T. cruzi compreende populações heterogêneas classificadas nas linhagens TCI e TCIIa-e. Neste estudo, foi caracterizado um grande número de isolados de mamíferos e vetores silvestres de diversas origens geográficas, além de isolados humanos da Amazônia. Análises filogenéticas baseadas em SSU rDNA e Cyb foram utilizadas para inferir relações entre linhagens e padrões biogeográficos. Além de análises ITS1 rDNA e RAPD para detectar polimorfismo intraespecífico. TCIIa circula em primatas e é transmitida por Rhodnius, no ecótopo arbóreo da Amazônia brasileira ocasionalmente infectando o homem. TCI é mais prevalente em macacos e no homem na Amazônia onde pode causar doença severa, como demonstramos no Nordeste. No Brasil, morcegos são infectados por três espécies de tripanossomas, incluindo uma nova linhagem de T. cruzi (TCbat). Foram caracterizados T. rangeli de macacos e morcegos. A linhagem TCIIc possui ampla distribuição no Brasil, associada com mamíferos e triatomíneos terrestres. Isolados TCIIa dos USA pertencem a uma linhagem, aparentemente ausente no Brasil. / T. cruzi comprises highly heterogeneous populations classified as TCI and TCIIa-e lineages. This study characterized large wild mammal and vector strains of various geographical origins, and human isolates from Amazonia. Phylogenetic analysis using SSU rDNA and Cyb genes inferred relationships among lineages and their biogeographic patterns. ITS1 rDNA and RAPD detected intraspecific polymorphism. TCIIa circulates in primates in the Brazilian Amazon, transmitted by Rhodnius in arboreal ecotopes sporadically infecting humans. TCI is the most prevalent in the Amazonian primates and humans, and can induce severe Chagas disease as demonstrated in a patient from Northeast Brazil. Bats of several biomes were found infected by three trypanosome species, including a new lineage of T. cruzi denominated TCbat. Isolates from monkeys and bats were also molecularly characterized. The lineage TCIIc showed to be widespread in Brazil, and was associated to terrestrial mammals and triatomines. TCIIa from the USA corresponds to an independent lineage, probably absent in Brazil.

Orientador: Maurício Dutra Zanotto / Banca: Juliana Parisotto Poletine / Banca: José Geraldo Carvalho Amaral / Resumo: Para a geração de híbridos comerciais de porte baixo visando à colheita mecanizada em condições de safra é necessário a obtenção de linhagens. O presente trabalho teve como objetivo avaliar 111 linhagens de mamona, obtidas da População FCA Planta Baixa selecionadas para porte baixo. O trabalho foi desenvolvido no município de São Manuel - SP na Fazenda Experimental São Manuel, da Faculdade de Ciências Agronômicas, no Campus de Botucatu - UNESP. Estas linhagens foram avaliadas entre os meses de outubro de 2003 a setembro de 2004 utilizando-se o delineamento experimental de blocos ao acaso, com área útil da parcela de 3,0 m2, espaçamento entre linhas 0,60 m e 0,50 m entre plantas. As 111 linhagens foram divididas em quatro experimentos: 30 linhagens em três experimentos com quatro repetições e 21 linhagens em um experimento com duas repetições. Após o completo desenvolvimento das plantas, avaliou-se a altura de 10 plantas por parcela (m) desde a superfície do solo até o ápice do racemo mais alto, bem como foram tomados dados de peso dos grãos em kg.ha -1, corrigidos por covariância para estande ideal de 10 plantas por parcela e teor de água de 10%. Os dados obtidos foram submetidos à análise de variância. Os quadrados médios não foram significativos a 5% de probabilidade para a característica altura de plantas, indicando que não houve variação genética para este parâmetro. Os quadrados médios das análises de variância para a característica produtividade de grãos foram significativos, indicando existir variabilidade para a característica em nível de 5% de probabilidade. Para a característica altura de plantas, a média das linhagens e amplitude de variação entre os quatro experimentos foi de 1,20 m com amplitude de 0,33 a 1,68 m ou plantas anãs a baixas... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: For the generation of commercial hybrids with short height seeking to automated harvest in crop conditions, it's necessary the obtaining of lineages. The present work had as objective to evaluate 111 castor bean lineages, obtained from FCA short height plant population selected for low size. The work was developed in São Manuel municipal district, São Paulo State, in the Experimental Farm belonging to University of Agronomic Sciences, Botucatu Campus - UNESP. These lineages were appraised between October, 2003 and September, 2004, by using randomized complete blocks experimental design, with plot useful area of 3,0 m2, spacing between lines of 0,60 m and 0,50 m between plants. The 111 lineages were divided into four experiments: 30 lineages in three experiments with four replications and 21 lineages in one experiment with two replications. After plants complete development, the height of ten of them was evaluated, in each plot (m), from the soil surface to the apex of the highest bunch, as well as data of grain weight were taken, in kg ha-1, corrected by covariance for ideal stand of 10 plants per plot and water content of 10%. The obtained data were submitted to variance analysis. Medium squares were not significant to 5% of probability for the characteristic plant height, indicating that there was not genetic variation for this parameter. The medium squares from the variance analyses for the characteristic grains yield were significant, indicating the existence of genetic variability for this characteristic with 5% of probability. For the characteristic plant height, the average of the lineages and variation width among the four experiments was about 1,20 m with range from 0,33 to 1,68 m or dwarfish to short plants... (Complete abstract, click eletronic address below) / Mestre

