Thesis (Ph.D.)--Hong Kong Baptist University, 2006. / Thesis submitted to the Dept. of Religion and Philosophy. Includes bibliographical references (leaves 192-217)

Thesis (Ph.D.)--Duquesne University, 2008. / Title from document title page. Abstract included in electronic submission form. Includes bibliographical references (p. 285-298) and index.

Thesis (Ph. D.)--University of Missouri-Columbia, 2002. / Typescript. Vita. Includes bibliographical references (leaves 91-103). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2002. / Typescript. Vita. Includes bibliographical references (leaves 91-103). Also available on the Internet.

Microbes can protect their plant and animal hosts against infection by pathogens, parasites and parasitoids. These ‘defensive microbes' can provide a powerful line of defence beyond the host response and are becoming attractive candidates for disease control. In this thesis, I investigated how defensive microbes can interact with pathogens over evolutionary time by measuring the effects of co-passaging a defensive microbe (Enterococcus faecalis) and a pathogen (Staphylococcus aureus) within the Caenorhabditis elegans model host. In Chapter 1, I found that co-passaging drove the evolution of reduced pathogen virulence as a by-product of adaptation to microbe-mediated defence. Moreover, I show that the mechanism of pathogen resistance to the defensive microbe can determine the direction of virulence evolution. In chapter two, I discovered that the co-passaged defensive microbe and pathogen populations had undergone coevolutionary interactions within host populations via fluctuating selection dynamics. I then showed that these dynamics resulted in patterns of pathogen local adaptation and increased genetic divergence. Finally, in chapter three, I revealed that these coevolutionary interactions significantly affected the costs and benefits of the defensive microbes to their hosts, but that the relationship between these costs and benefits prevented the transition of defensive microbes across the mutualism-parasitism continuum. Together, this thesis uncovers the potential for defensive microbes to shape the evolution of pathogens and demonstrates that defensive microbes can be an evolutionarily dynamic but stable form of host resistance towards infectious disease. As such, the data presented in this thesis have important implications for how we study host-parasite interactions in nature and question our current understanding of virulence evolution, pathogen local adaptation and the origin of defensive microbes.

Virtually all interacting species (such as hosts and parasites) are embedded within diverse communities. However, evolutionary interactions are typically considered in a pairwise species framework. Although coevolutionary theory suggests that multiple species interactions may provide greater opportunities for diversification, the impacts of community diversity on coevolution have not been directly tested. In this thesis I synthesize the findings from recent experimental work to assess the effects of increased species diversity on the patterns and processes of host and parasite evolution. I then investigate the effects of parasite diversity on host-parasite population dynamics and evolution using the pathogen Pseudomonas aeruginosa and five lytic bacteriophage parasites in a brief evolution experiment. Parasite diversity was manipulated by assembling phage communities with different number of species. Phage communities suppressed host populations more rapidly but also showed reduced phage density, likely due to inter-phage competition. The evolution of resistance allowed rapid bacterial recovery that was greater in magnitude with increases in phage diversity. These results were then followed up via longer term experimental coevolution of the same host and parasite communities. Here the data showed that greater parasite diversity accelerates coevolutionary arms races and drives more diversification among lineages. Coevolution between hosts and parasite communities drove more successive increases in host resistance coupled with increasingly frequent selective sweeps at the genomic level. Consistent with this, the most rapidly evolving host genes under coevolution with parasite communities were those involved in various host resistance strategies. These results demonstrate, at phenotypic and genomic levels, how areas of high community diversity may be hotspots for rapid evolution in interacting, antagonistic species. Finally, In the face of escalating antibiotic resistance, there is now an urgent need to develop alternative antimicrobials, these results may be relevant to the application of phages as therapeutics and they are discussed in that context.

