Origin and Examination of a Leafhopper Facultative Endosymbiont

Eukaryotes engage in intimate interactions with microbes that range in age and type of association. Although many conspicuous examples of ancient insect associates are studied (e.g., Buchneraaphidicola), fewer examples of younger associations are known. Here, we further characterize a recently evolved bacterial endosymbiont of the leafhopper Euscelidius variegatus (Hemiptera, Cicadellidae), called BEV. We found that BEV, continuously maintained in E. variegatus hosts at UC Berkeley since 1984, is vertically transmitted with high fidelity. Unlike many vertically transmitted, ancient endosymbioses, the BEV–E. variegatus association is not obligate for either partner, and BEV can be cultivated axenically. Sufficient BEV colonies were grown and harvested to estimate its genome size and provide a partial survey of the genome sequence. The BEV chromosome is about 3.8 Mbp, and there is evidence for an extrachromosomal element roughly 53 kb in size (e.g., prophage or plasmid). We sequenced 438 kb of unique short-insert clones, representing about 12% of the BEV genome. Nearly half of the gene fragments were similar to mobile DNA, including 15 distinct types of insertion sequences (IS). Analyses revealed that BEV not only shares virulence genes with plant pathogens, but also is closely related to the plant pathogenic genera Dickeya, Pectobacterium, and Brenneria. However, the slightly reduced genome size, abundance of mobile DNA, fastidious growth in culture, and efficient vertical transmission suggest that symbiosis with E. variegatus has had a significant impact on genome evolution in BEV

A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

<p>Abstract</p> <p>Background</p> <p>The 99% of bacteria in the environment that are recalcitrant to culturing have spurred the development of metagenomics, a culture-independent approach to sample and characterize microbial genomes. Massive datasets of metagenomic sequences have been accumulated, but analysis of these sequences has focused primarily on the descriptive comparison of the relative abundance of proteins that belong to specific functional categories. More robust statistical methods are needed to make inferences from metagenomic data. In this study, we developed and applied a suite of tools to describe and compare the richness, membership, and structure of microbial communities using peptide fragment sequences extracted from metagenomic sequence data.</p> <p>Results</p> <p>Application of these tools to acid mine drainage, soil, and whale fall metagenomic sequence collections revealed groups of peptide fragments with a relatively high abundance and no known function. When combined with analysis of 16S rRNA gene fragments from the same communities these tools enabled us to demonstrate that although there was no overlap in the types of 16S rRNA gene sequence observed, there was a core collection of operational protein families that was shared among the three environments.</p> <p>Conclusion</p> <p>The results of comparisons between the three habitats were surprising considering the relatively low overlap of membership and the distinctively different characteristics of the three habitats. These tools will facilitate the use of metagenomics to pursue statistically sound genome-based ecological analyses.</p

A Benchmark of Parametric Methods for Horizontal Transfers Detection

Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different methods applied to the same genomes were published. The use of artificial genomes in which all HGT parameters are controlled allows testing different methods in the same conditions. The results of this benchmark concerning 16 representative parametric methods showed a great variety of efficiencies. Some methods work very poorly whatever the type of HGTs and some depend on the conditions or on the metrics used. The best methods in terms of total errors were those using tetranucleotides as criterion for the window methods or those using codon usage for gene based methods and the Kullback-Leibler divergence metric. Window methods are very sensitive but less specific and detect badly lone isolated gene. On the other hand gene based methods are often very specific but lack of sensitivity. We propose using two methods in combination to get the best of each category, a gene based one for specificity and a window based one for sensitivity

Sequence-Based Prediction of Type III Secreted Proteins

The type III secretion system (TTSS) is a key mechanism for host cell interaction used by a variety of bacterial pathogens and symbionts of plants and animals including humans. The TTSS represents a molecular syringe with which the bacteria deliver effector proteins directly into the host cell cytosol. Despite the importance of the TTSS for bacterial pathogenesis, recognition and targeting of type III secreted proteins has up until now been poorly understood. Several hypotheses are discussed, including an mRNA-based signal, a chaperon-mediated process, or an N-terminal signal peptide. In this study, we systematically analyzed the amino acid composition and secondary structure of N-termini of 100 experimentally verified effector proteins. Based on this, we developed a machine-learning approach for the prediction of TTSS effector proteins, taking into account N-terminal sequence features such as frequencies of amino acids, short peptides, or residues with certain physico-chemical properties. The resulting computational model revealed a strong type III secretion signal in the N-terminus that can be used to detect effectors with sensitivity of ∼71% and selectivity of ∼85%. This signal seems to be taxonomically universal and conserved among animal pathogens and plant symbionts, since we could successfully detect effector proteins if the respective group was excluded from training. The application of our prediction approach to 739 complete bacterial and archaeal genome sequences resulted in the identification of between 0% and 12% putative TTSS effector proteins. Comparison of effector proteins with orthologs that are not secreted by the TTSS showed no clear pattern of signal acquisition by fusion, suggesting convergent evolutionary processes shaping the type III secretion signal. The newly developed program EffectiveT3 (http://www.chlamydiaedb.org) is the first universal in silico prediction program for the identification of novel TTSS effectors. Our findings will facilitate further studies on and improve our understanding of type III secretion and its role in pathogen–host interactions