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2016-01-29T10:59:58Z No. of bitstreams: 2 Dissertação - Marielton dos Passos Cunha - 2015.pdf: 3794305 bytes, checksum: 63dd946c15b0a01f4a247e2bd60fa1e2 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-01-29T11:01:41Z (GMT) No. of bitstreams: 2 Dissertação - Marielton dos Passos Cunha - 2015.pdf: 3794305 bytes, checksum: 63dd946c15b0a01f4a247e2bd60fa1e2 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2016-01-29T11:01:41Z (GMT). No. of bitstreams: 2 Dissertação - Marielton dos Passos Cunha - 2015.pdf: 3794305 bytes, checksum: 63dd946c15b0a01f4a247e2bd60fa1e2 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2015-04-17 / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / Dengue viruses (DENV) serotypes 1, 2, 3, and 4 have been causing yearly outbreaks in Brazil. Nevertheless, the population structure of the viruses transmitted in Goiás state is not well understood. In this study, we investigated the phylogenetic pattern of DENV samples identified in Goiânia, Goiás, Brazil during the 2012/2013 epidemic. Therefore, the entire region of the gene of the envelope (E) protein (1485bp) of 16 DENV-1 samples as well as partial region of this gene (363bp) of seven DENV-4 samples were sequenced. Phylogenetic analysis showed that DENV-1 belongs to the genotype V and presents itself divided into two clades, suggesting co-circulation of two distinct lineages in this region. Still, the molecular analyzes indicated a significant change in the amino acid level E348 position. For DENV-4, the sequences were segregate in a monophyletic group and are classified as genotype II American subclade. The molecular and phylogenetic analysis showed that the region suffered multiple introductions by dengue virus. This is the first report of co-circulation of two lineages of DENV-1, and the circulation of DENV-4 in Goiás state. / Os vírus dengue (DENV) sorotipos 1, 2, 3 e 4 tem causado surtos anuais no Brasil. No entanto, a estrutura populacional dos vírus transmitidos em Goiás não é bem compreendida. Neste estudo, investigamos o padrão filogenético de amostras do DENV identificadas em Goiânia, Goiás, Brasil, durante a epidemia de 2012/2013. Para isso, a região completa do gene codificante da proteína do envelope (E) (1485pb) de 16 amostras DENV-1 assim como a região parcial deste gene (363pb) de sete amostras DENV-4, foram sequenciadas. A análise filogenética mostrou que o DENV-1 pertence ao genótipo V e apresenta-se dividido em dois clados, sugerindo a cocirculação de duas linhagens distintas na região. Ainda, as análises moleculares indicaram uma alteração significativa na posição do aminoácido E348. Para DENV-4, as sequências segregaram em um grupo monofilético, sendo classificadas como genótipo II subclado americano. As análises moleculares e filogenéticas indicaram que a região sofreu múltiplas introduções pelo DENV. Este é o primeiro relato de cocirculação de duas linhagens de DENV-1, assim como circulação do DENV-4 no estado de Goiás.

