We applied culture-independent, next-generation sequencing (NGS) high throughput pyrosequencing, to characterize the microbial communities associated with near shore seawater in Broward County, FL. These waters flow over coral reef communities, which are part of the Florida reef tract, and are close to shore where bathers frequent. Through a close partnership with the NOAA FACE program, 38 total seawater samples were taken from 6 distinct locales -the Port Everglades and Hillsboro Inlets, Hollywood and Broward wastewater outfalls, and the associated reef waters-over the course of one year. Tagged 16S rRNA amplicons were used to generate longitudinal taxonomic profiles of marine bacteria and archaea for one year. 236,322 rRNA quality checked sequences with an average length of 250 base pairs were generated. Sequences were found to vary significantly due to seasonal effects, but depth showed no significant correlation. The most abundant taxa among these samples included Synechococcus, Pelagibacteraceae (SAR11), Bacteroidetes, various Proteobacteria, and Archaea, such as Thermoplasmata. Other taxa found, albeit in low numbers, were the Thiotrichales, and some members of which can indicate pollution, the Alteromonadales, a biofilm forming order. Inlet sequences were found to be significantly different from the outfall and reef communities by various analyses. Unifrac analysis of microbial beta diversity showed a significant clustering pattern for the inlet samples. Precipitation during the three days before and after sampling was low meaning there was little to no high terrestrial runoff during the sampling days. Higher levels of turbidity were seen at the inlet sites and significantly affected the growth of surface colonizing and biofilm forming bacterial families such at the Rhodobacteraceae and Flavobacteriaceae. This study represents one of the first to apply NGS analyses for a deep analysis of microbial community dynamics in these S. Florida waters.

No description available.

>Magister Scientiae - MSc / The class Actinobacteria consists of a heterogeneous group of filamentous, Gram-positive bacteria that colonise most terrestrial and aquatic environments. The industrial and biotechnological importance of the secondary metabolites produced by members of this class has propelled it into the forefront of metagenomics studies. The Ethiopian Rift Valley lakes are characterized by several physical extremes, making it a polyextremophilic environment and a possible untapped source of novel actinobacterial species. The aims of the current study were to identify and compare the eubacterial diversity between three geographically divided soda lakes within the ERV focusing on the actinobacterial subpopulation. This was done by means of a culture-dependent (classical culturing) and culture-independent (DGGE and ARDRA) approach. The results indicate that the eubacterial 16S rRNA gene libraries were similar in composition with a predominance of α-Proteobacteria and Firmicutes in all three lakes. Conversely, the actinobacterial 16S rRNA gene libraries were significantly different and could be used to distinguish between sites. The actinobacterial OTUs detected belonged to both the Rubrobacterales and Actinomycetales orders with members of the genus Arthrobacter being found in all three lakes. Geochemical properties were significantly different between the lakes, although more than one property attributed to the variance between community compositions. The diversity detected in the culture-based study differed significantly and all isolates belonged to the genus Streptomyces. Two novel strains were characterized by means of phylogenetic (16S rRNA gene sequence), physiological, morphological and biochemical analyses. Both novel isolates were capable of growing under "extreme" conditions- pH 12, 10% NaCl and 45°C. Partial enzyme characterization revealed that both strains produced xylanase enzymes that were active at pH 6.5 and 8.5 with an increase in activity up to 45°C. The results obtained revealed a previously undetected diversity of actinobacteria in the Ethiopian Rift Valley with a potentially novel subpopulation adapted to haloalkaline conditions. The low 16S rRNA sequence similarity of a substantial proportion of the libraries suggests that culture-based isolation may play a vital role in deciphering the community fingerprint. / The National Research Foundation and the Norwegian Research Council