Etude de l'interface sol-structure dans les milieux granulaires à l'aide d'un nouvel appareil de cisaillement annulaire

Many civil engineering problems involve interaction between soil and structural elements. The load transfer takes place in a very thin zone of soil, called interface. A new apparatus, the ring simple shear apparatus, has been developed in order to investigate the behaviour of interface between a granular material and a steel structural element. In a first time, a detailed description of this new apparatus is presented. The principle of the test with the ring simple shear apparatus consists to shear the intern part of a ring soil sample by a steel cylinder in rotation. The end effects are reduced and the loss of material is nil. Normal stresses are directly measured at the interface with specifically designed cells. Then, monotonous test are described, performed with Hostun RF sand and Hostun 14-10 gravel samples. A synthesis underlines the main factors which affect the interface behaviour : initial radial external pressure, limit conditions, density of the sample and roughness of the structural element. A visualisation of the grain motion inside the interface has been performed with three studies : direct visualisation during test with 14-10 gravel, realisation of test with Schneebeli roll sample, with an adapted configuration of the apparatus and numerical simulation with a distinct element code, called LMGC. This approach, at a microscopic level, shows the fundamental role of the media micro structure in the formation of the interface, where grains undergo large displacements and rotation. At this end of this work, a synthesis of first cyclic tests is presented. The major part of the amplitude of shearing is analysed.De nombreux ouvrages de génie civil nécessitent une bonne connaissance du mode de transmission des efforts de la structure vers le sol. Ce transfert se fait à travers une fine couche de sol, appelée interface. Un nouvel appareil, l'appareil de cisaillement simple annulaire a été développé pour analyser le comportement d'interface entre un matériau granulaire et un élément de structure en acier. Dans un premier temps, nous proposons une description détaillée de ce nouvel appareil. Le principe de l'essai à l'appareil de cisaillement simple annulaire consiste à cisailler la partie interne d'un échantillon de sol annulaire par un cylindre métallique en rotation. Les effets de bord sont très réduits et la perte de matériau est nulle. Des capteurs de contrainte totale ont été développés pour permettre une mesure locale de la contrainte radiale au sein de l'interface. Ensuite, des essais sous sollicitation monotone sont présentés, réalisés sur des échantillons de sable d'Hostun RF et de gravier d'Hostun 14~10. Une synthèse met en évidence l'influence des différents paramètres contrôlant le comportement de l'interface : la pression radiale initiale de confinement, les conditions aux limites, l'état de compacité de l'échantillon et la rugosité de l'élément de structure. La visualisation du mouvement des grains au sein de la couche d'interface a été menée à partir des trois études : visualisation directe au cours d'essais sur le gravier 14-10, réalisation d'essais sur des rouleaux de Schneeball, avec une configuration adaptée de l'appareil et simulation numérique par éléments distincts avec le logiciel L.M.G.C. Cette approche, au niveau microscopique, met en exergue le rôle fondamental de la microstructure du milieu, dans la formation de la couche d'interface où les grains subissent de grands déplacements tangentiels et de fortes rotations. A la fin de ce mémoire est présentée une synthèse des premiers essais réalisés sous sollicitation cyclique. Le rôle primordial de l'amplitude de cisaillement a été mis en évidence

Plan de préparation à une pandémie mondiale dans les animaleries de laboratoire : l’exemple du Covid-19

Coping ethically with drastic changes such as those occurring in times of pandemics is a very difficult challenge for animal facilities and researchers using animals for scientific purposes. It is quite impossible in fact to deal with such situations without a dedicated contingency plan. Any disaster plan will not do because, fortunately, pandemics are rare events and, as such, they are not included in all plans. We present here different avenues to cope with the drastic changes that may occur in the case on a pandemic, focusing on each and every action to optimize the minimal conservation of models and, at the same time, for ensuring continuous high standards of animal welfare. The proposed approach is a graduated one, considering research, researchers, animal caretakers, supply chain and logistics.Faire face de façon éthique aux changements drastiques tels que ceux imposés par une pandémie est un défi très complexe pour les animaleries et les chercheurs utilisant des animaux à des fins scientifiques. Il est en effet tout à fait impossible de faire face à de telles situations sans un plan d’urgence spécifique. Un plan générique de gestion des catastrophes ne peut pas suffire car, heureusement, les pandémies sont des événements rares et, à ce titre, elles ne sont généralement pas prévues dans ces plans. Nous présentons ici différents outils pour faire face aux changements drastiques qui peuvent survenir dans le cas d’une pandémie, en nous concentrant sur l’optimisation de la conservation des modèles de recherche tout en garantissant des normes élevées et continues de bien-être animal. L’approche proposée est graduée, en tenant compte de la recherche, des chercheurs, des techniciens animaliers, de la chaîne d’approvisionnement et de la logistique.Gonin Patrick, Delis Philippe, Lerat Hervé. Plan de préparation à une pandémie mondiale dans les animaleries de laboratoire : l’exemple du Covid-19. In: Bulletin de l'Académie Vétérinaire de France tome 173, 2020. pp. 92-97