Made available in DSpace on 2017-07-10T17:48:15Z (GMT). No. of bitstreams: 1 Paulo_Roberto_Poggere.pdf: 1235913 bytes, checksum: d755c1fed9bce078365b85e719b7f835 (MD5) Previous issue date: 2009-03-06 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The present study had as objective evaluates the performance, chemical composition, morphometrics reasons and yield of the fillet of three tilápia lineages: Supreme (SUP), Chitralada (CHIT) and Bouaké (BOU). The used experimental design was randomized entirely, composed by 3 treatments and 6 repetitions. 18 concrete tanks were used, where 30 fingerlings were stocked, with medium initial weight of 2,03 ± 0,25 g, 1,65 ± 0,06 g and 1,57 ± 0,11 g for SUP, CHIT and BOU respectively, totaling 540 fingerlings, being 180 fingerlings for each lineage. The fish were fed 3 times a day, with commercial diet of the type crumbed with 42% of CP for the alevinagem phase, and extruded with the levels of 36% CP for the growth phase and 32% CP for the fattening phase. The amount of diet was adjusted through the medium weight and temperature of the water. The biometry were accomplished biweekly, being captured 30% of the copies of each tank. The zootechnical indexes and the length data along the time were appraised through ANCOVA. The filet income was evaluated through ANOVA. Already the morphometrics reasons, were analyzed starting from MANOVA. For the zootechnical indexes, there were significant effects of the lineages on the Tax of Growth (TG), Earnings of Biomass (EB) and Final (FW) Weight. For TG and FW, CHIT differed significantly of the other ones, presenting largest TG and FW (2,543 g/day and 307 g), while SUP and BOU didn't differ significantly amongst themselves. In EB, CHIT and SUP they presented the best result (7.207,40 and 6.898,15 g, respectively), differing significantly of BOU. With relationship the morphometrics reasons, there was significant difference among the lineages. Already in the yield of the fillet without skin (YF), there were not significant effects among the lineages. The chemical composition of the fillet presented significant differences for ethereal (EE) extract and crude protein (CP) protein. For EE, the three lineages differed statistically amongst themselves, and BOU presented the largest value with 1,42%, following by SUP and CHIT. For CP, SUP (20,79%) and BOU (20,73%) they only differed of CHIT. For the growth in length, CHIT presented the largest value of L¥, with 27,39 cm, following by SUP (27,16 cm) and BOU (26,67 cm). Regarding the value of k (growth tax in length), SUP presented the largest value (0,4456), following by CHIT with 0,4349 and BOU (0,4141). In the growth in weight, CHIT obtained the largest value for W¥ with 534,15 g, following by SUP with 516,20 g and BOU 454,76 g. However, SUP was superior in the coefficient of growth alométrico (q) with 3,2442, being respectively the values of 3,2206 and 3,1773 for CHIT and BOU. It was verified that CHIT obtained the best results for TG, FW, EB and tenor of EE in the filet in comparison with SUP and BOU, besides presenting morphometrics reasons that provide a rounder format of his body being the lineage more adapted for cultivation in those imposed conditions and weight strip / O presente estudo teve como objetivo avaliar o desempenho produtivo, composição química, razões morfométricas e rendimento do filé de três linhagens de tilápia: Supreme (SUP), Chitralada (CHIT) e Bouaké (BOU). O delineamento experimental utilizado foi inteiramente casualizado, composto por três tratamentos e seis repetições. Foram utilizados 18 tanques de concreto, onde foram estocados 30 alevinos, com peso inicial médio de 2,03 ± 0,25 g, 1,65 ± 0,06 g e 1,57 ± 0,11 g para SUP, CHIT e BOU respectivamente, totalizando 540 alevinos, sendo 180 alevinos para cada linhagem. Os peixes foram alimentados três vezes ao dia, com ração comercial do tipo farelada com 42% de PB para a fase de alevinagem, e extrusada com os níveis de 36% PB para a fase de crescimento e 32% PB para a fase de engorda. A quantidade de ração foi ajustada através do peso médio e temperatura da água. As biometrias foram realizadas quinzenalmente, sendo capturados 30% dos exemplares de cada tanque. Os índices zootécnicos e os dados de comprimento ao longo do tempo foram avaliados através da ANCOVA, o rendimento de filé foi avaliado através da ANOVA e as razões morfométricas, foram analisadas a partir de MANOVA. Para os índices zootécnicos, houveram efeitos significativos das linhagens sobre a Taxa de Crescimento (TC), Ganho em Biomassa (GB) e Peso Final (PF). Para a TC e PF, a CHIT diferiu significativamente das outras, apresentando a maior TC e PF (2,543 g/dia e 307 g), enquanto a SUP e BOU não diferiram significativamente entre si. No GB, a CHIT e SUP apresentaram o melhor resultado (7.207,40 e 6.898,15 g, respectivamente), diferindo significativamente da BOU. Com relação as razões morfométricas, houve diferença significativa entre as linhagens. Já no rendimento de filé sem pele (RF), não houveram efeitos significativos entre as linhagens. A composição química do filé apresentou diferenças significativas para extrato etéreo (EE) e proteína bruta (PB). Para o EE, as três linhagens diferiram estatisticamente entre si, sendo que a BOU apresentou o maior valor com 1,42%, seguida da SUP e CHIT. Para PB, a SUP (20,79%) e BOU (20,73%) somente diferiram da CHIT. Para o crescimento em comprimento, a CHIT apresentou o maior valor de L¥, com 27,39 cm, seguida da SUP (27,16 cm) e BOU (26,67 cm). Com relação ao valor de k (taxa de crescimento em comprimento), a SUP apresentou o maior valor (0,4456), seguida da CHIT com 0,4349 e BOU (0,4141). No crescimento em peso, a CHIT obteve o maior valor para W¥ com 534,15 g, seguida da SUP com 516,20 g e BOU 454,76 g. Entretanto, a SUP foi superior no coeficiente de crescimento alométrico (q) com 3,2442, sendo os valores de 3,2206 e 3,1773 para CHIT e BOU respectivamente. Verificou-se que CHIT obteve os melhores resultados para TC, PF, GB e teor de EE no filé em comparação SUP e BOU; além de apresentar razões morfométricas que proporcionam um formato mais arredondado do seu corpo, sendo a linhagem mais adaptada para cultivo nessas condições impostas e faixa de peso

