Access to abstract restricted until 07/2016. / Eco-typology and the tree of life in Milton's Paradise lost -- The Matthew Bible, eco-typology and the tree of life in Milton's Eden -- The Geneva Bible, eco-typology and the fruit of the living word in Paradise lost -- Speed's 'Genealogies', the King James Bible and the seed of grace in the later books of Paradise lost. / Department of English

In Renaissance culture there was an iconographic and literary language of trees, related to the motif of the tree of life, an ancient symbol of immortality associated with paradise. The properties of trees were used to express a range of ideas, including the death and resurrection of Christ, the fall and regeneration of political regimes, and virtue and vice within the individual soul. The juxtaposition of the tree of knowledge with the tree of life, as motifs of sterility and fertility, expressed aspects of the human condition and constructions of spiritual history and destiny. This thesis explores the language of trees in visual art and a range of English Renaissance texts from the late-sixteenth to the mid-seventeenth century: two plays by Shakespeare, two country-house poems, and a prose treatise on growing fruit-trees. Each of the writers drew on arboreal metaphors and motifs in unique and innovative ways. However there are numerous parallels and connections between the texts, and with contemporary and antecedent visual art, to justify considering these works together. In Shakespeare’s tragedy Titus Andronicus (1594) Lavinia, when she has her hands cut off, is metaphorically described as a tree with lopped branches and linked with the stricken political entity of Rome. Shakespeare evokes the tree of virtue, the classical myth of Daphne, and the arboreal language of virtue and vice. In the late tragicomedy Cymbeline (1610), the king is symbolized in a dream vision as a tree, with its cut branches representing the princes who are initially stolen but then reunited with the king. The tree represents the family tree as well as the political state, two interlinked concepts in the play and in contemporary iconography and ideology. Since Cymbeline’s reign heralded the Nativity, the prophecy of the lopped and regenerated tree invokes the idea of Christ as the tree of life and the fruit of the tree of Jesse. In both plays, Shakespeare’s tree imagery comments on the exercise of political power and the resultant health of the state. Shakespeare’s contemporary Aemilia Lanyer wrote “The Description of Cooke-ham” (1611), part of a published volume of poetry entitled Salve Deus Rex Judaeorum. In the poem she imagines a prominent tree on the estate as the tree of life. An abstract metaphor is envisaged as part of the physical landscape. The motif transforms the estate to sacred terrain, enabling her to claim access to a space she is otherwise excluded from by class and gender. Lanyer links the sap from the tree of life with her writing, seeking to legitimize her claim as a female poet. Such strategies are part of her bid for patronage from the Countess of Cumberland, her primary dedicatee. In another country-house poem, Andrew Marvell’s “Upon Appleton House, to my Lord Fairfax” (1651), the poet creates a forest of the mind in which he explores different aspects of the language of trees. The speaker imagines himself encircled by vines and crucified by thorns, in imitation of Christ as the tree of life, while a fallen oak tree suggests the regicide. He takes on various roles including that of the enigmatic Green Man. I place Marvell’s imagery in the context of the Civil War and the relationship with his employer Lord Fairfax. Marvell’s exploration of arboreal motifs also subjects Christian tree of life imagery to the challenge of its pagan antecedents and reflects anxieties over the natural processes that threaten metaphors of regeneration. Lastly, in Ralph Austen’s A Treatise of Fruit-trees and Spiritual Use of an Orchard (1653), the author blends advice on horticultural practices in growing fruit-trees with religious metaphors. For Austen, gardening is both a physical and a metaphysical pursuit. His readers are expected to plant fruit-trees in orchards that evoke the idea of Christ as the tree of life and related ideas. His use of the motif is part of his advocacy of agricultural and social reform, motivations that were part of those in the circle surrounding Samuel Hartlib. Austen’s text is situated at the end of the English Renaissance and at the beginnings of the Scientific Revolution, when emblematic and symbolic frameworks for interpreting the natural world were subject to new pressures derived from empirical and rationalistic outlooks. What becomes apparent from these works is that tree metaphors were literalized, just as they had been in visual art, and given a new naturalism as they were projected onto landscapes. Symbolic trees merged with botanical trees in imagined landscapes, creating hybrid terrains that were both descriptive and mythical. Recognition of the language of trees in Renaissance culture opens up new readings of both canonical and lesser-known texts and highlights the porous disciplinary border between literature and art. Our historical readings are richer for understanding the potent language of trees. Overall the thesis highlights the importance and cultural preoccupation with trees in European visual and literary traditions.