A Cylinder Shear Apparatus

International audienceStudies of the interface between soil and an element of structure are actively carried out, considering the importance of the behavior of such interfaces in civil engineering applications such as deep foundations, retaining structures, and soil reinforcement. In the past a wide variety of different testing devices have been used, such as the modified direct or simple shear apparatus, pull-out devices, and annular shear apparatuses. Here a new shear device, the cylinder shear apparatus, is presented that has been designed to enhance our shear testing possibilities. This new shear device allows, as ring shear devices, significant shear displacements with an improved homogeneity of the interface. It allows also the control of the normal confining stress, stress control in a direction parallel to the interface, and visualization of the interface kinematics. The cylinder shear apparatus gives also the possibility of performing tests with natural granular material and/or with Schneebeli's rollers, with dry, saturated, drained and undrained samples and continuous pore fluid pressure monitoring

Alize-Lcpc Airfield pavement, a new software for the rational design of airport pavement

Alize-Lcpc is the reference software for roads and motorways pavement design in France since more than thirty years. It is a rational method, based on the computation of the resilient stresses and strains in roadways by the classical multi-layer elastic linear model. The design is carried out by comparing these calculated values in all the layers, to the admissible stresses and/or strains values which are evaluated according to the fatigue characteristics of the materials (bounded materials) or their rutting behavior due to plasticization (untreated materials and soils), taking into account the cumulative traffic specified for the pavement. In France, the adaptation of the road design approach to airport pavement is now in progress, leading to the development of a specific version of Alize-Lcpc software dedicated to the design of both flexible and rigid airport pavements. This paper firstly sums up the basis of the French rational pavement approach. It describes the possibilities of the new software, which are illustrated by an example of thickness design for a flexible pavement

A complete workflow applied on an oil reservoir analogue to evaluate the ability of 4D seismics to anticipate the success of a chemical enhanced oil recovery process

In an Enhanced Oil Recovery (EOR) process, one of the main difficulties is to quickly evaluate if the injected chemical products actually improve oil recovery in the reservoir. The efficiency of the process can be monitored in the vicinity of wells, but it may take time to estimate it globally in the reservoir. The objective of this paper is to investigate the ability of 4D seismics to bridge this gap and to help predict the success or breakdown of a production strategy at reservoir scale. To that purpose, we consider a complete workflow for simulating realistic reservoir exploitation using chemical EOR and 4D seismic modeling. This workflow spans from geological description to seismic monitoring simulation and seismic attributes analysis, through geological and reservoir modeling. It is applied here on a realistic case study derived from an outcrop analog of turbiditic reservoirs, for which the efficiency of chemical EOR by polymer and surfactant injection is demonstrated. For this specific field monitoring application, the impact of both waterflooding and proposed EOR injection is visible on the computed seismics. However, EOR injection induces a more continuous water front that can be clearly visible on seismics. In this case, the EOR efficiency can thus be related to the continuity of the water front as seen on seismics. Nevertheless, in other cases, chemical EOR injections may have more moderate impacts, or the field properties may be less adapted to seismic monitoring. This points out the importance of the proposed workflow to check the relevance of seismic monitoring and to design the most adapted monitoring strategy. Numerous perspectives are proposed at the end of the paper. In particular, experts of the different disciplines involved in the proposed workflow can benefit from the availability of a complete set of well-controlled data of various types to test and improve their own tools. In contrast, the non-experts can easily and quickly benefit from “hands-on” experiments for understanding the involved phenomena. Furthermore, the proposed workflow can be directly applied to geological reservoirs all over the world

WASPS: Web-Assisted Symbolic Plasmid Synteny Server

International audienceMotivation: Comparative plasmid genome analyses require complex tools, the manipulation of large numbers of sequences and constitute a daunting task for the wet bench experimentalist. Dedicated plasmid databases are sparse, only comprise bacterial plasmids and provide exclusively access to sequence similarity searches. Results: We have developed Web-Assisted Symbolic Plasmid Synteny (WASPS), a web service granting protein and DNA sequence similarity searches against a database comprising all completely sequenced natural plasmids from bacterial , archaeal and eukaryal origin. This database pre-calculates orthologous protein clustering and enables WASPS to generate fully resolved plasmid synteny maps in real time using internal and user-provided DNA sequences. Availability and implementation: WASPS queries befit all current browsers such as Firefox, Edge or Safari while the best functionality is achieved with Chrome. Internet Explorer is not supported. WASPS is freely accessible at https:// archaea.i2bc.paris-saclay.fr/wasps/