The basking shark, Cetorhinus maximus, has historically been a target of international fisheries, leading to well-documented declines in parts of its global distribution. Currently, the basking shark is listed as globally ‘Vulnerable’ and regionally ‘Endangered’ (North Pacific and Northeast Atlantic) on the IUCN Red List of Threatened Species, rendering the species an international conservation priority. Here, we assessed the global matrilineal genetic population structure and evolutionary history of the basking shark by completing the first whole mitochondrial genome sequence level survey of animals sampled from three globally widespread geographic regions: the western North Atlantic (n = 11), the eastern North Atlantic (n = 11), and within New Zealand territorial waters (n = 12). Despite the relatively large amount of sequence data assessed (~16,669 bp per individual), whole mitogenome analyses showed no evidence of population differentiation (ΦST = -0.047, P > 0.05) and very low nucleotide diversity (π = 0.0014 ± 0.000) across a global seascape. The absence of population structure across large distances and even between ocean basins is indicative of long-dispersal by this species, including an ability to cross known biogeographic barriers known to differentiate populations of other highly vagile pelagic fishes. Notably, evolutionary analyses of the mitogenome sequences revealed two globally sympatric but evolutionary divergent lineages, with a Bayesian framework estimated coalescence time of ~2.46 million years ago. Coalescent-based Bayesian skyline analysis uncovered subtle evidence of Pleistocene demographic flux for this species, including a potential decline in female effective population size. Thus, historical population changes may be responsible for the occurrence of the two highly divergent, yet sympatric lineages, as population declines may have resulted in the loss of intermediate haplotypes and resulted in an overall loss of genetic diversity. This work supports the recognition of basking sharks as a single matrilineal global population, and as such requires the application of a cooperative multiagency and international approach to fisheries management to conserve this highly vulnerable and ecologically unique species.