Orientador: Jair Lopes Junior / Banca: Elio Carlos Ricardo / Banca: Renato Eugenio da Silva Diniz / Resumo: A teoria evolutiva desempenha papel fundamental dentro das ciências biológicas, dado que possibilita a organização e a unificação do corpo de conhecimentos desta área. Em concordância com esta perspectiva, o ensino-aprendizagem de Biologia deve salientar a centralidade e a importância da evolução para este componente curricular. Entretanto, as pesquisas brasileiras sobre ensino de evolução biológica evidenciam uma série de obstáculos para a construção de conteúdos referentes à teoria evolutiva, bem como para a adoção da evolução como eixo central da disciplina de Biologia. A constatação e o reconhecimento de tais dificuldades impõem questões sobre os subsídios oferecidos pelos documentos oficiais da educação básico do Estado de São Paulo e pelas pesquisas acadêmicas sobre o ensino de evolução para enfrentamento das mesmas. Nesta perspectiva, poder-se-ia demarcar correspondências entre, de um lado, os indicadores de aprendizagem derivados das pesquisas acadêmicas sobre o ensino de conteúdos relacionados ao tema origem e evolução da vida e, de outro lado, o contexto escolar no qual ocorrem os processos de ensino-aprendizagem desta temática. Considerando as diferentes dimensões em relação às quais tais correspondências poderiam ser analisadas, o presente trabalho concentrou ênfase em investigar se os indicadores de aprendizagem referentes ao tema evolução derivados das pesquisas acadêmicas equivalentes ou consistentes com os descritores preconizados pelas matrizes de referência do Sistema de Avaliação de Rendimento Escolar do Estado de São Paulo (SARESP). Nestes termos, objetivamos com este estudo investigar e caracterizar as possíveis correspondências entre os descritores e as habilidades preconizadas em documentos oficiais da educação básica do Estado de São Paulo e os indicadores de aprendizagem expostos pelas pesquisas... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The evolutionary theory plays a fundamental role in the biological sciences, data that makes possible the organization and unification of the corpus of knowledge in this area. In agreement with this perspective, the Biology teaching and learning must highlight the centrality and the importance of the evolution for this curriculum component. However, the Brazilian researches on the teaching of biological evolution show a series of obstacles to building contents concerning to the evolutionary theory, as well as the adoption of the evolution as the central axis of the biology discipline. The fact and the recognition of these difficulties impose questions about the subsidies offered by official documents of the basic education in the State of São Paulo and by the academic researches on the teaching of evolution in order to face them. In this perspective, it could be able to demarcate correspondences between, on one hand, the learning, indicators derived from academic research on teaching content related to the subject origin and evolution of the life and on the other hand, the school context in which occur the teaching and learning processes of this subject. Considering the different dimensions on which such matches could be analyzed, this study focused emphasis on investigating whether the indicators of learning on the subject of evolution derived from academic researches would be equivalent to or consistent with the descriptors recommended by the matrices of reference of the Evaluation System of the School Performance of the State of São Paulo (SARESP). In these terms, this study aimed to investigate and characterize the possible matches between descriptors and the skills recommended in official documents of the basic education in the State of Sao Paulo and the indicators of learning exhibited by academic... (Complete abstract click electronic access below) / Mestre

Meiotic recombination is a fundamental biological process in sexually reproducing organisms, enabling offspring to inherit novel combinations of mutations, and ensuring even segregation of chromosomes into gametes. Recombination is initiated by programmed Double Strand Breaks (DSBs), the genomic locations of which are determined in most mammals by PRDM9, a rapidly evolving DNA-binding protein. In crosses between different mouse subspecies, certain Prdm9 alleles cause infertility in hybrid males, implying a critical role in fertility and speciation. Upon binding to DNA, PRDM9 deposits a histone modification (H3K4me3) typically found in the promoters of expressed genes, suggesting that binding might alter the expression of nearby genes. Many other questions have remained about how PRDM9 initiates recombination, how it causes speciation, and why it evolves so rapidly. This body of work investigates these questions using complementary experimental and analytical methodologies. By generating a map of human PRDM9 binding sites and applying novel sequence analysis methods, I uncovered new DNA-binding modalities of PRDM9 and identified sequence-independent factors that predict binding and recombination outcomes. I also confirmed that PRDM9 can affect gene expression by binding to promoters, identifying candidate regulatory targets in meiosis. Furthermore, I showed that PRDM9’s DNA-binding domain also mediates strong protein-protein interactions that produce PRDM9 multimers, which may play an important functional role. Finally, by generating high-resolution maps of PRDM9 binding in hybrid mice, I provide evidence for a mechanism to explain PRDM9-mediated speciation as a consequence of the joint evolution of PRDM9 and its binding targets. This work reveals that PRDM9 binding on one chromosome strongly impacts DSB formation and/or repair on the homologue, suggesting a novel role for PRDM9 in promoting efficient homology search and DSB repair, both critical for meiotic progression and fertility. One consequence is that PRDM9 may play a wider role in mammalian speciation.

