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Search Results: 1 - 10 of 6110 matches for " Stéphane Cruveiller "
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Horizontal gene transfer may explain variation in θs
Rohan Maddamsetti,Philip J. Hatcher,Stéphane Cruveiller,Claudine Médigue,Jeffrey E. Barrick,Richard E. Lenski
Quantitative Biology , 2012,
Abstract: Martincorena et al. estimated synonymous diversity ({\theta}s = 2N{\mu}) across 2,930 orthologous gene alignments from 34 Escherichia coli genomes, and found substantial variation among genes in the density of synonymous polymorphisms. They argue that this pattern reflects variation in the mutation rate per nucleotide ({\mu}) among genes. However, the effective population size (N) is not necessarily constant across the genome. In particular, different genes may have different histories of horizontal gene transfer (HGT), whereas Martincorena et al. used a model with random recombination to calculate {\theta}s. They did filter alignments in an effort to minimize the effects of HGT, but we doubt that any procedure can completely eliminate HGT among closely related genomes, such as E. coli living in the complex gut community. Here we show that there is no significant variation among genes in rates of synonymous substitutions in a long-term evolution experiment with E. coli and that the per-gene rates are not correlated with {\theta}s estimates from genome comparisons. However, there is a significant association between {\theta}s and HGT events. Together, these findings imply that {\theta}s variation reflects different histories of HGT, not local optimization of mutation rates to reduce the risk of deleterious mutations as proposed by Martincorena et al.
Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer
Philippe Remigi,Delphine Capela,Camille Clerissi,Léna Tasse,Rachel Torchet,Olivier Bouchez,Jacques Batut,Stéphane Cruveiller,Eduardo P. C. Rocha,Catherine Masson-Boivin
PLOS Biology , 2014, DOI: 10.1371/journal.pbio.1001942
Abstract: Horizontal gene transfer (HGT) is an important mode of adaptation and diversification of prokaryotes and eukaryotes and a major event underlying the emergence of bacterial pathogens and mutualists. Yet it remains unclear how complex phenotypic traits such as the ability to fix nitrogen with legumes have successfully spread over large phylogenetic distances. Here we show, using experimental evolution coupled with whole genome sequencing, that co-transfer of imuABC error-prone DNA polymerase genes with key symbiotic genes accelerates the evolution of a soil bacterium into a legume symbiont. Following introduction of the symbiotic plasmid of Cupriavidus taiwanensis, the Mimosa symbiont, into pathogenic Ralstonia solanacearum we challenged transconjugants to become Mimosa symbionts through serial plant-bacteria co-cultures. We demonstrate that a mutagenesis imuABC cassette encoded on the C. taiwanensis symbiotic plasmid triggered a transient hypermutability stage in R. solanacearum transconjugants that occurred before the cells entered the plant. The generated burst in genetic diversity accelerated symbiotic adaptation of the recipient genome under plant selection pressure, presumably by improving the exploration of the fitness landscape. Finally, we show that plasmid imuABC cassettes are over-represented in rhizobial lineages harboring symbiotic plasmids. Our findings shed light on a mechanism that may have facilitated the dissemination of symbiotic competency among α- and β-proteobacteria in natura and provide evidence for the positive role of environment-induced mutagenesis in the acquisition of a complex lifestyle trait. We speculate that co-transfer of complex phenotypic traits with mutagenesis determinants might frequently enhance the ecological success of HGT.
Experimental Evolution of a Plant Pathogen into a Legume Symbiont
Marta Marchetti,Delphine Capela,Michelle Glew,Stéphane Cruveiller,Béatrice Chane-Woon-Ming,Carine Gris,Ton Timmers,Véréna Poinsot,Luz B. Gilbert,Philipp Heeb,Claudine Médigue,Jacques Batut,Catherine Masson-Boivin
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1000280
Abstract: Rhizobia are phylogenetically disparate α- and β-proteobacteria that have achieved the environmentally essential function of fixing atmospheric nitrogen in symbiosis with legumes. Ample evidence indicates that horizontal transfer of symbiotic plasmids/islands has played a crucial role in rhizobia evolution. However, adaptive mechanisms that allow the recipient genomes to express symbiotic traits are unknown. Here, we report on the experimental evolution of a pathogenic Ralstonia solanacearum chimera carrying the symbiotic plasmid of the rhizobium Cupriavidus taiwanensis into Mimosa nodulating and infecting symbionts. Two types of adaptive mutations in the hrpG-controlled virulence pathway of R. solanacearum were identified that are crucial for the transition from pathogenicity towards mutualism. Inactivation of the hrcV structural gene of the type III secretion system allowed nodulation and early infection to take place, whereas inactivation of the master virulence regulator hrpG allowed intracellular infection of nodule cells. Our findings predict that natural selection of adaptive changes in the legume environment following horizontal transfer has been a major driving force in rhizobia evolution and diversification and show the potential of experimental evolution to decipher the mechanisms leading to symbiosis.
Pricing and Hedging in Stochastic Volatility Regime Switching Models  [PDF]
Stéphane Goutte
Journal of Mathematical Finance (JMF) , 2013, DOI: 10.4236/jmf.2013.31006
Abstract:

