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Elucidating the molecular machinery of an evolutionary novelty: Single-cell transcriptomics of Arcella intermedia and characterization of gene expression during shell formation / Elucidando a maquinaria molecular de uma novidade evolutiva: transcriptomica single-cell de Arcella intermedia e caracterização da expressão gênica durante a formação de tecaSousa, Alfredo Leonardo Porfirio de 14 February 2019 (has links)
The present dissertation aims to shed light on the molecular machinery involved in the process of shell formation (thecagenesis) in Arcella (Arcellinida : Amoebozoa). Arcellinida are single-celled testate amoebae organisms, characterized by the presence of an outer shell (test or carapace); it is a monophyletic lineage of Amoebozoa, sister group to a naked amoeboid lineage. No homologous structure to shell is present in the sister group of Arcellinida, thus it is considered an evolutionary novelty. The origin and evolution of the shell in Arcellinida are currently open questions; deciphering its formation process is a key step to address these questions. During each reproductive process by budding division, these organisms build a new shell. In the span of more than a century, several authors have described the thecagenesis process on Arcellinida, primarily focusing on the genus \\textit, based on cyto-morphological evidence. Conversely, the absence of molecular data has impaired advances on describing the molecular aspects of shell formation. In this study, we designed and applied a molecular framework to identify candidate genes and develop a molecular model for the shell formation process in Arcella; we based this framework on single-cell RNA-sequencing, gene expression profiling, Gene Ontology analysis, and comparative analysis of cyto-morphological with newly generated molecular data. We identify and propose a set of 539 genes as the candidate genes for shell formation, based on expression profiling and biological process assignment. We propose a model for the the shell formation process, which describes the mechanistic aspect of this process, hypothetically based on a molecular machinery conserved in Eukaryotes. Additionally, we identified a massive expansion of the Rab GTPase family, a protein likely to be involved on the process of shell formation. In the lights of the present study, we briefly discuss possible evolutionary scenarios involved on the origin and evolution of the shell and present future perspectives; we propose the shell of Arcellinida as a prosperous model to study the origin and evolution of evolutionary novelties, as well as other evolutionary questions / A presente dissertação tem como objetivo lançar luz sobre a maquinaria molecular envolvida no processo de formação de teca (tecagênese) em \\textit (Arcellinida: Amoebozoa). Arcellinida são amebas tecadas unicelulares, caracterizadas pela presença de uma teca (carapaça ou concha) externa; é uma linhagem monofilética de Amoebozoa, grupo irmão de alguns organismos amebóides nus. Nenhuma estrutura homóloga à carapaça está presente no grupo irmão de Arcellinida, sendo considerada como uma novidade evolutiva. A origem e evolução da carapaça em Arcellinida são questões em aberto; Decifrar seu processo de formação é um passo fundamental para abordar essas questões. Durante todo processo reprodutivo, por divisão por brotamento, estes organismo constroem uma nova concha. No decorrer de mais de um século, vários autores descreveram o processo de tecagênese nestes organismos, focando principalmente no gênero \\textit, baseados em evidências cito-morfológicas. Enquanto isso, a ausência de dados moleculares impede avanços na descrição dos aspectos moleculares da formação de conchas. Neste estudo, projetamos e aplicamos uma \\textit molecular para identificar genes candidatos e desenvolver um modelo molecular para o processo de formação de teca em \\textit; Baseamos este \\textit em sequenciamento de RNA \\textit, perfil de expressão