocean basins and can extend for over 1000’s of kilometers. Upon reaching the end of these channels, flows lose their confinement, decelerate, and deposit their sediment load; this is what we read in textbooks. However, sea floor observations have shown the opposite: turbidity currents tend to erode the seafloor upon losing confinement. Here we use a state-of-the-art scaling method to produce the first experimental turbidity currents that erode upon leaving a channel. The experiments reveal a novel flow mechanism, here called flow relaxation, that explains this erosion. Flow relaxation is rapid flow deformation resulting from the loss of confinement, which enhances basal shearing of the turbidity current and leads to scouring. This flow mechanism plays a key role in the propagation of submarine channel systems

The importance of soil and vegetation characteristics for establishing ground nesting bee aggregations

Most bee species are ground-nesters, yet knowledge on the nesting behaviour of this diverse group remains sparse. Evidence on the effectiveness of ground-nesting bee species as crop pollinators is growing, but there is limited information on their nesting habits and preferences and how to manage habitats to enhance populations on farms. In this study, artificially prepared plots of bare soil were constructed with the aim to attract ground-nesting bees to nest in a commercial orchard in Kent, UK. Nine soil parameters were measured to determine their preferred soil properties: hydraulic conductivity, soil compaction, soil moisture, soil temperature, soil stoniness, soil organic matter, soil root biomass, soil texture and vegetation cover. Eighteen non-parasitic ground-nesting bee species (7 Andrena, 9 Lasioglossum, 1 Halictus and 1 Colletes spp.) were recorded in the study plots. Soil stoniness and soil temperature at 10cm depth were positively correlated, and vegetation cover and hydraulic conductivity were negatively correlated with the number of ground-nesting bees on the plots. We show that artificially created habitats can be exploited for nesting by several ground-nesting bee species. This study’s findings can inform management practices to enhance ground-nesting bee populations in agricultural and urban areas

Genetic analysis of members of the species Oropouche virus and identification of a novel M segment sequence

Oropouche virus (OROV) is a public health threat in South America, and in particular Northern Brazil, causing frequent outbreaks of febrile illness. Using a combination of deep sequencing and Sanger sequencing approaches we have determined complete genome sequences of eight clinical isolates that were obtained from patient sera during an Oropouche fever outbreak in Amapa state, northern Brazil in 2009. We also report complete genome sequences of two OROV reassortants isolated from two marmosets in Minas Gerais state, southeast Brazil in 2012 that contain a novel M genome segment. Interestingly, all ten isolates posses a 947 nucleotide long S segment that lacks 11 residues in the S segment 3' UTR compared to the recently redetermined Brazilian prototype OROV strain BeAn19991. OROV maybe circulating more widely in Brazil and in the non-human primate population than previously appreciated and the identification of yet another reassortant highlights the importance of bunyavirus surveillance in South America

Erratum: Correction: A latitudinal phylogeographic diversity gradient in birds (PLoS biology (2017) 15 4 (e2001073))

[This corrects the article DOI: 10.1371/journal.pbio.2001073.]

Interferon-stimulated gene (ISG)-expression screening reveals the specific antibunyaviral activity of ISG20

Bunyaviruses pose a significant threat to human health, prosperity and food security. In response to viral infections, interferons (IFNs) upregulate the expression of hundreds of interferon stimulated genes (ISGs) whose cumulative action can potently inhibit the replication of bunyaviruses. We used a flow cytometry-based method to screen the ability of ∼500 unique ISGs from humans and rhesus macaques to inhibit the replication of Bunyamwera orthobunyavirus (BUNV), the prototype of both the Peribunyaviridae family and Bunyavirales order. Candidates possessing antibunyaviral activity were further examined using a panel of divergent bunyaviruses. Interestingly, one candidate, ISG20, exhibited potent antibunyaviral activity against most viruses examined from the Peribunyaviridae, Hantaviridae and Nairoviridae families, whereas phleboviruses (Phenuiviridae) largely escaped inhibition. Similar to other viruses known to be targeted by ISG20, the antibunyaviral activity of ISG20 is dependent upon its functional ribonuclease activity. Through use of an infectious VLP assay (based on the BUNV minigenome system), we confirmed that gene expression from all 3 viral segments is strongly inhibited by ISG20. Using in vitro evolution, we generated a substantially ISG20-resistant BUNV and mapped the determinants of ISG20 sensitivity/resistance. Taken together, we report that ISG20 is a broad and potent antibunyaviral factor yet some bunyaviruses are remarkably ISG20 resistant. Thus, ISG20 sensitivity/resistance could influence the pathogenesis of bunyaviruses, many of which are emerging viruses of clinical or veterinary significance

Positive association between population genetic differentiation and speciation rates in New World birds

An implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, but its significance as a rate-limiting control on phylogenetic speciation dynamics remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. By pairing population genetics datasets from173 NewWorld bird species (\u3e17,000 individuals) with phylogenetic estimates of speciation rate, we show that the population differentiation rates within species are positively correlated with their speciation rates over long timescales. Although population differentiation rate explains relatively little of the variation in speciation rate among lineages, the positive relationship between differentiation rate and speciation rate is robust to species-delimitation schemes and to alternative measures of both rates. Population differentiation occurs at least three times faster than speciation, which suggests that most populations are ephemeral. Speciation and population differentiation rates are more tightly linked in tropical species than in temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest that the processes responsible for population differentiation are tied to those that underlie broad-scale patterns of diversity