Duas linhagens filogenéticas principais (LI e L2) foram definidas em Trypanosoma cruzi, com base em sequências de genes de rDNA e mini-exon e análise por RAPD (Souto et al. 1996). Neste trabalho investigamos a estrutura e atividade dos promotores do cistron ribossômico das duas linhagens de T. cruzi. O promotor da cepa Dm28 (L2) foi clonado e sua seqüência foi comparada com seqüências publicadas da região homóloga de CL (L1) e La Cruz (L2). A identidade entre os dois promotores de L2 foi de 98%, e entre estes e o de L1 foi de 82%. O ponto de início de transcrição foi mapeado, apresentando a mesma localização nas duas linhagens. A atividade dos promotores de L1 e L2 foi determinada em construções plasmidiais contendo o gene reporter da cloranfenicol acetil transferase (CAT). Experimentos de expressão transitória mostraram que o promotor de L1 foi funcional apenas em isolados de L1, enquanto que o promotor de L2 foi funcional em ambas as linhagens. A expressão do promotor de L2 em isolados de L1 foi maior do que a do promotor homólogo. Analisamos ainda a atividade dos dois promotores em um grupo de isolados que apresentam dois tipos de cistrons ribossômicos (grupo 1/2). Neste grupo de cepas observamos que ambos os promotores presentes nas construções são funcionais, embora o promotor de L2 induza maior expressão de CAT. Por outro lado, demonstramos que nestes isolados apenas o cistron ribossômico de tipo 2 é expresso in vivo. Neste trabalho analisamos ainda a eficiência de entrada das construções plasmidiais nas cepas de T. cruzi; caracterizamos a atividade de regiões do promotor de L2 e a eficiência do processo de \"trans-splicing\" para gerar mRNA de CAT contendo a seqüência de mini-exon na extremidade 5\'. / Two major phylogenetic lineages (L1 and L2) have been defined in Trypanosoma cruzi based on rDNA and mini-exon sequences and RAPD analysis (Souto et al., 1996). In the present work we have investigated the structure and activity of ribosomal RNA promoters from the two T. cruzi lineages. The promoter region of Dm28 strain (L2) was cloned and its sequence was compared with the homologous regions from the CL (L1) and La Cruz (L2) strains, whose sequences were previously published. The identity found between promoters of the two L2 strains was 98%, while the identity between L2 and L1 promoters was 82%. The transcription start point mapped in the two Lineages showed the same localization. The activity of L1 and L2 promoters was investigated through the use of plasmid constructs bearing bacterial chloramphenicol acetyl transferase (CAT) as reporter gene. Experiments of transient expression showed that the L1 promoter drove high CAT activity in L1 isolates, but essentially no activity in L2 strains. On the other hand, L2 promoter was functional in both Lineages. The expression driven by L2 promoter in L1 isolates was higher than that driven by the homologous promoter. We have also analysed the activity of both L1 and L2 promoters in a particular group of T. cruzi isolates (group 1/2) which contains two types of rRNA cistrons. It was observed that both promoters were functional in this group of strains, although L2 promoter drove higher CAT activity. This is an interesting result since we have shown that in group 1/2 isolates only the type 2 rRNA cistron is expressed in vivo. In the present study, we have also analysed the transfection efficiency of the plasmid constructs in T. cruzi strains; the activity of segments of the L2 promoter; and the efficiency of the \"trans-splicing\" process involved in the generation of mature CAT mRNA containing the mini-exon sequence at the 5\' end.