gênica, análise de \\textit{Gene Ontology} e análise comparativa de dados cito-morfológicos e moleculares. Nós identificamos e propomos um conjunto de 539 genes como genes candidatos para a formação de carapaça, com base no perfil de expressão e na atribuição de processos biológica. Propomos um modelo para o processo de formação de carapaça, que descreve o aspecto mecanicista deste processo, hipoteticamente baseado em um mecanismo molecular conservado em Eucariotos. Além disso, identificamos uma expansão maciça da família gênica das Rab GTPase, gene provavelmente envolvida no processo de formação de carapaça. À luz do presente estudo, discutimos brevemente possíveis cenários evolutivos envolvidos na origem e evolução da teca e apresentamos perspectivas futuras; propomos a teca dos Arcellinida como próspero modelo para estudar a origem e evolução das novidades evolutivas, bem como outras questões evolutivas
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Taxonomia dos Arcellinida Kent, 1880 (Protista: Ramicristates) do parque ecológico do rio Tietê / Taxonomy of the Arcellinida Kent, 1880 (Protista: Ramicristates) of the Tiete River Ecological Park.Lahr, Daniel José Galafasse 13 April 2006 (has links)
O presente trabalho explora os aspectos taxonomicos, ecologicos, morfologicos, biometricos e biogeograficos dos Arcellinida Kent, 1880 coletados no Parque Ecologico do Rio Tiete, Sao Paulo Brasil. Foram encontrados organismos pertencentes a cerca de 30 taxons nominais, no entanto, a revisao da literatura, novos dados morfologicos obtidos atraves do Microscopio Eletronico de Varredura e medidas biometricas realizadas com grande numero de individuos permitem afirmar que muitos destes taxons estao se referindo a mesma entidade na natureza. Logo, na presente pesquisa sao descritas, com detalhes de distribuicao geografica, morfologia ultra-estrutural, morfometria e ecologia, especies pertencentes a quatro familias e cinco generos: Difflugia corona Wallich, 1864; Difflugia gramen Penard, 1902; Difflugia lanceolata Penard, 1890; Difflugia claviformis Penard, 1899; Difflugia gigantea Chardez, 1967; Centropyxis aculeata (Ehrenberg, 1838); Netzelia wailesi (Ogden, 1980); Lesquereusia modesta Rhumbler, 1895; Lesquereusia mimetica Penard, 1911; Arcella hemisphaerica Perty, 1852; Arcella gibbosa Penard, 1890; Arcella discoides Ehrenberg, 1871 e Arcella brasiliensis Cunha, 1913. Sao discutidas inovacoes taxonomicas para que a comparacao de dados obtidos usando tecnicas atuais com aqueles reportados na literatura tradicional seja feita da maneira mais explicita possivel, de modo a delimitar melhor o conceito taxonomico de cada especie abordada. / The present survey explores the taxonomic, ecologic, morphologic, biometric and biogeographic aspects of the Arcellinida Kent, 1880 collected at the Ecological Park of the Tiete River, Sao Paolo Brazil. Around 30 nominal taxa were identified, however, a review of the literature and new morphologic data obtained via the Scanning Electron Microscope and biometric measures with a large number of individuals allow the inference that many of these taxa are referring to the same natural entity. Therefore, the present work describes species from four families and five genera, along with details about geographic distribution, ultra-structural morphology, morphometry and ecology: Difflugia corona Wallich, 1864; Difflugia gramen Penard, 1902; Difflugia lanceolata Penard, 1890; Difflugia claviformis Penard, 1899; Difflugia gigantea Chardez, 1967; Centropyxis aculeata (Ehrenberg, 1838); Netzelia wailesi (Ogden, 1980); Lesquereusia modesta Rhumbler, 1895; Lesquereusia mimetica Penard, 1911; Arcella hemisphaerica Perty, 1852; Arcella gibbosa Penard, 1890; Arcella discoides Ehrenberg, 1871 e Arcella brasiliensis Cunha, 1913. Taxonomic innovations are discussed in order to make comparison of recent data with those reported on traditional literature a more explicit practice, allowing a better understanding of each species taxonomic concept.
