L’élément mariner Mos1 est un élément mobile de classe II, sans spécificité d’insertion évidente, hormis un dinucléotide TA dupliqué lors de l’insertion. Pourtant, des travaux antérieurs révèlent l’existence de deux sites préférentiels d’insertion : le gène bactérien cat, codant une chloramphénicol acétyl-transférase et le locus du rDNA chez Caenorhabditis elegans. Le premier objectif de ce travail a été d’évaluer l’attractivité du gène cat dans différents contextes plasmidiques et chromosomiques, par des tests in vitro et en bactéries. Le second objectif était de faire le point sur les sites d’insertions de l’élément Mos1 à partir des données disponibles in vitro et in vivo. Une analyse statistique a révélé que l’insertion de Mos1 était préférentiellement ciblée dans des TA regroupés en motifs TATA ou TAxTA, ou localisés dans des régions riches en AT. Pour finir, le gène cat a servi de modèle pour déterminer que, si la courbure et la flexibilité de l’ADN n’expliquaient pas l’attractivité des sites préférentiels, la sélection du site d’insertion de Mos1 était dépendante de l’hélicité de la cible et que l’intervention de facteurs protéiques codés par l’hôte n’est pas à exclure. / The mariner Mos1 element is a class-II transposable element with no obvious insertion specificity, without TA dinucléotide duplicated during transposition. However, two insertion hotspots were previously suspected: the bacterial cat gene, encoding a chloramphenicol acetyl-transferase, and rDNA locus in Caenorhabditis elegans. In a first time, this work aims at investigate the cat gene attractiveness in different plasmidic or chromosomic supports, using in vitro and in bacteria assays. Secondly, we aims at synthesize what is known about Mos1 insertion sites in vitro and in vivo. Statistical analyzes showed that Mos1 insertions preferentially occurred in TA dinucléotides clusterred in TATA or TAxTA, or located in AT-rich regions. Hotspots attractiveness could not be related with DNA curvature or bendability, but supercoiling is essential for the cat gene to be a hotspot. The cat gene was used as a model to determine that influence of host proteic factor in integration target selection could not be excluded.

No description available.

The new elements in "The Ancient Mariner" were partly responsible for the unfavorable early reviews which vary much from the high praise the poem receives today. The purpose of this study is to record critical opinion of the poem from the contemporary reviews of 1798 to the intensive critical analysis of the 1960's.

This study attempts to discover in the early poetry of Coleridge anticipations of the poetic excellence exhibited in "The Ancient Mariner." It begins by explaining that the years from 1787, the date of his first recorded poem, to 1798, when he travelled to Germany, may be divided into three periods: 1787 to 1794, the years spent at school and university; 1794 to 1796, the years of his discipleship to two eighteenth-century rationalists, Godwin and Hartley; and 1797 to 1798, the years of his happy fellowship with the Wordsworths. The poetry has markedly different characteristics in each of these periods. The study proceeds by discussing the poetry under three headings: ideas, imagery and symbolism, and form. Noticeable progress towards the degree of achievement found in "The Ancient Mariner" appears in each of these areas. Chapter One, which discusses Coleridge's ideas, begins by establishing that from 1787 to 1798 the poetry is characterized by attempts to explain and offer a solution for evil and suffering. From 1787 to 1794 Coleridge advocated a simple and trite schoolroom morality, largely based on Church-of-England doctrine. Then he turned to the rationalism of Godwin and Hartley, accepting their concept of necessity, of the mind as a tabula rasa, of private property and institutionalism as the prime sources of evil, and of environment, reason and necessity as forces working toward the perfection of man. Rejecting Godwin's atheism, he subscribed to Hartley's system, in which these same concepts were placed in a Christian framework. However, disillusioned by the sterility of rationalism, and by the failure of the French Revolution to advance the morality of society, he retired to Nether Stowey in December, 1796, confused in mind and depressed in spirit. There he established a more meaningful concept of morality. It was based on faith in man's mind, as was Godwin's, and was focused on religion, as was Hartley's. But, unlike the system of either master, it found its motivation in will rather than reason. "The Ancient Mariner" embodies this concept of morality. In Chapter Two the study proceeds by categorizing the imagery and symbolism in "The Ancient Mariner" into three groups, or clusters, and showing that each appears, at least in nucleus, throughout the early poetry. The first cluster, which describes the Mariner, from 1787 to 1794 is associated with poet figures, from 1794 to 1796 is associated with political and social reformers and the spiritually regenerate. In 1797 and 1798 it is associated with individuals who, through an act of self-less will, have achieved a degree of moral and spiritual regeneracy, or who have a mission to enlighten other men. The second cluster is related