Thesis (D. Min.)--Western Seminary, Portland, OR, 2009. / Abstract. Includes bibliographical references (leaves 197-206).

Not too much is known today about religion of ancient Mesoamerica, and it will only be through an intensive comparative study of the various deities as presented in the heiroglyphic manuscripts and native writings, and of the symbolic religious art in the architectural and sculptural remains, that greater knowledge of the subject will be gained. The "Tree of Life," one of the most striking religious symbols of the area, may be one key to such knowledge.

My dissertation addresses two aspects of eukaryotic evolution, 1) the organization of eukaryotic diversity and 2) genomic variation in Foraminifera. The bulk of eukaryotic diversity is microbial with plants and animals representing just two of the estimated 75 lineages of eukaryotes. Among these microbial lineages, there are many examples of dynamic genome processes. Elucidating the origin and evolution of genome features requires a robust phylogenetic framework for eukaryotes. Taxon-rich molecular analyses provide a mechanism to test hypothesized evolutionary relationships and enable placement of diverse taxa on the tree of life. These analyses result in a well-resolved eukaryotic tree of life. Relaxed molecular clock analyses of this taxon-rich dataset place the origin on eukaryotes in the Paleoproterozoic, and suggest that all of the major lineages of eukaryotes diverged before the Neoproterozoic. This robust scaffold of the tree of eukaryotes is also used to elucidate common themes in genome evolution across eukaryotes. Mapping dynamic genome features onto this tree demonstrates that they are widespread in eukaryotes, and suggests that a common mechanism underlies genome plasticity. Foraminifera, a diverse lineage of marine amoebae, provide a good model system for investigating genome dynamics because they amplify portions of their genome and go through ploidy cycles during their life cycle. Assessment of nuclear dynamics in one species of Foraminifera, Allogromia laticollaris strain CSH, reveals that genome content varies according the life cycle stage and food source, which may differentially impact organismal fitness. The inclusion of diverse microbial eukaryotes enables better resolution of eukaryotic relationships and improves our understanding the dynamic nature of eukaryotic genomes.

The ocean plays essential roles in Earth's biochemistry. Most of the nutrient transformations that fuel trophic webs in the ocean are mediated by microorganisms. The extent of phylogenetic and metabolic diversity of key culture and uncultured marine microbial clades started to be revealed due to progress in sequencing technologies, however we still lack a comprehensive understanding of the evolutionary processes that led to the microbial diversity we see in the ocean today. In this dissertation, I apply phylogenomic and comparative genomic methods to explore the evolutionary genomics of bacterial and archaeal clades that are relevant due to their abundance and biogeochemical activities in the ocean. In Chapter 1, I review relevant literature regarding the evolutionary genomics of marine bacteria and archaea, with emphasis on the origins of marine microbial diversity and the evolution of genome architecture. In Chapter 2, I use a comparative framework to get insights into the evolutionary forces driving genome streamlining in the Ca. Marinimicrobia, a clade widely distributed in the ocean. This project shows that differences in the environmental conditions found along the water column led to contrasting mechanisms of evolution and ultimately genome architectures. In Chapter 3, I assess the phylogenetic signal and congruence of marker genes commonly used for phylogenetic studies of bacteria and archaea and propose a pipeline and a set of genes that provide a robust phylogenetic signal for the reconstruction of multi-domain phylogenies. In Chapter 4, I apply a phylogeny-based statistical approach to evaluate how tightly genome size in bacteria and archaea is linked to evolutionary ii history, including marine clades. I