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A polyphasic study of Xanthomonas hortorum in the genomic era : ocus on X. hortorum pv. vitians, the causal agent of the bacterial leaf spot of lettuce
No full textLe genre Xanthomonas représente un réservoir majeur d’espèces bactériennes phytopathogènes. Parmi celles-ci, les différents pathovars de X. hortorum s’attaquent à une grande variété d’espèces végétales phylogénétiquement distantes. La bactériose foliaire de la laitue, causée par X. hortorum pv. vitians, est l’une des de ces pathologies dont les conséquences pour les cultures sont les plus importantes à l’échelle mondiale. Toutefois, les questions liées à l’étiologie de cette maladie infectieuse végétale nécessitaient une étude approfondie pour être élucidées. De plus, les aspects moléculaires et génétiques de l’interaction hôte-pathogène et de l’adaptation environnementale n’avaient jamais été investigués. À travers une approche mixte alliant les principes de la taxonomie polyphasique et le criblage par Tn-seq des gènes contribuant à la valeur sélective de X. hortorum pv. vitians en conditions in vitro et in planta, cette étude entend répondre à ces problématiques en se reposant sur les dernières évolutions dans le champ de la génomique. La taxonomie de X. hortorum a tout d’abord été remaniée en proposant sa combinaison avec X. cynarae. Ensuite, le génome essentiel de X. hortorum pv. vitians a été caractérisé et distingué entre gènes conservés et gènes accessoires « égoïstes » acquis par transferts horizontaux. Enfin, les gènes et fonctions importants pour la valeur sélective du pathogène lors des phases successives épiphytes et endophytes de l’interaction avec la laitue ont été identifiés. Ces travaux révèlent la complexité insoupçonnée de l’espèce X. hortorum et éclairent les bases génétiques de la plasticité écologique de X. hortorum pv. vitians.The genus Xanthomonas constitutes a major reservoir of phytopathogenic bacterial species. Among them, the pathovars of X. hortorum attacks a wide variety of phylogenetically distant botanical species. The bacterial leaf spot of lettuce caused by X. hortorum pv. vitians is one of the most destructive of these diseases at a worldwide scale. However, substantial interrogations remain regarding the etiology of this disease. Moreover, the molecular and genetic determinants sustaining the host-pathogen interaction and the environmental adaptation have never been investigated. Through a mixed approach combining the principles of polyphasic taxonomy and the genome-wide Tn-seq screening of genes contributing to the fitness of X. hortorum pv. vitians in in vitro and in planta conditions, this study aims at solving these issues using the latest developments in the field of genomics. First, investigations on the taxonomy of this phytopathogenic bacteria led to reconsider the genomic diversity existing within the species and to propose the combination of X. hortorum and X. cynarae. Then, the essential genome of X. hortorum pv. vitians was characterized and essential genes were discriminated between core and “selfish” accessory ones, the latter being acquired through horizontal gene transfer events. At last, a comprehensive overview of the genes and functions required for the fitness of X. hortorum pv. vitians during the successive epiphytic and endophytic phases of the lettuce infection was provided. This work reveals the unsuspected complexity of the X. hortorum species and enlighten the genetic bases of the ecological plasticity of X. hortorum pv. vitians
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Recombination and base composition evolution : experimental evidence of GC-biased gene conversion in Bacteria
No full textLa composition en base des génomes varie très fortement entre espèce bactériennes, avec une gamme de taux de G+C génomique s'étalant de 13% jusqu’à 75%. Ce phénomène est connu depuis plus de 50 ans, mais sa signification biologique reste fortement débattue. Des expériences d'accumulation de mutations ont permis de démontrer que ces variations de G+C sont principalement dues à des différences de patron mutationnel.Cependant, ces expériences ont également montré que la grande majorité des génomes ont un taux de G+C supérieur à celui attendu à l'équilibre mutationnel. Deux forces évolutives peuvent expliquer cet écart: la sélection naturelle et la conversion génique biaisée vers GC (gBGC) – processus non-adaptatif lié à des biais de réparation des mésappariements au cours de la recombinaison homologue.Le phénomène de gBGC a été bien caractérisé chez plusieurs eucaryotes, et plusieurs indices suggèrent qu'il pourrait également affecter des bactéries. Mon travail de thèse a été consacré à déterminer empiriquement si la recombinaison homologue provoque de la gBGC chez des bactéries. Pour cela nous avons réalisé des expériences de transformation chez *Acinetobacter baylyi* et *Bacillus subtilis* puis analysé les produits de recombinaison. Le séquençage des génomes de clones transformants a permis de quantifier les fréquences de conversion parmi 