1,720,967 research outputs found
Understanding the paleo-evolution of flowering plants for the challenges of modern agriculture
No full textLes plantes à fleurs, également connues sous le nom d'Angiospermes, ont évolué il y a plus de 300 millions d'années, se diversifiant et colonisant la plupart des habitats terrestres pour devenir les plantes prédominantes de notre écosystème actuel. La disponibilité de nombreuses bases de données publiques donnant accès à des génomes d'Angiospermes offre l'opportunité d'étudier les gènes et les fonctions biologiques qui ont façonné l'évolution de ces plantes jusqu'à nos jours. Dans ce contexte, l'objectif de ce projet de recherche est de comprendre les mécanismes sous-jacents à l'évolution des génomes de plantes à fleurs, notamment la polyploïdie (le doublement du contenu génomique) et ceci à différentes échelles : des chromosomes, des gènes et des séquences.Une analyse de génomique comparée portant sur 84 espèces offre un aperçu approfondi de l'évolution des plantes à fleurs modernes. En effet, cette approche a permis non seulement de révéler (1) la datation de l'émergence des principales familles botaniques et celle à l'origine des Angiospermes, mais également d'estimer la date des évènements de polyploïdisation qui ont jalonné l'évolution de ces espèces. Dans ce cadre évolutif, ont été mis en évidence (2) la nature et les fonctions biologiques des gènes à la base des plantes à fleurs et à la base des grandes familles botaniques, (3) les gènes conservés et leur évolution en termes de séquences nucléotides et d'acides aminés, (4) l'impact de la polyploïdie sur l'évolution des gènes et (5) les fonctions biologiques différenciant des traits d'histoire de vie acquis au cours de l'évolution. Notre analyse de génomique comparée nous a enfin permis (6) d'exploiter pour l'ensemble des espèces travaillées les gènes associés à des caractères d'intérêt agronomique clés connus chez quelques espèces : on parle de recherche translationnelle.D'un point de vue de la recherche cognitive, ces travaux de thèse, basés sur une génomique comparée impliquant 84 espèces d'Angiospermes, ont enrichi notre compréhension de l'évolution des génomes de plantes et les événements qui ont conduit à la diversité des plantes à fleurs contemporaines. D'un point de vue de la recherche finalisée, l'analyse de la conservation des gènes d'intérêt agronomique entre les espèces modèles et/ou pivots et les espèces d'intérêt agronomique offre une opportunité d'exploiter les connaissances acquises sur la fonction d'un gène chez une espèce pour l'ensemble des espèces où la conservation d'un tel gène est démontrée. Les résultats présentés dans ces travaux de thèse ouvrent de nouvelles perspectives tant pour la recherche fondamentale, en termes de compréhension de l'évolution des espèces, que pour la recherche appliquée, en vue de l'amélioration variétale des espèces d'intérêt agronomique à partir des connaissances disponibles chez les espèces modèles.Flowering plants, also known as Angiosperms, evolved over 300 million years ago, diversifying and colonizing most terrestrial habitats to become the predominant plants in our current ecosystem. The access to numerous public databases providing Angiosperm genomes offers an opportunity to study the genes and their associated biological functions that have shaped the evolution of these plants to the present day. In this context, the objective of this research project is to understand the mechanisms underlying the evolution of flowering plant genomes, in particular polyploidy (Whole Genome Duplication - WGD) and this at different scales: chromosomes, genes and sequences.A comparative genomic analysis of 84 species offers in-depth insights into the evolution of modern flowering plants. Indeed, this approach made it possible not only to reveal (1) the dating of the emergence of the main botanical families and that at the origin of the Angiosperms, but also to estimate the date of the polyploidization events which marked the evolution of these species. In this evolutionary context, (2) the nature and biological functions of the genes at the base of flowering plants and at the base of the major botanical families have been highlighted, (3) the conserved genes and their evolution in terms of sequences nucleotides and amino acids, (4) the impact of polyploidy on gene evolution and (5) the biological functions differentiating life history traits acquired during evolution. Our comparative genomic analysis has finally enabled us (6) to exploit, for all the species studied, the genes associated to key traits of agronomic interest known in a few species: this is the concept of translational research.From a fundamental research point of view, this thesis work, based on a comparative genomics investigation of 84 species of Angiosperms, has enriched our understanding of the evolution of plant genomes and the events that shaped the diversity of contemporary flowering plants. From an applied research point of view, the analysis of the genes of agronomic interest conserved between the model and/or pivot species and crop species offers an opportunity to exploit the knowledge acquired on the function of a gene in a species for all the species where the conservation of such a gene is demonstrated. The results presented in this thesis work open new perspectives both for fundamental research, in terms of understanding the evolution of species, and for applied research, to gain better insights in crops' improvement from knowledge gained in model species
Dataset for "Bacterial genome annotation" and "AMR gene detection" workflows
No full text<p>This dataset is associated with the workflows "Bacterial genome annotation" and "AMR gene detection in an assembled bacterial genome".</p>
Recurrences and consequences of polyploidy events on gene evolution in angiosperms: Comparative analysis of 80 genomes
No full textInternational audiencePolyploidy is the inherited condition of having more than two complete sets of chromosomes resulting from whole genome duplication. Polyploidization is quite common in the plant kingdom (~50% of current flowering plants are polyploid) and is associated with the origin of new species: it plays a fundamental role in plant evolution. Indeed, it is considered as a major factor of speciation, diversification and ecological adaptation of plants. But what are the genes and functions and more particularly the plant processes that are most impacted by polyploidy?The research project aims to understand the evolution and conservation of flowering plant genomes (angiosperms) by comparing the genomes of 80 species. A study of the genes conserved between these species has revealed a method for calibrating these angiosperms according to the age of their polyploidization events. In addition, this is supplemented by knowledge of the function of genes that have been conserved in single copy or multiple copy from comparative functional annotation analysis. Finally, we know that polyploidization makes it possible to gain genes, but we also know that when these species return to a diploid state during their evolution, genes are lost due to the diploidization of these genomes. A quantification of these genes is possible and knowing the function of these genes gained or lost after polyploidization will make it possible to learn more about the genomic mechanisms at the origin of the adaptive success of angiosperms over nearly 250 million years of evolution
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe 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
No full text“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
No full textWe 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
Dispelling the Myths Behind First-author Citation Counts
No full textWe 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
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