Submitted by Irene Nascimento (irene.kessia@ufpe.br) on 2016-08-12T19:39:07Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese_versão_final_biblioteca_português.pdf: 2265965 bytes, checksum: 707851ccf48e28513fc34178bca7c739 (MD5) / Made available in DSpace on 2016-08-12T19:39:07Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese_versão_final_biblioteca_português.pdf: 2265965 bytes, checksum: 707851ccf48e28513fc34178bca7c739 (MD5) Previous issue date: 2016-03-04 / Capes / Cromossomos holocêntricos apresentam atividade cinetocórica difusa e essa organização favorece, em teoria, rápidas variações cromossômicas numéricas e o acúmulo de DNA satélite (DNAsat) predominantemente nas regiões terminais dos cromossomos. O gênero de plantas Rhynchospora (Cyperaceae), um dos diversos grupos com esse tipo cromossômico, apresenta espécies com cariótipos entre 2n = 4 e 2n = 58, cuja variação é atribuída à poliploidia e a eventos de quebra/fusão, levando a disploidias. Quanto à distribuição de DNAsat, o único relato até o momento revelou uma baixa proporção dessas sequências, com o único repeat identificado (Tyba) associado aos holocentrômeros. Com o intuito de entender como a estrutura centromérica difusa interfere na organização de sequências ao longo do cromossomo e na evolução do cariótipo como um todo, foram realizadas uma análise de reconstrução dos números cromossômicos ancestrais de Rhynchospora em um contexto filogenético e a caracterização de DNAsats em três espécies do gênero. O complemento cromossômico 2n = 10 foi indicado como o mais provável para o ancestral do gênero, tendo sido mantido em diferentes taxa. A maioria dos clados mostrou números estáveis e a homoplasia de cariótipos foi observada em uma frequência relativamente baixa. Os genomas de R. ciliata/R. globosa e R. tenuis apresentaram duas e uma família(s) de DNAsat, respectivamente, com um padrão de condensação típico (blocos condensados em intérfase). Uma localização preferencial nos terminais cromossômicos foi observada apenas para os DNAsat de R. globosa. Três tipos de cromatina foram revelados pela distribuição dessas sequências: (1) associadas à heterocromatina e presente na forma de cromocentros em intérfase e blocos nos cromossomos metafásicos (R. ciliata e R. globosa); (2) compactados em interfase mas parcialmente descondensados em metáfase e não diretamente associados à heterocromatina (R. ciliata e R. tenuis); ou (3) associados aos holocentrômeros (R. ciliata e R. tenuis). De forma geral em Rhynchospora, os eventos de fusão e fissão parecem atuar localmente no remodelamento dos cariótipos e as sequências satélites não mostram uma tendência única de distribuição. A estrutura centromérica difusa, portanto, não determina em larga escala a dinâmica evolutiva dos cromossomos do gênero. / Holocentric chromosomes show diffuse kinetochore activity, what would lead to fast evolution of chromosome numbers and a biased distribution of satellite repeats. The plant genus Rhynchospora (Cyperaceae) possesses holocentric chromosomes and shows a large chromosome number variation (2n = 4 to 2n = 58) attributed to polyploidy and frequent fusion/fission events, leading to dysploidy. Regarding satellite repeats (satDNA), the only investigated species showed a low proportion of these sequences, with the single family identified associated to the holocentromeres. In the present work, aiming to better understand how the diffuse centromere organisation could interfere with the distribution of satellite repeats along the chromosomes and with the karyotype evolution as a whole, we combined a reconstruction of Rhynchospora chromosome numbers in a phylogenetic framework and the characterisation of satellite repeats in three selected species. The karyotype with 2n = 10 was suggested as the ancestral state and was maintained in different lineages. Most of the clades showed stable chromosome number and recurrent karyotypes changes (leading to homoplasies) were detected in low frequency. All Rhynchospora species analysed (R. ciliata, R. globosa and R. tenuis) showed a higher diversity of satellite repeats than R. pubera, with most of the repeats showing a typical condensation profile (clustered in interphase). A preferential terminal location on chromosomes was only observed for R. globosa satDNAs. These sequences, however, might represent different chromatin types, organized in distinct ways: (1) associated to the heterochromatin and clustered in interphase and metaphase (identified in R. ciliata and R. globosa only); (2) clustered in interphase but partially decondensed in metaphase and not associated to heterochromatin domains (R. ciliata e R. tenuis); (3) associated to the holocentromeres (R. ciliata e R. tenuis). Taken together, at least for Rhynchospora, fusion/fission events may not act in a broader way in the reshuffling of karyotypes and satellite repeats distribution do not appeared to be biased towards the chromosome termini. A non-localized centromere, therefore, must not constrain, in a large scale, the chromosome evolution of the genus.

