The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays

Background: Ribosomal 5S genes are well known for the critical role they play in ribosome folding and functionality. These genes are thought to evolve in a concerted fashion, with high rates of homogenization of gene copies. However, the majority of previous analyses regarding the evolutionary process of rDNA repeats were conducted in invertebrates and plants. Studies have also been conducted on vertebrates, but these analyses were usually restricted to the 18S, 5.8S and 28S rRNA genes. The recent identification of divergent 5S rRNA gene paralogs in the genomes of elasmobranches and teleost fishes indicate that the eukaryotic 5S rRNA gene family has a more complex genomic organization than previously thought. The availability of new sequence data from lower vertebrates such as teleosts and elasmobranches enables an enhanced evolutionary characterization of 5S rDNA among vertebrates.Results: We identified two variant classes of 5S rDNA sequences in the genomes of Potamotrygonidae stingrays, similar to the genomes of other vertebrates. One class of 5S rRNA genes was shared only by elasmobranches. A broad comparative survey among 100 vertebrate species suggests that the 5S rRNA gene variants in fishes originated from rounds of genome duplication. These variants were then maintained or eliminated by birth-and-death mechanisms, under intense purifying selection. Clustered multiple copies of 5S rDNA variants could have arisen due to unequal crossing over mechanisms. Simultaneously, the distinct genome clusters were independently homogenized, resulting in the maintenance of clusters of highly similar repeats through concerted evolution.Conclusions: We believe that 5S rDNA molecular evolution in fish genomes is driven by a mixed mechanism that integrates birth-and-death and concerted evolution

Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests

High-throughput sequencing (HTS) technologies have the potential to become one of the most significant advances in molecular diagnostics. Their use by researchers to detect and characterize plant pathogens and pests has been growing steadily for more than a decade and they are now envisioned as a routine diagnostic test to be deployed by plant pest diagnostics laboratories. Nevertheless, HTS technologies and downstream bioinformatics analysis of the generated datasets represent a complex process including many steps whose reliability must be ensured. The aim of the present guidelines is to provide recommendations for researchers and diagnosticians aiming to reliably use HTS technologies to detect plant pathogens and pests. These guidelines are generic and do not depend on the sequencing technology or platform. They cover all the adoption processes of HTS technologies from test selection to test validation as well as their routine implementation. A special emphasis is given to key elements to be considered: undertaking a risk analysis, designing sample panels for validation, using proper controls, evaluating performance criteria, confirming and interpreting results. These guidelines cover any HTS test used for the detection and identification of any plant pest (viroid, virus, bacteria, phytoplasma, fungi and fungus-like protists, nematodes, arthropods, plants) from any type of matrix. Overall, their adoption by diagnosticians and researchers should greatly improve the reliability of pathogens and pest diagnostics and foster the use of HTS technologies in plant health

A comprehensive accretion model for glaciated icing conditions

International audienceIcing has been identified as a major hazard for aviation safety since the beginning of aeronautical engineering. This paper is focused on ice crystal icing (ICI) which is related to ice accretion for an aircraft in flight in the presence of ice particles. Liquid water is necessary for the ice crystals to stick to the walls of the internal components of an aircraft engine. Emphasis is put on the glaciated conditions where the required liquid water comes from the melting of the ice crystals themselves when they enter a warm environment (the engine core). ICI represents an important concern for flight safety in addition to classical supercooled water icing where the accreted ice only derives from the instantaneous freezing of supercooled liquid droplets when they hit an obstacle. A semi-empirical model which accounts for the influence of the ice crystals on the mass and momentum balance equations is proposed. It accounts for the liquid transport in the porous ice layer and for the ice crystal sticking efficiency. The physics is extremely complicated and not completely understood. Therefore, several adjustable parameters are used in the model. However, the model predictions agree well with the existing experimental data. In particular, the model is able to predict typical conical accretion shapes that are never found in classical supercooled water icing conditions. Moreover, the influence of the ice crystal melting ratio on the accretion shapes is properly accounted for

Revisited Model for Supercooled Large Droplet Impact onto a Solid Surface

International audienceA rationally based methodology is proposed to derive a new mass loss empirical model for supercooled large droplets. The numerical results from the ONERA two-dimensional trajectory solver and the experimental results from the NASA Papadakis supercooled large droplet database are combined to get both the impinging and the deposited mass flow rates at each point of the test model. These data are used to derive a new model for the collection efficiency. It allows clearly separating the influence of the kinetic energy, which is the dominating effect close to the leading edge, from the influence of the angle of incidence, which is the most influent parameter close to the impingement limits. Moreover, the model can be used for both supercooled large droplets and small droplets