present evidence suggesting that phylogenetic history and environmental complexity are strong drivers of genome size in prokaryotes. Lastly, in Chapter 5, I estimate the emergence time of marine bacterial and archaeal clades in the context of the Prokaryotic Tree of Life and demonstrate that the diversification of these groups is linked to the three main oxygenation periods occurring throughout Earth's history. I also identify the metabolic novelties that likely led to the colonization of marine realms. Here I present methodological frameworks in the fields of comparative genomics and phylogenomics to study the evolution of marine microbial diversity and show evidence suggesting that the main evolutionary processes leading to the extant diversity seen in the ocean today are intimately linked to geological and biological innovations occurring throughout Earth's history. / Doctor of Philosophy / The ocean plays essential roles in the functioning of our planet. Many of the nutrient's transformation happening in marine environments are mediated by microorganisms, whose metabolic activities underpin higher trophic levels. The identity of the most prevalent marine microbial groups has been reveled during the last two decades through sequencing technologies. Despite having a great progress in our understanding of the functions that these microorganisms have in the ocean; we still lack information about the evolutionary processes that allowed their diversification and colonization into marine realms. In this work, I developed and applied computational strategies to disentangle the evolutionary genomics of marine microorganisms. One particularity about most these marine groups is that they have very small genomes. To explore the evolutionary forces driving their genome reduction, I analyzed a broad set of genomes of Marinimicrobia, a bacterial group widely distributed in the ocean. This analysis shows that genome reduction in Marinimicrobia is driven by negative selection, an evolutionary force that allows the deletion of non-essential genes, subsequently leading to genome reduction. Moreover, I developed a benchmarked pipeline for the reconstruction of phylogenetic trees to study the evolutionary relationships of microorganisms. This pipeline allowed me to link the diversification of the main marine groups and the geological periods in which they first emerged. I discovered that the colonization of these groups happened during three different periods, which are coincident with the main oxygenation events occurring across Earth's history. Moreover, the diversification of vi marine microbial groups was associated with the acquisition of genes to exploit the newly created niches that followed the oxygenation of the atmosphere and the ocean. Overall, my work shows that the diversification of the marine microbial clades that are essential for the functioning of the ocean is intimately linked to the redox state of the ocean and the atmosphere throughout Earth's history.

Ce mémoire étudie l’influence du monologue intérieur sur l’immersion d’un spectateur lorsqu’il audiovisionne une œuvre filmique narrative. Plus particulièrement, il s’intéresse à décrire les différents mécanismes perceptifs impliqués lors du traitement de l’information sensorielle et de quelles façons ces derniers influencent la production et la perception d’un discours intérieur chez le spectateur. S’inscrivant dans une perspective cognitiviste fonctionnaliste, ce mémoire explore différentes hypothèses et concepts rattachés aux processus attentionnels, mémoriels et langagiers chez l’être humain, eux-mêmes fortement impliqués lors du décodage d’une œuvre fictive et narrative. La recherche proposée permet de revisiter la théorie générale du PECMA flow développée par Torben Grodal (1997), qui conçoit l’expérience cinématographique en tant que flux de traitement sensoriel. L’approche transhistorique et intersectorielle préconisée dans le cadre de ce mémoire permet d’aborder certaines conceptions matérialistes liées aux fonctionnements physiologique et neurologique du cerveau humain, en les combinant à différentes théories issues des