This master thesis focuses on the phylogeny of hybridogenous and polyploid genus Curcuma from family Zingiberaceae using Next-Generation Sequencing data from hundreds to thousands nuclear loci. This approach seems to be better than widely used cpDNA and ITS sequencing especially in the case of hybridogenous and polyploid groups. Data for phylogeny reconstruction were generated using Hybridization-based sequencing (Hyb-Seq) method which combines target enrichment and genome skimming strategies. Data analysis was performed primarily using pipeline HybPhyloMaker especially created for Hyb-Seq data analysis. Twenty-seven species from the genus Curcuma and three outgroup species were sequenced in this work. Phylogenetic trees based on all 1 154 and 811 selected nuclear low- copy genes show high support values of all nodes which is in contrast to plastome and rDNA phylogeny with lower support values in some nodes and incongruences in topology compared to low-copy genes phylogeny. Phylogenetic networks inferred from low-copy genes, lineage movement analysis and monophyly tests agree with published hypotheses of interlineage hybrid origin of three species - C. vamana, C. myanmarensis and C. roscoeana. These analyzes show likely hybrid origin of C. candida too with parents from the group Curcuma I and basal...

A protein, B0238.11, was identified in a yeast one-hybrid screen to bind to the ribosomal intergenic spacer region (IGS) of Caenorhabditis elegans. Proteins interacting with this region of the DNA have been implicated in ribosome biogenesis in other model organisms, so it is also possible that B0238.11 plays a role in RNA transcription by interacting with RNA polymerase I or other transcription machinery. Thus, the goal of this study was to further characterize the structure and function of B0238.11. I used yeast two-hybrid experiments to identify proteins that interact with B0238.11 within the nucleus. RPS-0, K04G2.2, DPY-4, EFT-3, PAL-1, and B0238.11, itself, were found to bind to B0238.11. Additionally, I analysed the amino acid sequence of B0238.11 using in silico bioinformatics methods to determine its structure and putative function and also to identify and characterize the other interacting proteins. I found that B0238.11 contains a high-mobility group box domain, which is also found in HMO1P in yeast and UBF in vertebrates. These other proteins also bind to the IGS, are known to form homodimers and have been implicated in the initiation of ribosomal RNA transcription. Here I scrutinize the validity of the interaction between each protein and B0238.11. I conclude that B0238.11 is likely to be a C. elegans homolog of UBF and present an updated interactome map for B0238.11. / Synopsis: I carried out yeast two-hybrid assay to find proteins interacting with B0238.11 (O16487_CAEEL). I found that this protein's DNA-binding profile and protein interaction profile mimic other HMG-box containing proteins UBF and HMO1P which are involved in ribosomal RNA transcription initiation. Acknowledgements: I would like to thank my supervisor, Dr. Teresa J. Crease, for not only giving me the opportunity to investigate an interesting topic in Molecular Biology, but also for her patient guidance, encouragement and sound advice. I feel extremely lucky to have a supervisor who cared so much about my work, who responded to my questions and queries so promptly, and was always available to discuss project and career related matters. I would also like to thank Dr. Todd Gillis and Dr. Terry Van Raay for their careful consideration of this project and timely constructive criticisms that helped shape my project. I would like to thank all the members of my committee for helping me see things from different perspectives and helping me develop and critical and mature understanding of the scientific process. I must also express my gratitude to Dr. Robin Floyd for allowing me to build upon his work and Dr. Marian Walhout, at the University of Massachusetts, for providing the Caenorhabditis elegans complimentary DNA library. A large part of this project would not have been possible without the people at the genomics facility in the Department of Integrative Biology, I commend their professionalism and punctuality in delivering results. Completing this work would have been all the more difficult were it not for the support and friendship provided by my peers Shannon Eagle, Tyler Elliott, Nick Jeffery, Joao Lima, Sabina Stanescu, Fatima Mitterboeck and Paola Pierossi. And finally, I would like to thank my parents and siblings Sara Omar and Ali Omar for their continued support through good times and bad, and letting me use their laptops when mine broke down.

Alstonia scholaris is an evergreen tree native to Southeast Asia and Australia. It is commonly used as a medicinal plant throughout these regions. In the present study, an endophyte of the genus Xylaria was isolated from a stem of Alstonia scholaris, its mycelia and exudate extracted, and the extract assayed for growth inhibition of HeLa cancer cells in vitro. Several known compounds were isolated and identified based on NMR, infrared, and mass spectral data. The compounds identified are 19,20-epoxycytochalasin C; 19,20epoxycytochalasin D; and xylobovide. Two other compounds, fusaric acid and dehydrofusaric acid, were discovered in an endophyte of the Hypocreales family inhabiting the plant Acmena Graveolens.