We consider general regime switching stochastic volatility models where both the asset and the volatility dynamics depend on the values of a Markov jump process. Due to the stochastic volatility and the Markov regime switching, this financial market is thus incomplete and perfect pricing and hedging of options are not possible. Thus, we are interested in finding formulae to solve the problem of pricing and hedging options in this framework. For this, we use the local risk minimization approach to obtain pricing and hedging formulae based on solving a system of partial differential equations. Then we get also formulae to price volatility and variance swap options on these general regime switching stochastic volatility models.

 

Analysis of Relationships between Port Activity and Other Sectors of the Economy: Evidence from Cote d’Ivoire  [PDF]
Nomel Paul Stéphane Essoh
American Journal of Industrial and Business Management (AJIBM) , 2013, DOI: 10.4236/ajibm.2013.33042
Abstract:

This research paper aims to study the correlation between the port activity and the activity of the different services sectors. By comparing trends between them and analyzing the causality relationships between the port traffic and the other economic sectors, our study tends to present how the activity of the port of Abidjan could have a decisive effect on the local economy. To meet our objectives, correlation analysis and statistical test tools Eviews and other techniques have been run with data provided by local agencies and port authority. By doing so, our research study finds that there is existing correlation between port activity and activity generated by the other services sectors and its contribution can accelerate the economic growth.

Cote d’Ivoire’s Commodities Export and Shipping: Challenges for Port Traffic and Regional Market Size  [PDF]
Nomel P. Stéphane Essoh
American Journal of Industrial and Business Management (AJIBM) , 2014, DOI: 10.4236/ajibm.2014.45031
Abstract:

The global integration with the growth of the world population generated a constant need of goods where trade took place with both inputs and ready-made products. Although this global need has led to a diversification of exports of goods, it still requires special commodities from tropical Africa and trade partners in West Africa that may supply more their specialized products which can be moved in cargo between destinations. This paper identifies especially Cote d’Ivoire’s commodities export and shipping market structure with its main agricultural products which makes him the world’s dominant producer and exporter of cocoa beans. It develops the importance of export crops structure for local economy driven by the international demand for cocoa beans. And it finally could indicate in our future study whether the possibility of pricing power and export taxes affecting the shipping market has a decisive impact on the port traffic and accelerates growth.

Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles
David Vallenet, Patrice Nordmann, Valérie Barbe, Laurent Poirel, Sophie Mangenot, Elodie Bataille, Carole Dossat, Shahinaz Gas, Annett Kreimeyer, Patricia Lenoble, Sophie Oztas, Julie Poulain, Béatrice Segurens, Catherine Robert, Chantal Abergel, Jean-Michel Claverie, Didier Raoult, Claudine Médigue, Jean Weissenbach, Stéphane Cruveiller
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0001805
Abstract: Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.
Experimental Evolution of a Plant Pathogen into a Legume Symbiont
Marta Marchetti equal contributor,Delphine Capela equal contributor,Michelle Glew equal contributor,Stéphane Cruveiller,Béatrice Chane-Woon-Ming,Carine Gris,Ton Timmers,Véréna Poinsot,Luz B. Gilbert,Philipp Heeb,Claudine Médigue,Jacques Batut,Catherine Masson-Boivin
PLOS Biology , 2010, DOI: 10.1371/journal.pbio.1000280
Abstract: Rhizobia are phylogenetically disparate α- and β-proteobacteria that have achieved the environmentally essential function of fixing atmospheric nitrogen in symbiosis with legumes. Ample evidence indicates that horizontal transfer of symbiotic plasmids/islands has played a crucial role in rhizobia evolution. However, adaptive mechanisms that allow the recipient genomes to express symbiotic traits are unknown. Here, we report on the experimental evolution of a pathogenic Ralstonia solanacearum chimera carrying the symbiotic plasmid of the rhizobium Cupriavidus taiwanensis into Mimosa nodulating and infecting symbionts. Two types of adaptive mutations in the hrpG-controlled virulence pathway of R. solanacearum were identified that are crucial for the transition from pathogenicity towards mutualism. Inactivation of the hrcV structural gene of the type III secretion system allowed nodulation and early infection to take place, whereas inactivation of the master virulence regulator hrpG allowed intracellular infection of nodule cells. Our findings predict that natural selection of adaptive changes in the legume environment following horizontal transfer has been a major driving force in rhizobia evolution and diversification and show the potential of experimental evolution to decipher the mechanisms leading to symbiosis.
An Aspect-Oriented Approach for Use Case Based Modeling of Software Product Lines  [PDF]
Stéphane S. SOMé, Pauline ANTHONYSAMY
Journal of Software Engineering and Applications (JSEA) , 2009, DOI: 10.4236/jsea.2009.24032
Abstract: Software Product Line Development advocates software reuse by modeling common and variable artefacts separately across members of a family of products. Aspect-Oriented Software Development aims at separation of concerns with “aspects” to increase modularity, reusability, maintainability and ease of evolution. In this paper, we apply an as-pect-oriented use case modeling approach to product line system modeling. A use case specification captures stake-holders concerns as interactions between a system and its actors. We adapt our previous work with the introduction of a “variability” relationship for the expression of variabilities. This relationship is used to model variable and common behaviours across a family of products as use cases. A variability composition mechanism enables building of executa-ble behaviour models for each member of a product line family by integrating common elements with the applicable variable elements.
Three Patterns of Motion Which Change the Perception of Emotional Faces  [PDF]
Alhadi Chafi, Loris Schiaratura, Stéphane Rusinek
Psychology (PSYCH) , 2012, DOI: 10.4236/psych.2012.31014
Abstract: The aim of the study was to focus on the relationship between motion and emotion. Relying on studies in Behavioral Neurology and Social Psychology, it is believed motion is one of the core components of Emotion. The study uses basic emotional faces (i.e., Happy, Surprised, Fearful, Sad, Disgusted and Angry) which are presented displaying patterns of motion (i.e., a Parabolic motion, a Translational motion and a Wave-like motion). Hypotheses are that the wave-like motion will increase perceived intensities and arou- sal related to positive emotional faces (i.e., Happy and Surprised), and simplify their recognition. Otherwise, the parabolic motion is hypothesized to increase perceived intensities and arousal related to negative emotional faces (i.e., Angry, Disgusted, Fearful and Sad), while enhancing their recognition. Results sho- wed that “Happy” is the most recognized face and “Fearful” is the least recognized one. Concerning Perceived Intensity, an Emotional Face main effect and an Interaction Motion Pattern × Emotional Face were obtained. Finally, the Arousal dimension yielded two main effects, one for the Emotional Face and one for the Motion Pattern. On one hand, results we found are very promising in understanding the part played by motion in Arousal. On the other hand, further research still has to be done so as to question the exact effects of the Translational, Parabolic and Wave-like motion patterns, especially in more dynamic contexts.
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