2023 régions recombinantes chez *A. baylyi*, et 549 régions recombinantes chez *B. subtilis*. Nous avons également ré-analysé les données issues d'expériences similaires publiées pour deux autres espèces : *Helicobacter pylori*, *Streptococcus pneumoniae*. Dans trois des quatre espèces analysées, nous avons observé un biais de réparation en faveur des bases GC, ce qui constitue une preuve directe de l'existence de la gBGC chez ces bactéries. L'intensité du biais que nous avons mesuré est compatible avec celui nécessaire pour expliquer l'écart entre la composition en base observée et celle attendue à l'équilibre mutationnel. Nos observations démontrent que ce processus non-adaptatif peut affecter fortement l'évolution des génomes de bactéries, qui, en raison des grandes tailles de population supposées, sont souvent perçus comme déterminés quasi-exclusivement par la sélection naturelle. De façon intéressante, nous avons constaté que la gBGC se manifeste différemment selon les contextes génomiques et selon les espèces : chez *A. baylyi*, nous avons observé un fort gBGC spécifiquement dans les tracts de conversion impliquant un seul SNP --- ce qui suggère un rôle possible de la machinerie BER (Base Excision Repair), comme cela a également été proposé chez les mammifères. A l'inverse, chez *H. pylori*, et *S. pneumoniae*, la gBGC se manifeste uniquement aux extrémités de longs tracts de conversion --- tout comme cela a été décrit chez la Levure. Cela suggère que différents mécanismes moléculaires sont à l'origine de la gBGC observée dans différentes lignées. Cette évolution convergente soulève la question des contraintes sélectives susceptibles de gouverner l'évolution de la gBGC. Ce manuscrit sera consacré à la description de la question des origines de la variabilité en composition en base connue, à la question de la recombinaison chez les procaryotes, et à la façon dont les deux processus conjoints permettent d'apporter du poids à l'hypothèse de la conversion génique biaisée.Genomic base composition is widely variable among Bacteria, with a genomic G and C content ranging from 13% to 75%. This observation has been acknowledged for more than fifty years, yet its biological significance remains quite debated. Mutation accumulation experiments have shown these variations mainly to be due to differences in mutational patterns. However, these experiments have also clearly shown that the great majority of genomes have a higher GC content than expected under the sole action of mutations. Two evolutionary forces can explain this departure: natural selection acting on the base composition, or GC-biased gene conversion (gBGC), a non-adaptative process linked to the repair of mismatch occurring during homologous recombination. This phenomenon of gBGC has been well described in Eukaryotes, and much evidence suggests that it could also affect Bacteria. My Ph.D. project has been focused on the experimental determination of whether homologous recombination leads to gBGC in Bacteria too. And so we performed genome-wide transformation experiments with *Acinetobacter baylyi* and *Bacillus subtilis* and analyzed recombination products. Whole-genome sequencing of transformant clones leads us to quantify conversion frequencies among 2023 conversion tracts in *A. baylyi*, and *549* conversion tracts in *B. subtilis*. We also re-analyzed data coming from similar published experiments performed in *Helicobacter pylori* and *Streptococcus pneumoniae*. In three of the four analyzed species, we detected a significant conversion bias in favor of G and C bases, which constitutes a direct proof of the existence of gBGC in Bacteria. The measured bias intensity stands within a range that could explain the gap between observed base composition and base composition expected at mutational equilibrium. Our observations demonstrate that this non-adaptive process can deeply affect the genome evolution of Bacteria, which, owing to the alleged large effective population size, are often perceived as being determined by the sole action of natural selection. Interestingly, we found that gBGC occurs differently with regards to genomic contexts and species: in *A. baylyi*, we found a strong gBGC specifically associated with short conversion tracts, which suggests it might be due to the BER machinery (Base Excision Repair), as it has been proposed in Mammals as well. On the other hand, in *H. pylori* and *S. pneumoniae*, gBGC occurs on long conversion tracts extremities --- as has been described for Yeast. This suggests that different molecular mechanisms are causing gBGC in different lineages. This convergent evolution raises the question of selective constraints that might govern the evolution of gBGC.This manuscript is focused on the description of the question of the origin of the variability in base composition, of recombination within Prokaryotes, and of how the two processes jointly might give weight to the GC-biased gene conversion hypothesis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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