Os peixes apresentam uma grande diversidade quanto a sua morfologia, seus habitats e também sua biologia. São encontrados em lagos, córregos, estuários e oceanos, constituindo assim mais de 50% do número total das espécies de vertebrados conhecidas atualmente. Essa fauna tem sido objeto de um número expressivo de estudos citogenéticos e moleculares, tendo-se já conhecimento não só das relações cromossômicas, mas também da sistemática de vários grupos. Essas pesquisas têm investigado não somente o número e fórmula cromossômica, mas também a presença de cromossomos sexuais diferenciados, presença de cromossomos supranumerários, padrões de distribuição da heterocromatina, localização das regiões organizadoras de nucléolo, padrões de bandamento de restrição e replicação, permitindo a localização de diferentes classes de DNAs repetitivos, bem como a identificação de homeologias cromossômicas que auxiliam a compreensão da evolução cariotípica dos grupos. Os estudos moleculares, por sua vez, têm se tornado cada vez mais importantes nesse grupo e têm fornecido dados fundamentais não só no que diz respeito à filogenia dos grupos, como também em relação a regiões repetitivas do DNA e sua importância no genoma. A união dessa área com a Citogenética tem permitido uma maior e melhor compreensão sobre os processos evolutivos associados às alterações de seqüências específicas do genoma visíveis tanto a níveis cromossômicos, quanto moleculares. O gênero Gymnotus (Teleostei: Gymnotiformes) inclui representantes com características biológicas peculiares, o que os torna objeto de estudo de diversas áreas da Biologia. Estudos sobre o gênero incluem sua caracterização cariotípica, estudo das regiões organizadoras de nucléolo (RONs) polimórficas, bem como estudos envolvendo marcadores moleculares, os quais conjuntamente com a Citogenética permitiram a análise de filogenética molecular, com inferência na evolução cromossômica, permitindo uma melhor compreensão das relações dentro do gênero. No presente trabalho foram levados a efeito estudos sobre as regiões heterocromáticas e os DNAs repetitivos desse grupo, para uma melhor compreensão da organização e localização dessas seqüências no genoma e a identificação de possíveis marcadores moleculares. Foram efetuados ainda, estudos envolvendo a evolução cariotípica das espécies G. carapo e G. sylvius, localização de genes ribossômicos e análise molecular do gene ribossômico 5S juntamente com seu espaçador não transcrito, propiciando uma melhor compreensão da evolução dessa família gênica em Gymnotus. / Fishes present a great diversity in relation to their morphology, habitat and biology. They are found in lakes, rivers, estuaries and oceans, comprising more than 50% of the total number of known vertebrates. Cytogenetic and molecular aspects of the fish fauna have been extensively studied, providing information about their chromosomal relationships and also about the systematic status of several groups. These researches have focused on the description of both chromosomal number and formula as well as the presence of differentiated sex chromosomes, occurrence of B-chromosomes, patterns of heterochromatin distribution, localization of nucleolar organizer regions, restriction or replication banding profiles allowing to locate distinct classes of repetitive DNAs and to identify chromosomal homeologies in order to understand the karyotypic evolution in distinct groups. On the other hand, molecular studies have become of utmost importance in this group, providing essential data about phylogeny of many groups and about repetitive DNA regions and their role in the genome. The union between this approach and cytogenetics has favored a better comprehension about the evolutionary processes associated with visible alterations in specific sequences within the genome at both chromosomal and molecular levels. The genus Gymnotus is composed of representatives with peculiar biological features, which turn them suitable for studies in a variety of biology approaches. Genetic studies in this genus comprise karyotype characterization, analysis of polymorphic NORs, besides studies of molecular markers that, coupled with cytogenetics, have fostered molecular phylogenetic analyzes with inferences on their chromosomal evolution, which have led to a better understanding about the interrelationships in the group. In the present work, we carried out studies about the heterochromatic regions and the repetitive DNAs in this group for a better comprehension about the organization and localization of these sequences in the genome and identification of potential molecular markers. Furthermore, studies related to the karyotype evolution in the species G. carapo and G. sylvius, location of ribosomal genes and molecular analysis of both 5S ribosomal gene and its non-transcribed spacer were performed to provide a better comprehension about the evolution of this gene family in Gymnotus.