to the murder of the Albatross. From 1787 to 1794 murder is treated as the inevitable consequence of living in an evil world, as an act committed consciously by men helpless to do otherwise. From 1794 to 1796 murder is treated as an act of self-interest, and of opposition to God, an act which violates the laws of reason and nature. During 1797 and 1798 murder is treated as the inevitable result of a purely sensual mind, in contrast to a spiritual mind. The final cluster, nature imagery and symbolism, is characterized by duality throughout the early poetry. From 1787 to 1794 the positive and negative aspects of nature describe happiness and unhappiness in Coleridge's personal life, and successes and failures of his poetic imagination. From 1794 to 1796 the duality contrasts the self-centered, ignorant mind to the enlightened, rational mind, which senses divine order in creation. During 1797 and 1798 the dualism contrasts the vision of the sensual man to that of the spiritual man. Chapter Three discusses the three kinds of form in poetry: external form, technique and internal form. Poetry is differentiated from prose by having pleasure as its immediate end. Pleasure is provided by an intuitive recognition of unity in multeity. Therefore form in poetry must be characterized by unity. External form is the relation of various thoughts and feelings to each other in the framework of a poem. Almost all Coleridge's poems have a well-unified external form. The success of this kind of form is most fully expressed in a poem such as "The Ancient Mariner," in which a unified symbolic level is super-imposed upon a unified narrative level. Technique is the way in which a poet expresses his thoughts and feelings. The various elements of technique - diction, imagery, metre, rhyme and stanza form - are well unified when they are the best and most natural expression of the poet's thoughts and feelings, and therefore mutually support and explain each other. The technique of the early poetry is noticeably weak; its mastery in "The Ancient Mariner" is the product of ten years of apprenticeship. Internal form is the proportion between the degree of thought and the degree of feeling in a poem. In all good poems thought and feeling give rise to and balance each other; they are unified. The greatest and best poems contain deep thought - a sense of spirituality in the midst of social and political reform - and deep feeling - a love which concerns itself with the changes in individual men. Deep thought and deep feeling can occur only with the achievement of the ultimate end of poetry: moral or intellectual truth. The poetry of 1787 to 1794 is characterized by an overbalance of feeling, that of 1794 to 1796, by an overbalance of thought. "The Ancient Mariner" contains a fusion of deep thought and deep feeling conveyed on the symbolic level. Enchanting the reader through the pleasure yielded by the perfect harmony of all the parts, and suggesting to him through symbolic patterns that it contains deep truths of human experience, the poem draws him back into itself, that he might discover these truths, find greater unity, and achieve more pleasure. / Arts, Faculty of / English, Department of / Graduate

The shortage of qualified merchant marines in the United States requires State Maritime Academy (SMA) leaders to develop competitive retention strategies to retain merchant mariners aboard training vessels. The purpose of this single case study was to identify retention strategies that U.S. SMA leaders used to retain mariners aboard training ships. The conceptual framework of this study was Vroom's expectancy theory. The study participants consisted of 5 SMA leaders overseeing the mariners aboard a training vessel. Semistructured interviews and review of SMA documents pertaining to employment strategies provided the study data. The data analysis included collecting and coding data, and using the constant comparative method to identify the themes. Four themes related to successful retention strategies emerged from the data analysis: (a) the monetary value of employment and benefits must be comparable to what is available in the maritime industry, (b) professional development is necessary to maintain maritime industry credentials and improve employee performance within the organization, (c) recognition and understanding of the uniqueness of being a mariner as a profession is important to mariners, and (d) transparency and trust increase communication and improve retention. The findings of this study contribute to positive social change by providing best practices for SMA leaders to integrate retention strategies to improve employment satisfaction, enhance the training of mariners on U.S. waterways, and increase longevity of qualified mariners, which could create a healthy and positive work environment.