sciences humaines et des sciences sociales rattachées au soi dialogique, au soi narratif, de même qu’aux processus de traitement ascendant et descendant. Enfin, l’analyse d’un extrait tiré de The Tree of Life (2011), du réalisateur Terrence Malick, démontre comment l’expérience d’audiovisionnement d’un film peut concourir à mettre en place un recul nécessaire avec le récit, qui s’avère primordial dans l’actualisation et la perception d’un monologue intérieur « immertiel » chez le sujet. À l’aide des notions développées au cours des différents chapitres et s’appuyant sur le modèle du PECMA flow, le mémoire illustre comment une œuvre filmique peut concourir à faire émerger, en parallèle de l’audiovisionnement, une conversation intérieure toute particulière dans l’esprit du spectateur, qui participe directement à son immersivité filmique. Une attention particulière sera accordée à l’usage de la voix-over au cinéma, afin de démontrer comment son traitement dans l’œuvre à l’étude en fait un élément du langage cinématographique qui favorise l’élaboration d’un trialogue entre le sujet pensant confronté à son propre monologue intérieur et sa position de spectateur récepteur du ou des discours transmis par le film. / This master’s thesis studies the influence of the inner monologue on the immersion of a spectator when he/she audioviews a narrative film work. More specifically, it is interested in describing the different perceptual mechanisms involved in the processing of sensory information and the ways in which these influence the production and perception of an inner speech in the viewer. From a functionalist cognitive perspective, this dissertation explores different hypotheses and concepts related to attentional, memory and language processes in humans, which are themselves strongly involved in the decoding of a fictional and narrative work. The proposed research allows us to revisit the general theory of PECMA flow developed by Torben Grodal (1997), which conceives the cinematic experience as a sensory processing flow. The transhistorical and intersectorial approach adopted in this dissertation allows us to address certain materialist conceptions related to the physiological and neurological functioning of the human brain, by combining them with different theories from the humanities and social sciences related to the dialogical self, the narrative self, as well as bottom-up and top-down processing. Finally, the analysis of an excerpt from The Tree of Life (2011), by director Terrence Malick, demonstrates how the experience of audio-viewing a film can contribute to the establishment of a necessary distance from the narrative, which proves to be essential in the actualization and perception of an “immertial” inner monologue in the subject. Using the notions developed in the different chapters and based on the PECMA flow model, the master’s thesis illustrates how a filmic work can contribute to the emergence, in parallel to the audiovisioning, of a very particular inner conversation in the spectator's mind, which directly participates in his filmic immersiveness. A particular attention will be paid to the use of the voice-over in cinema, to demonstrate how its treatment in the work under study makes it an element of the cinematographic language that favors the elaboration of a trialogue between the thinking subject confronted with its own inner monologue and its position of receiver of the discourse(s) transmitted by the film.

This paper outlines a model of human development to help guide contemplative practice in parenting and facilitate prayerful understanding of parent-child development with a focus upon one's own parent-child relationship. The model draws from the tree of life symbolism represented by the cross and the spiral and further elaborated through symbolic interpretations of the seed, root, stem, branch, leaf, and fruit. Contemplative prayer is seen as a path of self-development that allows parents to respond to children with goodness, love, wisdom, and justice. / Graduation date: 1992