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Taxonomia dos Arcellinida Kent, 1880 (Protista: Ramicristates) do parque ecológico do rio Tietê / Taxonomy of the Arcellinida Kent, 1880 (Protista: Ramicristates) of the Tiete River Ecological Park.Daniel José Galafasse Lahr 13 April 2006 (has links)
O presente trabalho explora os aspectos taxonomicos, ecologicos, morfologicos, biometricos e biogeograficos dos Arcellinida Kent, 1880 coletados no Parque Ecologico do Rio Tiete, Sao Paulo Brasil. Foram encontrados organismos pertencentes a cerca de 30 taxons nominais, no entanto, a revisao da literatura, novos dados morfologicos obtidos atraves do Microscopio Eletronico de Varredura e medidas biometricas realizadas com grande numero de individuos permitem afirmar que muitos destes taxons estao se referindo a mesma entidade na natureza. Logo, na presente pesquisa sao descritas, com detalhes de distribuicao geografica, morfologia ultra-estrutural, morfometria e ecologia, especies pertencentes a quatro familias e cinco generos: Difflugia corona Wallich, 1864; Difflugia gramen Penard, 1902; Difflugia lanceolata Penard, 1890; Difflugia claviformis Penard, 1899; Difflugia gigantea Chardez, 1967; Centropyxis aculeata (Ehrenberg, 1838); Netzelia wailesi (Ogden, 1980); Lesquereusia modesta Rhumbler, 1895; Lesquereusia mimetica Penard, 1911; Arcella hemisphaerica Perty, 1852; Arcella gibbosa Penard, 1890; Arcella discoides Ehrenberg, 1871 e Arcella brasiliensis Cunha, 1913. Sao discutidas inovacoes taxonomicas para que a comparacao de dados obtidos usando tecnicas atuais com aqueles reportados na literatura tradicional seja feita da maneira mais explicita possivel, de modo a delimitar melhor o conceito taxonomico de cada especie abordada. / The present survey explores the taxonomic, ecologic, morphologic, biometric and biogeographic aspects of the Arcellinida Kent, 1880 collected at the Ecological Park of the Tiete River, Sao Paolo Brazil. Around 30 nominal taxa were identified, however, a review of the literature and new morphologic data obtained via the Scanning Electron Microscope and biometric measures with a large number of individuals allow the inference that many of these taxa are referring to the same natural entity. Therefore, the present work describes species from four families and five genera, along with details about geographic distribution, ultra-structural morphology, morphometry and ecology: Difflugia corona Wallich, 1864; Difflugia gramen Penard, 1902; Difflugia lanceolata Penard, 1890; Difflugia claviformis Penard, 1899; Difflugia gigantea Chardez, 1967; Centropyxis aculeata (Ehrenberg, 1838); Netzelia wailesi (Ogden, 1980); Lesquereusia modesta Rhumbler, 1895; Lesquereusia mimetica Penard, 1911; Arcella hemisphaerica Perty, 1852; Arcella gibbosa Penard, 1890; Arcella discoides Ehrenberg, 1871 e Arcella brasiliensis Cunha, 1913. Taxonomic innovations are discussed in order to make comparison of recent data with those reported on traditional literature a more explicit practice, allowing a better understanding of each species taxonomic concept.
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Phylogenics and Patterns of Molecular Evolution in AmoebozoaLahr, Daniel J.G. 01 September 2011 (has links)
My dissertation explores several aspects of the relationship between morphological and molecular evolution in amoeboid lineages:
Chapter 1 - General Introduction: This chapter provides an overview of the most pressing issues in Amoebozoa phylogeny that are dealt with in the remainder of the thesis
Chapter 2 - Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new generation high fidelity DNA polymerase: This chapter addresses the methodological difficulty in the study of large gene families, the generation of artifactual sequences by recombination during PCR.
Chapter 3 - Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent expansions: This chapter explores intriging patterns of evolution in the actin gene families of testate amoebae.
Chapter 4 - Comprehensive phylogenetic reconstruction of Amoebozoa based on concatenated analysis of SSU-rDNA and actin genes: A deep phylogenetic analyses of the Amoebozoa, enables exploration of well supported taxonomic units within the group.
Chapter 5 - Interpreting the evolutionary history of the Tubulinea (Amoebozoa), in light of a multigene phylogeny: This chapter explores a more restrict taxonomic unit within the Amoebozoa - the Tubulinea - based on an expanded sample of genes and taxa.
Chapter 6 - The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms: This chapter asks whether the null-hypothesis that amoebae are asexual is consistent with current phylogenetic evidence
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