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.

yes / Recent studies portend a rising global spread and adaptation of human- or healthcare- associated pathogens. Here, we analyse an international collection of the emerging, multi-drug-resistant, opportunistic pathogen Stenotrophomonas maltophilia from 22 countries to infer population structure and clonality at a global level. We show that the S. maltophilia complex is divided into 23 monophyletic lineages, most of which harbour strains of all degrees of human virulence. Lineage Sm6 comprises the highest rate of human-associated strains, linked to key virulence and resistance genes. Transmission analysis identifies potential outbreak events of genetically closely related strains isolated within days or weeks in the same hospitals.

yes / Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto, as well as two lineages (L5 and L6) traditionally referred to as Mycobacterium africanum. Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known of their genomic diversity, phylogeography and evolution. Here, we analysed the genomes of 350 L5 and 320 L6 strains, isolated from patients from 21 African countries, plus 5 related genomes that had not been classified into any of the known MTBC lineages. Our population genomic and phylogeographical analyses showed that the unclassified genomes belonged to a new group that we propose to name MTBC lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure and genetic diversity. Finally, we could not confirm the previous association of drug-resistance markers with lineage and sublineages. Instead, our results indicate that the association of drug resistance with lineage is most likely driven by sample bias or geography. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of TB in Africa and globally.

No description available.

Genome evolution is not always shaped by a Darwinian-fashion of vertical inheritance from ancestral lineages. The historical gene content of a species contains many atypical gene sequences showing high similarity to those of distantly related taxa. This evolutionary phenomenon is referred to as lateral gene transfer (LGT). Lateral gene transfer permits the exchange of genetic material across lineages, completely ignoring any concept of taxonomic boundary. The rapid acquisition of foreign genes into bacterial genomes has greatly obscured the historical phylogeny of prokaryotes. In this thesis we calculate the rate of LGT on a Bacillaceae phylogeny, to determine the extent to which it controls species evolution. First, we examined the evolution of the phylogeny according to a simple model of maximum likelihood. We assume equal rates of gene insertion and deletion on the phylogeny and show high rates of evolution in the genomes of B. anthracis, B. cereus, and B. thuringiensis (Bc group), representative of adaptive evolution. We then improved the model to account for differential rates of gene insertion and deletion, thus offering a more realistic model of gene evolution. Again, we demonstrate that members of the Bc group are rapidly evolving, with the rate of gene insertion being significantly higher than the rated of gene deletion. Finally, we evaluate the sole effect of LGT on the phylogeny in a simple birth-death analysis with immigration. We show that LGT is the main vehicle of gene acquisition when the number of gene families substantially increases from external taxa to members of the Bc group. Collectively, our findings suggest that the Bacillaceae genome is rapidly expanding, and that laterally transferred genes may facilitate adaptive evolution and subsistence in a new niche. / Thesis / Master of Science (MSc)