Made available in DSpace on 2014-06-11T19:24:49Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-01-30Bitstream added on 2014-06-13T19:47:28Z : No. of bitstreams: 1 silva_csf_me_bauru.pdf: 2718844 bytes, checksum: 6fd94a4eeb1edb620cf29512bc9deb3f (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A teoria evolutiva desempenha papel fundamental dentro das ciências biológicas, dado que possibilita a organização e a unificação do corpo de conhecimentos desta área. Em concordância com esta perspectiva, o ensino-aprendizagem de Biologia deve salientar a centralidade e a importância da evolução para este componente curricular. Entretanto, as pesquisas brasileiras sobre ensino de evolução biológica evidenciam uma série de obstáculos para a construção de conteúdos referentes à teoria evolutiva, bem como para a adoção da evolução como eixo central da disciplina de Biologia. A constatação e o reconhecimento de tais dificuldades impõem questões sobre os subsídios oferecidos pelos documentos oficiais da educação básico do Estado de São Paulo e pelas pesquisas acadêmicas sobre o ensino de evolução para enfrentamento das mesmas. Nesta perspectiva, poder-se-ia demarcar correspondências entre, de um lado, os indicadores de aprendizagem derivados das pesquisas acadêmicas sobre o ensino de conteúdos relacionados ao tema origem e evolução da vida e, de outro lado, o contexto escolar no qual ocorrem os processos de ensino-aprendizagem desta temática. Considerando as diferentes dimensões em relação às quais tais correspondências poderiam ser analisadas, o presente trabalho concentrou ênfase em investigar se os indicadores de aprendizagem referentes ao tema evolução derivados das pesquisas acadêmicas equivalentes ou consistentes com os descritores preconizados pelas matrizes de referência do Sistema de Avaliação de Rendimento Escolar do Estado de São Paulo (SARESP). Nestes termos, objetivamos com este estudo investigar e caracterizar as possíveis correspondências entre os descritores e as habilidades preconizadas em documentos oficiais da educação básica do Estado de São Paulo e os indicadores de aprendizagem expostos pelas pesquisas... / The evolutionary theory plays a fundamental role in the biological sciences, data that makes possible the organization and unification of the corpus of knowledge in this area. In agreement with this perspective, the Biology teaching and learning must highlight the centrality and the importance of the evolution for this curriculum component. However, the Brazilian researches on the teaching of biological evolution show a series of obstacles to building contents concerning to the evolutionary theory, as well as the adoption of the evolution as the central axis of the biology discipline. The fact and the recognition of these difficulties impose questions about the subsidies offered by official documents of the basic education in the State of São Paulo and by the academic researches on the teaching of evolution in order to face them. In this perspective, it could be able to demarcate correspondences between, on one hand, the learning, indicators derived from academic research on teaching content related to the subject origin and evolution of the life and on the other hand, the school context in which occur the teaching and learning processes of this subject. Considering the different dimensions on which such matches could be analyzed, this study focused emphasis on investigating whether the indicators of learning on the subject of evolution derived from academic researches would be equivalent to or consistent with the descriptors recommended by the matrices of reference of the Evaluation System of the School Performance of the State of São Paulo (SARESP). In these terms, this study aimed to investigate and characterize the possible matches between descriptors and the skills recommended in official documents of the basic education in the State of Sao Paulo and the indicators of learning exhibited by academic... (Complete abstract click electronic access below)