Experimental and numerical investigations on aircraft icing at mixed phase conditions

International audienceSince the beginning of civil aviation, icing is a severe weather hazard for aircraft operation. In this context, the phenomenon of ice crystal icing has been identified as a risk for flight safety in the recent past. Ice crystals can accrete on warm components such as heated stagnation pressure probes and engine compressor blades. Liquid melt water or additional liquid droplets in the icing cloud enable the ice particles to stick to the component surface and to form a cohesive ice accretion layer. In this paper, we present results of comprehensive icing wind tunnel tests on ice crystal ice accretion together with results of complementary simulations by means of the ONERA icing code IGLOO2D. The experiments show a strong influence of ambient temperature on the icing process. In agreement with literature findings, ice particle sticking ability can be correlated with the ice cloud composition. Correlations between accretion shape and growth rate have been identified. IGLOO2D separates accretion abrasion by particle impact from the efficiency with which those particles stick to the deposit. Comparisons of computational and experimental results indicate that this sticking efficiency has the greatest effect on ice shapes at low Mach numbers, at least for the particle sizes and conditions used in the experiments. The experimental and numerical findings of this study can be considered as complementary to existing knowledge on ice crystal icing. Therefore, the experimental results are provided to an international benchmark of test cases for icing code validation

An implicit time marching Galerkin method for the simulation of icing phenomena with a triple layer model

International audienceIn the context of more electrical aircraft and reduction of fuel consumption, aircraft manufacturers are moving towards more complex and transient ice protection systems. The operating of these systems involves several unsteady heat and mass transfer phenomena. Modelling and numerical simulation play an important role in the investigation of these unsteady phenomena. In this paper, a model for unsteady ice build-up and melting is presented. The model is based on a triple layer assumption. In addition, a tailored numerical methodology for solving the governing partial differential equations is also described. It is based on a Galerkin finite element method and a Gauss-Seidel like implicit time marching scheme. The global method is validated and its capabilities are demonstrated on several cases

Direct numerical simulation of a freely decaying turbulent interfacial flow

International audienceWhereas Large Eddy Simulation (LES) of single-phase flows is already widely used in the CFD world, even for industrial applications, LES of two-phase interfacial flows, i.e. two-phase flows where an interface separates liquid and gas phases, still remains a challenging task. The main issue is the development of subgrid scale models well suited for two-phase interfacial flows. The aim of this work is to generate a detailed data base from direct numerical simulation (DNS) of two-phase interfacial flows in order to clearly understand interactions between small turbulent scales and the interface separating the two phases. This work is a first contribution in the study of the interface/turbulence interaction in the configuration where the interface is widely deformed and where both phases are resolved by DNS. To do this, the interaction between an initially plane interface and a freely decaying homogeneous isotropic turbulence (HIT) is studied. The densities and viscosities are the same for both phases in order to focus on the effect of the surface tension coefficient. Comparisons with existing theories built on wall-bounded or free-surface turbulence are carried out. To understand energy transfers between the interfacial energy and the turbulent one, PDFs of the droplet sizes distribution are calculated. An energy budget is carried out and turbulent statistics are performed including the distance to the interface as a parameter. A spectral analysis is achieved to highlight the energy transfer between turbulent scales of different sizes. The originality of this work is the study of the interface/turbulence interactions in the case of a widely deformed interface evolving in a turbulent flow

Eulerian and lagrangian ice-crystal trajectory simulations in a generic turbofan compressor

This study provides a comparison between an Eulerian and a Lagrangian approach for simulation of ice-crystal trajectories and impact in a generic turbofan compressor. The enginelike geometry consists of a one-and-a-half stage (stator-rotor-stator) compressor, in which the computed airflow is steady and inviscid. Both methods apply the same models to evaluate ice-crystal dynamics, mass and heat transfer, and phase change along ice-crystal trajectories. The impingement of the crystals on the blade surfaces is modeled assuming full deposition for comparison and validation purposes. Moreover, the effect of ice-crystal diameter and sphericity variations on impinging mass flux and particle melting ratio is briefly assessed. Then, a more realistic wall interaction model predicts rebound, shattering, or deposition as a function of impact parameters that is applied. When the full deposition model is activated, an excellent agreement is observed between the Eulerian and Lagrangian approaches for the impinging mass-flux profiles on each blade, while moderate differences appear for the melting curves. However, significant differences appear between both approaches when using the more realistic wall interaction model. The analysis of these results highlights the classic limitations of standard Eulerian and Lagrangian methods for this type of applications