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Transposable elements (TEs) are DNA regions that can move within and between genomes, causing great impact on the host organisms. The Tc1-Mariner superfamily stands out for being, probably, the DNA transposons superfamily with greater distribution in nature, being ubiquitous in eukaryotes. In part of this work, we characterize elements of the mariner family in Neotropical drosophilids, which were obtained through amplification with degenerated primers. The primers were designed for the catalytic domain region of mariner transposase allowing amplification of a wide range of mariner-like sequences. A sum of twenty-three species have mariner-like sequences belonging to three subfamilies (mellifera, mauritiana and irritans). These elements present a patchy distribution and incongruences with the host phylogeny, suggesting horizontal transmission events between drosophilids and even between drosophilids and species of other families, subfamilies and orders. Moreover, some sequences present open reading frames, conserved catalytic motifs and evidence for the action of a strong purifying selection, which suggest yhat they originated from active elements. In another part of the work, we characterize Paris-like elements (belonging to Tc1 family), through searches in the twelve Drosophila genomes available. These searches, enabled us to find five new Paris-like elements (one in D. ananassae, one in D. pseudoobscura, one in D. persimilis, one in D. mojavensis and one in D. willistoni), with a copy number ranging from two to seven. Three species have putatively active elements. The evolutionary analysis of these elements suggests that they have envolved through vertical transmission associated with some events of stochastic loss in the analysed species. / Elementos transponíveis (TEs) são regiões do DNA que podem se mover dentro e entre genomas, causando grande impacto na evolução dos organismos. A Superfamília Tc1-Mariner se destaca por ser, provavelmente, a superfamília de transposons de DNA com maior distribuição na natureza, sendo ubíqua em eucariotos. Em parte desse trabalho, caracterizamos elementos da família mariner em drosofilideos Neotropicais para os quais obtivemos amplificação com primers degenerados. Os primers foram construídos na região do domínio catalítico da transposase de mariner o que permite amplificar uma ampla gama de sequências relacionadas à mariner. Um total de 23 espécies apresentou sequências relacionadas à mariner pertencentes a três subfamílias (mellifera, mauritiana e irritans). Esses elementos apresentaram uma distribuição descontínua e incongruências com a filogenia das espécies hospedeiras, o que sugere eventos de transmissão horizontal entre drosofilideos e, até mesmo entre drosofilideos e espécies de outra família, superfamília e ordem. Além disso, algumas sequências apresentaram um quadro aberto de leitura, os motivos catalíticos conservados e uma forte seleção purificadora atuando, o que sugere que esses elementos sejam provenientes de elementos ativos. Em outra parte do trabalho, caracterizamos as sequências relacionadas ao elemento Paris (pertencentes à família Tc1), com buscas nos doze genomas de Drosophila disponíveis. Nessas buscas,foram encontrados cinco novos elementos relacionados à Paris (um em D. ananassae, um em D. pseudoobscura, um em D. persimilis, um em D. mojavensis e um em D. willistoni), com um número de cópias variando de dois a sete. Três espécies apresentaram elementos potencialmente ativos. A análise evolutiva desses elementos sugere que estão sendo mantidos por transmissão vertical, com alguns eventos de perda estocástica nas espécies analisadas.

Les Eléments Transposables (ET) sont des parasites du génome caractérisés par leur capacité à se répliquer plus rapidement que les autres éléments génétiques du génome. La régulation par la voie des piARN joue un rôle essentiel pour limiter l’expansion des ET dans les lignées germinales des animaux.La première question posée est comment le génome répond face à une nouvelle invasion par un ET. Dans ce but, nous avons introduit le transposon de Classe II mariner (sous-famille mos1) chez D. melanogaster, qui ne contient naturellement pas l’élément. Nous avons montré, qu’après son amplification autonome dans le génome, l’élément avait atteint un équilibre en termes de nombre de copies, depuis qu’une régulation de novo par les piARN avait été acquise.Deuxièmement, nous avons étudié la mobilisation de l’élément mariner au cours du processus de colonisation des régions géographiques tempérées. A partir d’un large panel de populations naturelles nous avons trouvé que l’activité moyenne de mariner était remarquablement augmentée dans les populations non-Africaines en comparaison aux populations Africaines. Ces variations peuvent s’expliquer par un fort polymorphisme d’expression (transcriptionnel et traductionnel) des gènes de la voie des piARN.Le troisième chapitre soutient que la forte activité des ET dans la lignée germinale mâle est un phénomène global chez les drosophiles. Par ailleurs, le contenu en ET chez les espèces sœurs (D. melanogaster et D. simulans) a fortement divergé et, cela a affecté la réponse associée à la production des piARN. Chez D. melanogaster, de nombreux « burst » de transposition ont eut lieu récemment. Ces familles d’ET sont activement réprimées par les piARN dans l’ovaire et donc, se retrouvent massivement surexprimés dans les testicules. Chez D. simulans, nous pensons que la réponse par les piARN résulte principalement d’une régulation passée qui semble être la relique d’anciennes invasions d’ET.La voie des piARN est supposé être « garante de l’intégrité du génome » de