Orientador: Shirlei Maria Recco Pimentel / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T03:30:46Z (GMT). No. of bitstreams: 1 Bruschi_DanielPacheco_D.pdf: 18653513 bytes, checksum: 6cab8e91377d38b25d3a8a77e634c16a (MD5) Previous issue date: 2014 / Resumo: Dificuldades na identificação de populações e delimitação taxonômica de espécies, evidências de espécies crípticas e padrões biogeográficos diversos fazem dos anuros gênero Phyllomedusa (Hylidae, Phyllomedusinae) um interessante candidato a estudos taxonômicos e evolutivos. Na presente tese, foram realizados estudos visando acessar diferentes níveis de diferenciação entre os táxons e possibilitar inferência de eventos e processos envolvidos na diversificação das espécies, contribuindo no melhor entendimento das questões taxonômicas e evolutivas do gênero. Utilizando citogenética, filogenia molecular e filogeografia, investigamos aspectos da evolução cromossômica e molecular em representantes do gênero Phyllomedusa. No primeiro capítulo avaliamos o status taxonômico de populações atribuídas à P. hypochondrialis e P. azurea, utilizando dados morfológicos, cromossômicos e filogenia molecular. Reforçamos a dificuldade de distinção entre estas duas espécies baseado somente em seus caracteres de diagnose, já que estes se sobrepõem quando a amostragem é ampliada. Destacamos variações inter- e intrapopulacionais na posição da NOR em P. hypochondrialis. No segundo capítulo, para entender essa variação em P. hypochondrialis, delimitar as populações brasileiras de P. azurea e estimar a diversidade genética entre populações de P. nordestina, foi realizada uma análise filogeográfica dessas três espécies. As inferências filogenéticas indicaram forte estruturação regional entre as populações de P. hypochondrialis amostradas, recuperando quatro clados bem suportados. Processos demográficos históricos foram importantes na distribuição das variações de NOR, sendo que os clados demograficamente estáveis exibiram conservada posição de NOR no par 8, enquanto as populações que experenciaram eventos de rápida expansão demográfica exibiram variação neste marcador. A história evolutiva dessa espécie foi influenciada pela interação entre eventos geomorfológicos na transição Mioceno-Plioceno, que persistiram por episódios de flutuações climáticas ocorridas durante o Pleistoceno. As populações distribuídas dentro de domínios de cerrado demostraram uma recente colonização durante o Pleistoceno, sendo que hipotetizamos que sucessivos ciclos de expansão/retração de matas de galeria permitiram a colonização desta linhagem neste bioma. Recuperamos P. azurea parafilética em relação à P. nordestina. Interessantemente, os dois clados divergentes de P. nordestina estão separados pelo rio São Francisco (SF), definindo um clado localizado na margem esquerda e outro na margem direita desse rio. A estimativa do tempo de divergência entre estes dois grupos são condizentes com o reposicionamento histórico do curso deste rio no nordeste brasileiro, que deve ter contribuído no isolamento destes grupos por um processo de vicariância. Esta barreira geográfica teve papel fundamental na divergência entre as duas linhagens, suportada pelo alto nível de diferenciação entre os grupos de margens opostas do rio e ausência de fluxo gênico entre os grupos. Sugerimos futura reavaliação da taxonomia de populações distribuídas na margem esquerda do rio SF. A história evolutiva de P. azurea, foi marcada por um profundo evento de perda de diversidade genética, que deve ter contribuído para a rápida fixação dos alelos exclusivos encontrados nesta população. No terceiro capítulo, uma abordagem integrativa foi utilizada para descrição de uma nova espécie, filogeneticamente relacionada às espécies do grupo de P. hypochondrialis que habitam ambientes de altitude, condizente com a área na qual o táxon foi encontrado, revelando um interessante padrão biogeográfico. No quarto e quinto capítulo, descrevemos citogeneticamente cinco espécies (P. vaillantii, P. tarsius, P. bahiana, P. distincta e P. ayeaye). Observamos cariótipos conservados, possibilitando o reconhecimento de homeologias cromossômicas. Apesar de ainda existirem lacunas na citogenética do gênero, variações interessantes na posição da NOR reportam uma alta razão de transposição de sítios de rDNA no genoma destes representantes e alertam para seu papel na evolução cromossômica no gênero / Abstract: We conducted cytogenetic, phylogenetic and phylogeographical studies to investigate aspects of chromosomal and molecular evolution in the Neotropical tree frogs of the genus Phyllomedusa genus (Hylidae, Phyllomedusinae), which have been the subject of extensive taxonomical debate. In the first chapter, the study focuses on the morphological variation found in populations attributed to P. hypochondrialis, and examines whether this variation is interspecific or inter-population. The results of this analysis support the need for a thorough revision of the phenotypic features used to discriminate P. azurea and P. hypochondrialis, given the considerable overlap found in these characters when more populations are samples. We also report inter- and intra-population variability in the NOR of P. hypochondrialis. In the second chapter, we use phylogeographic approaches to evaluate the source of the karyotype variation found within P. hypochondrialis, provide a better delimitation of the Brazilian populations of P. azurea, and estimate the genetic diversity within P. nordestina. These three species are closely related, but are associated with distinct South American morphoclimatic domains. Our results reveal a deep genetic structuring in the P. hypochondrialis populations, based four well-supported clades with a low migration signal among haplogroups. The evolutionary history of this species has been influenced by the interaction between the geomorphological changes occurring in the Miocene-Pliocene that have persisted through the episodes of climatic fluctuation that occurred during the Pleistocene. The populations of the Cerrado domain appear to have colonized this region during the Pleistocene period, when successive cycles of forest expansion and retraction may have facilitated expansion into this biome via gallery forests. We were able to recognize two cryptic lineages within the P. nordestina populations, differentiated by the São Francisco River in northeastern of Brazil. Estimates of coalescence time indicated a process of divergence between two geographic clades of P. nordestina during the Pliocene-Pleistocene transition, which is temporally congruent with historical modifications to the course of the São Francisco River. This geographic barrier has had a primary role in the divergence of lineages, supported by the high differentiation between populations from opposite margins of the river and the absence of gene flow between haploclades. A strong signature of genetic decline marks the evolutionary history of the Brazilians populations of P. azurea. While more extensive surveys are needed, Brazilian populations of this species appear to be restricted to the Pantanal biome. In the third chapter, we describe a new species of the P. hypochondrialis group, diagnosed using molecular, morphological and chromosomal approaches. The new species is closely related phylogenetically with all the highland species of the clade, revealing an interesting biogeographical pattern. Finally, in chapters four and five, we present cytogenetic data on four species of the genus Phyllomedusa (P. vaillantii, P. tarsius, P. distincta, P. bahiana and P. ayeaye). We found conservative karyotypes, permitting the recognition of chromosomal homologies. Despite the gaps in the chromosomal studies of this genus, the inter- and intraspecific variation found in the number and location of rDNA sites reflects the rapid rate of evolution of this character in Phyllomedusa, and highlights the important role of this sequence in the chromosomal evolution of this genus / Doutorado / Biologia Celular / Doutor em Biologia Celular e Estrutural