O estudo sobre a cinética de incorporação de uridina em ácidos nucleicos permitiu estabelecer que o tamanho do \"pool\" de precursores permanece constante na presença de concentrações de uridina exógena acima de aproximadamente1 µM. Concluiu-se ainda que todo o sistema de tomada de uridina, medido pela sua incorporação em ácidos nucleicos, apresenta um Km de 5,1 µM e opera a uma velocidade máxima de 11 pmoles/min/l,3 x 107 células. Um estudo análogo, em presença de rifampicina, possibilitou calcular que a meia vida de RNAs mensa - geiros em B. subtilis é de 2 minutos e que 44% da radiatividade incorporada em RNA num determinado instante se encontra na fração de RNA estável (ribossômico e de transferência). A análise do mecanismo de transcrição dos genes para RNA ribossômico foi abordada por meio do estudo do alongamento de cadeias de rRNA já iniciadas, em presença de rifampicina. As relações iniciais de radiatividade incorporada em rRNA 16S e 23S, quando rifampicina e uridina tritiada são adicionadas concomitantemente, bem corno a cinética de decaimento de marcação presente em ambas as espécies de rRNA sugerem que os genes para RNA ribossômico 16S e 23S são cotranscritos nessa ordem, em B. subtilis. Levando-se em consideração essas e outras evidências, propõe-se o seguinte relacionamento estrutural para a unidade de transcrição: [Obs.: Ver no arquivo em PDF] Os resultados experimentais foram comparados com modelos teóricos descritos no Apêndice. A existência de um mecanismo de cotranscrição para os genes responsáveis pela síntese de rRNA em procariotos e eucariotos parece sugerir que esse mecanismo, de fundamental importância, instalou-se precocemente e foi mantido durante a evolução. / The kinetics of uridine incorporation into nucleic acids has shown that the precursor pool size remains constant in the presence of exogenous uridine concentrations above 1 µM, approximately. It has also been shown that the whole system of uridine uptake, as measured by the incorporation of uridine into nucleic acids, has an apparent Km of 5.1 µM and operates at a maximal rate of 11 pmoles/min/ 1.3 x 107 cells. The incorporation, in the presence of rifampicin, made it possible to calculate the half life of the messenger RNA\'s in B.subtilis as being 2 minutes. In any given instant, 44% of the radioactivity incorporated into RNA belongs to the stable RNA fraction (ribosomal and transfer). The analysis of the ribosomal RNA genes transcription mechanism was undertaken by a study of the rRNA chain elongation in the presence of rifampicin. The initial ratios of radioactivity incorporated in 16S and 23S rRNA\'s, when rifampicin and tritiated uridine are concomitantly added, and the decay kinetics of the radioactivity present in both rRNA species, suggest that the 16S and 23S rRNA genes are cotranscribed, in that order, in B.subtilis. Taking into consideration these and other evidences, the following structural relationships are proposed for the transcriptional unit: The experimental results were compared with theoretical models described in the Appendix. The existence of a cotranscription mechanism for the rRNA genes in prokaryotes and eukaryotes seems to suggest that such mechanism, being of fundamental importance, established itself very early and was maintained through evolution.

Rickettsia rickettsii é o agente etiológico da Febre Maculosa das Montanhas Rochosas, que no Brasil é transmitida pelos carrapatos Amblyomma cajennense e A. aureolatum. Para elucidar os mecanismos de virulência sobre seus vetores, construímos bibliotecas subtrativas utilizando RNA de A. aureolatum infectados ou não com o patógeno. Com a análise bioinformática, foram obtidas 56 sequências únicas com expressão induzida e 12 com expressão reprimida pela infecção. Após a validação dos dados por RT-qPCR 3 genes foram caracterizados por RNAi: uma hebraeína, uma proteína dissulfeto isomerase (PDI) e uma proteína com domínio Kunitz-type. Um maior número de carrapatos adquiriu R. rickettsii quando a expressão gênica da hebraeína e da PDI foi silenciada, sugerindo que elas participam na defesa do carrapato contra a infecção. Nenhum efeito foi observado sobre a transmissão da bactéria para o hospedeiro ou sobre o fitness de carrapatos nos três genes analisados. O presente estudo apontou genes importantes que possibilitam uma melhor compreensão da relação carrapato-riquétsia. / Rickettsia rickettsii is the etiological agent of Rocky Mountain Spotted Fever and, in Brazil, it is transmitted by Amblyomma cajennense and A. aureolatum. To elucidate mechanisms of virulence to its vectors, we construct cDNA libraries with RNA of ticks A. aureolatum infected or not with this pathogen. After bioinformatic analysis, 56 unique sequences were obtained representing up-regulated genes and 12 down-regulated by infection. After data validation by RT- qPCR, 3 genes were characterizated by RNAi: a hebraein, a protein disulfide isomerase (PDI), and a protein with Kunitz-type domain. A higher number of ticks acquired R. rickettsii when the gene expression of hebraein and PDI was silenced, suggesting that both proteins participate in the defense of the tick against infection. No effect on the transmission of the bacterium to the host or on the fitness of ticks was observed after knockdown of the 3 analyzed genes. Data obtained by the present study pointed out important genes that provide information to better understand of the tick-rickettsia relationship.