par son rôle actif dans la défense contre les ET. Cependant, si la sélection naturelle purge les génomes de ces parasites délétères, il semble que les mécanismes de régulation de l’hôte contribuent au maintien de l’homéostasie du génome en limitant leur expansion, et quelque part en favoriser le maintien sur long terme. Ainsi, une autre interprétation pourrait être que la voie des piARN est « garante de la diversification du génome » de par son rôle à faciliter l’accumulation des ET. / Transposable Elements (TEs) are genomic parasites characterized by their ability to replicate faster than any other genetic element in the genomes. The piRNA mediated silencing is of central importance to limit TE expansion in the germline of animal species. The present dissertation explores the relationship between TEs and piRNAs alongside their evolutionary dynamics.The first question raised here was to understand how the genome responds to a new TE invasion. For that purpose, we injected a mariner Class II transposon into D. melanogaster genome that does not naturally contain the element. We found that, after its self-replication into the genome, the element have reached a copy number equilibrium since a de novo piRNA mediated regulation have been acquired.Second, we studied the mariner rewiring activity during the colonization of geographical temperate regions. From a large sampling of D. simulans natural populations, we found the mean activity of mariner to be strikingly higher in non-African populations compared to the African ones. These findings support the idea that selection acting on piRNA effector proteins has been of central importance to explain TE lineages diversification during colonization process.The third chapter provides evidences to propose that, the strong TE activity in testes, is a general phenomenon in Drosophila. We also observed that TE landscape divergence between the two sister species, have affected the genomic response mediated by the piRNAs. As a response of their recent bursts of transposition, TEs overexpressed in testes are preferentially silenced by piRNAs in D. melanogaster ovaries. By contrast, we assumed the D. simulans piRNA response to be the relic of a past regulation that still persists mostly against inactive TEs.The piRNA silencing in the germline, is assumed to be the “vanguard of genome” defense and integrity due to its active role against TEs. However, while natural selection purifies the genome from its deleterious parasites, it seems that the host regulation contributes to genome homeostasis by limiting their expansion, and somehow, favors their longterm maintenance. Thus, another interpretation would have been that piRNA silencing is the “vanguard of genome” diversification due to its active role in facilitating TE accumulation

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No description available.

La céréaliculture occupe une place importante dans l’agriculture mondiale et contribue à la sécurité alimentaire des populations. Pour assurer la production des céréales (orge, blé, avoine), il est nécessaire de lutter contre ses ravageurs, essentiellement les pucerons qui sont capables de transmettre plusieurs virus. L’analyse des génomes des pucerons tels que Rhopalosiphum padi, R. maidis, Sitobion avenae, Schizaphis graminum, de leur évolution et de leur relation avec les plantes hôtes (céréales) pourrait contribuer à la mise en place de moyens de lutte pour contrôler les populations de ces ravageurs. Dans ce contexte, cette étude s’est focalisée sur la recherche des éléments transposables des deux superfamilles Tc1-mariner-IS630 et des piggyBac. Les ETs, considérés comme des moteurs de la plasticité génomique et de l’évolution des espèces, sont utilisés en biotechnologie pour développer des outils de transfert de gènes. Dans un premier temps, nous avons recherché des éléments de la famille mariner, ou apparentés à cette famille, dans les génomes séquencés de trois espèces de pucerons : Acyrthosiphon pisum, Myzus persicae et Diuraphis noxia. Sur la base de similitude de séquences, nous avons pu caractériser 183 éléments répartis en trois clades. Le premier, commun aux trois espèces, correspond au clade de la sous-famille irritans DD34D. Il est subdivisé en trois tribus Macrosiphinimar, Batmar-like elements et Dnomar-like elements. Le deuxième comprend l’élément rosa DD41D qui appartient à une famille phylogénétiquement proche de mariner. Le troisième comprend des séquences avec de longues répétitions terminales inversées et inclut deux tribus DD40-41D. Ces deux derniers clades, plus répandus chez A. pisum, dérivent vraisemblablement d’un ancêtre commun et formeraient une nouvelle famille.Dans un deuxième temps, nous avons exploité les résultats de la recherche in silico pour identifier in vitro des éléments de la sous-famille irritans chez les pucerons des céréales et chez leur plante hôte. Deux types d’éléments délétées (MITEs) ont été identifiés chez les pucerons, l’un commun à toutes les espèces avec un pourcentage d’identité supérieur à 98% (Aphidmar) et l’autre spécifique à S. avenae (Samar2). Par ailleurs, les génomes des céréales (orge, blé, brachypodium, égilope) ont été analysés en utilisant comme requêtes des séquences d’éléments de la sous-famille irritans