Orientador: Nilton Luiz de Souza / Banca: Edson Luiz Furtado / Banca: Marli Teixeira de Almeida Minhoni / Banca: Luiz Eduardo Aranha de Camargo / Banca: Eiko Kuramae / Resumo: Rhizoctonia solani Kuhn (teleomorfico: Thanatephorus cucumeris (Frank) Donk) e um fungo basidiomycota, fitopatogeno anamorfico com uma ampla gama de hospedeiros, incluindo mais de 500 generos de plantas. Causam doencas em varias culturas importantes no mundo, infectando sementes, raizes, folhas, hastes e frutos. A diversidade genetica de 274 isolados de Rhizoctonia spp. coletados, em diversas partes do mundo, foram caracterizados utilizando-se a analise de sequencia da regiao ITS1-5.8S rDNA-ITS2, para avaliar o grau de variabilidade genetica dentro e entre grupos de anastomose (AGs), incluindo os isolados padroes dos respectivos AGs. A arvore filogenetica gerada pela analise das sequencias da regiao ITS foi suportada por 66% gbootstraph para a separacao em nove maiores grupos. De maneira geral, o agrupamento dos isolados de Rhizoctonia spp. ocorreu de acordo com os grupos de anastomose ja previamente determinados. A similaridade de sequencias entre isolados de mesmo hospedeiro, mas de diferente origem geografica foi elevada. Por exemplo, isolados de melao do Brasil e Espanha mostraram 97,2% de similaridade na regiao ITS1 e de 98,6 a 99,3 % na regiao ITS2. Isolados de batata do Brasil e da Espanha mostram similaridade de sequencia de 94%. Para melhorar a qualidade das sequencias da regiao ITS1-5.8S rDNA-ITS2 dos isolados CBS316.84 (Waitea circinata) e CBS569.83 (Ceratobasidium globisporum) foram gerados clones, e a analise das sequencias dos clones apresentaram variacao de 94,9 a 100 % de identidade 2 entre os clones do isolado CBS316.84 e de 91,9 ate 100 % para os clones do isolado CBS569.83. Os 44 isolados selecionados previamente, a partir do cladograma gerado da regiao ITS1-5.8S-ITS2 foram submetidos ao sequenciamento dos genes ATP sintase subunidade 6 mitocondrial (ATP6), fator de elongacao 1-alpha (EF-1ƒ¿), RNA polimerase 2 (RPB2) e a regiao ITS. As arvores filogeneticas baseadas na analise gneighbor-joiningh geradas a partir das... / Abstract: Rhizoctonia solani Kuhn (teleomorph: Thanatephorus cucumeris (Frank) Donk) is an anamorphic plant pathogenic basidiomycota fungus with a wide host range, including more than 500 genera of higher plants. Species cause disease in several important crops worldwide by infecting the seeds, roots, leaves, stems and fruits. Two hundred seventy four isolates from plant pathogenic fungus Rhizoctonia spp. collected worldwide was characterized using ITS1-5.8S rDNA-ITS2 sequence analysis to assess the degree of genetic variability within and among anastomosis groups (AGs), including tester isolates of the respective AGs. Within the ITS phylogenetic tree, there was support (66% bootstrap value) for the separation into nine major groups. In general the clustering isolates of Rhizoctonia species agreed with previously determined anastomosis groups. Nucleotide sequence similarity between isolates from the same host but from different geographic origin was high e.g. isolates from melon from Brazil and Spain showed from 97.2 % similarity in ITS1 region and 98.6 to 99.3 % in ITS2 region. Potato isolates from Brazil and Spain showed a sequence similarity about 94%. Several isolates from the same geographic origin were found closely related to different anastomosis groups such as isolates from potato, tomato, soybeans, beans, sugar beet and have been reported different symptoms around the world. Were generated cloning of ITS region from CBS 316.84 (Waitea circinata) and CBS 569.83 (Ceratobasidium globisporum) isolates to improve the sequence quality. The clones showed 94.9 to 100% and 91.9 to 100% identity respectively. Fourty four isolates were selected from the ITS1-5.8S rDNA-ITS2 phylogenetic tree for sequencing using the genes of ssembling the Fungal tree of Life (AFTOL) such as ATP 4 synthase subunit 6 mitocondrial (ATP6), elongation factor 1-alpha (EF-1ƒ¿) and RNA polymerase 2 (RPB2). The phylogenetic tree generated by sequences of EF-1ƒ¿ and RPB2 in general. / Doutor