L'expression des ARN mitochondriaux et chloroplastiques des plantes implique un grand nombre de modifications post-transcriptionnelles, parmi lesquelles l'épissage des introns est un processus essentiel. Sur la base de leur structure et des mécanismes d'épissage associés, les introns peuvent être classés en deux familles et ceux présents dans les organites des plantes appartiennent au groupe II. Les introns mitochondriaux et chloroplastiques de groupe II sont fortement dégénérés et ont perdu la capacité de s'auto-épisser in vivo. Leur élimination nécessite l’action de nombreux facteurs protéiques codés dans le noyau et importés dans les organites. Les protéines de liaison à l'ARN jouent un rôle prédominant dans ce processus complexe. Les protéines ribosomales sont des protéines abondantes se liant à l'ARN et peuvent être recrutées pour remplir diverses fonctions annexes. Au cours de ma thèse, j’ai étudié la fonction des protéines de type uL18 chez Arabidopsis, qui comprend 8 membres. Ces protéines partagent un domaine uL18 plutôt dégénéré, mais dont la structure est conservée, et dont la fonction initiale est de permettre l’association avec l’ARNr 5S. Nos résultats ont montré que cinq protéines de type uL18 sont adressées aux mitochondries et trois aux chloroplastes. Deux d’entre elles correspondent à de véritables protéines ribosomales uL18 associées aux ribosomes des organites, tandis que deux autres (uL18-L1 et uL18-L8) se sont transformées en facteurs d'épissage et sont nécessaires à l'élimination d’introns mitochondriaux ou chloroplastiques spécifiques. L'analyse d'un troisième membre de la famille, uL18-L5, a révélé qu'il participait à l'épissage de nombreux introns mitochondriaux. Mes résultats ont permis de révéler que les facteurs dérivés des protéines ribosomales uL18 jouent un rôle essentiel dans l’épissage des introns du groupe II mitochondriaux ou chloroplastiques chez les végétaux et que ces fonctions ciblent sot un seul intron ou bien plusieurs d’entre eux. / RNA expression in plant organelles implies a large number of post-transcriptional modifications in which intron splicing is an essential process. Based on RNA structures and splicing mechanisms, introns can be classified into two families and organellar introns of seed plants are categorized as group II. Organellar group II introns are highly degenerate and have lost the ability to self-splice in vivo. Their removal from transcripts is thus facilitated by numerous nuclear-encoded proteins that are post-translationaly imported into organelles. Among them, RNA binding proteins play predominant roles in this complex process. Ribosomal proteins are abundant RNA-binding proteins and could be recruited to carry out multifarious auxiliary functions. During my thesis, I investigated the function of the uL18 ribosomal-like protein family in Arabidopsis that comprises 8 members. The members of this protein family share a rather degenerate but structurally conserved uL18 domain whose original function is to permit association with the 5S rRNA. Our results showed that five uL18-Like proteins are targeted to mitochondria and three to chloroplasts. Two of these proteins correspond to real ribosomal uL18 proteins that incorporate into organellar ribosomes, while two other members (uL18-L1 and uL18-L8) have turned into splicing factors and are required for the removal of specific mitochondrial or plastid group II introns. The analysis of a third member, uL18-L5, revealed that it participated in the splicing of numerous mitochondrial introns. Our results revealed that uL18-like factors play essential roles in group II intron splicing in both mitochondria and plastids of plants and that these functions could target a single or multiple introns.

No description available.

No description available.