trouvés chez les aphides. Un seul contig de l’orge cultivar barke comprend un élément tronqué de 320 pb, flanqué par de l’ADN génomique de pucerons. La vérification in vitro de la présence de cette séquence chez plusieurs cultivars d’orge révèle deux types de séquences. Le premier est similaire à celui trouvé in silico chez l’orge, le second correspond à l’élément Samar2 délété de 7 nucléotides au niveau du point de cassure de la délétion initiale. Ceci suggère l’existence d’un transfert horizontal entre pucerons des céréales et l’orge. Enfin, l’abondance de données génomiques et la rareté des travaux approfondis portant sur les membres de la superfamille piggyBac, nous ont amenés à analyser in silico leurs caractéristiques, leur distribution et leur évolution. Un total de 117 séquences protéiques de PBLE (éléments autonomes) et de PGBD (éléments domestiqués), ont été utilisées comme requêtes. Quatre groupes structuraux de PBLE ont été définis en fonction de la présence ou absence de répétitions sub-terminales (directes/inversées). Toutefois, il n'existe aucune relation entre ces quatre groupes et la phylogénie des PBLE. Les PGBD soumis à une forte sélection purifiante, sont clairement structurés en neuf groupes dont un correspondant à un nouvel ensemble d’éléments domestiqués trouvé chez les Néopterygiens. L’analyse fine des PGBD révèle que le domaine catalytique de la transposase ancestrale n'est pas toujours conservé. La phylogénie générale des PBLE et des PGBD suggère des événements multiples de domestication des PGBD à partir de différents ancêtres PBLE. / Cereal farming plays an important role in world agriculture and contributes to the food security of the populations. To improve the production of cereals (barley, wheat, oats ...), it is necessary to fight against their pests, especially aphids, able to transmit several viruses. The analysis of aphid’s genomes such as Rhopalosiphum padi, R. maidis, Sitobions avenae and Schizaphis graminum, their evolution and their relationships with their host plants could contribute to define strategies against pest populations. In this context, this work focused on the analysis of transposable elements belonging to Tc1-mariner-IS630 and piggyBac superfamilies. Indeed, TEs are involved in genomic plasticity and evolution of species, and are also used in biotechnology to develop gene transfer tools. In the first chapter, we investigate three available genomes of aphids, namely Acyrthosiphon pisum, Myzus persicae and Diuraphis noxia, to search for elements of the mariner family or close to it. Based on sequence similarities, we were able to characterize 183 elements distributed in three clades. The first one, common to the three species, corresponds to the clade of irritans subfamily DD34D, and is subdivided into three tribes Macrosiphinimar, Batmar-like elements and Dnomar-like elements. The second one includes the rosa element DD41D belonging to a group close to the mariner family. The third one includes sequences with long Terminal Inverted Repeats and is subdivided into two DD40-41D tribes. These two latter clades, more common in A. pisum, likely derive from a common ancestor and would form a new family. In the second chapter, the results of in silico research were exploited, to identify in vitro, elements of the irritans subfamily in cereal aphids and in their host plants as well. Two types of deleted elements (MITEs) have been identified in aphids, one common to all species with a percentage of identity higher than 98% (Aphidmar) and the other one specific to S. avenae (Samar2). In addition, the genomes of cereals (barley, wheat, brachypodium, aegilops) were investigated using as queries sequences of irritans subfamily found in aphids. A single contig identified in Hordeum vulgare (cultivar barke) contains a 320 bp truncated element flanked by genomic DNA of aphids. The presence of this sequence was checked in several barley cultivars by an in vitro approach. Two types of sequences were found. The first one similar to that found in barley from the in silico approach, the second one corresponding to Samar2 element, lacking seven nucleotides at the breaking points of the initial deletion. This suggests a possible horizontal transfer between cereal aphids and barley. In the last chapter, the abundance of genomic data and the scarcity of in-depth research covering all members of the piggyBac superfamily led us to determine in silico their characteristic, their distribution and their evolution. A total of 117 proteic sequences of the PBLE (autonomous elements) and PGBD (domesticated elements) have been used as queries. Four structural groups of PBLE have been identified depending on the presence or absence of sub-terminal repeats (direct / inverted). However, there is no relationship between the structural groups and the phylogeny of these PBLE elements. PGBD are clearly structured into nine main groups including a new group of domesticated elements found in Neopterygii. The catalytic domain of the ancestral transposase is not always preserved, but all these domesticated elements are subjected to a strong purifying selection. The general phylogeny of PBLEs and PGBD suggests multiple and independent domestication events of PGBD from different PBLE ancestors.