Made available in DSpace on 2014-06-11T19:34:59Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-05-05Bitstream added on 2014-06-13T20:25:38Z : No. of bitstreams: 1 nakatani_ak_dr_fca.pdf: 853202 bytes, checksum: df12fbbfd3cd127e44acff93e2b14eff (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Rhizoctonia solani Kuhn (teleomorfico: Thanatephorus cucumeris (Frank) Donk) e um fungo basidiomycota, fitopatogeno anamorfico com uma ampla gama de hospedeiros, incluindo mais de 500 generos de plantas. Causam doencas em varias culturas importantes no mundo, infectando sementes, raizes, folhas, hastes e frutos. A diversidade genetica de 274 isolados de Rhizoctonia spp. coletados, em diversas partes do mundo, foram caracterizados utilizando-se a analise de sequencia da regiao ITS1-5.8S rDNA-ITS2, para avaliar o grau de variabilidade genetica dentro e entre grupos de anastomose (AGs), incluindo os isolados padroes dos respectivos AGs. A arvore filogenetica gerada pela analise das sequencias da regiao ITS foi suportada por 66% gbootstrap h para a separacao em nove maiores grupos. De maneira geral, o agrupamento dos isolados de Rhizoctonia spp. ocorreu de acordo com os grupos de anastomose ja previamente determinados. A similaridade de sequencias entre isolados de mesmo hospedeiro, mas de diferente origem geografica foi elevada. Por exemplo, isolados de melao do Brasil e Espanha mostraram 97,2% de similaridade na regiao ITS1 e de 98,6 a 99,3 % na regiao ITS2. Isolados de batata do Brasil e da Espanha mostram similaridade de sequencia de 94%. Para melhorar a qualidade das sequencias da regiao ITS1-5.8S rDNA-ITS2 dos isolados CBS316.84 (Waitea circinata) e CBS569.83 (Ceratobasidium globisporum) foram gerados clones, e a analise das sequencias dos clones apresentaram variacao de 94,9 a 100 % de identidade 2 entre os clones do isolado CBS316.84 e de 91,9 ate 100 % para os clones do isolado CBS569.83. Os 44 isolados selecionados previamente, a partir do cladograma gerado da regiao ITS1-5.8S-ITS2 foram submetidos ao sequenciamento dos genes ATP sintase subunidade 6 mitocondrial (ATP6), fator de elongacao 1-alpha (EF-1 ¿), RNA polimerase 2 (RPB2) e a regiao ITS. As arvores filogeneticas baseadas na analise gneighbor-joining h geradas a partir das... / Rhizoctonia solani Kuhn (teleomorph: Thanatephorus cucumeris (Frank) Donk) is an anamorphic plant pathogenic basidiomycota fungus with a wide host range, including more than 500 genera of higher plants. Species cause disease in several important crops worldwide by infecting the seeds, roots, leaves, stems and fruits. Two hundred seventy four isolates from plant pathogenic fungus Rhizoctonia spp. collected worldwide was characterized using ITS1-5.8S rDNA-ITS2 sequence analysis to assess the degree of genetic variability within and among anastomosis groups (AGs), including tester isolates of the respective AGs. Within the ITS phylogenetic tree, there was support (66% bootstrap value) for the separation into nine major groups. In general the clustering isolates of Rhizoctonia species agreed with previously determined anastomosis groups. Nucleotide sequence similarity between isolates from the same host but from different geographic origin was high e.g. isolates from melon from Brazil and Spain showed from 97.2 % similarity in ITS1 region and 98.6 to 99.3 % in ITS2 region. Potato isolates from Brazil and Spain showed a sequence similarity about 94%. Several isolates from the same geographic origin were found closely related to different anastomosis groups such as isolates from potato, tomato, soybeans, beans, sugar beet and have been reported different symptoms around the world. Were generated cloning of ITS region from CBS 316.84 (Waitea circinata) and CBS 569.83 (Ceratobasidium globisporum) isolates to improve the sequence quality. The clones showed 94.9 to 100% and 91.9 to 100% identity respectively. Fourty four isolates were selected from the ITS1-5.8S rDNA-ITS2 phylogenetic tree for sequencing using the genes of ssembling the Fungal tree of Life (AFTOL) such as ATP 4 synthase subunit 6 mitocondrial (ATP6), elongation factor 1-alpha (EF-1 ¿) and RNA polymerase 2 (RPB2). The phylogenetic tree generated by sequences of EF-1 ¿ and RPB2 in general.