A presente tese avaliou os efeitos de dois distúrbios de larga escala sobre estrutura das assembleias de macrófitas aquáticas em distintos ecossistemas neotropicais: uma grande depleção do nível da água no reservatório de Itaipu (Brasil/Paraguai) e os pulsos de cheia e seca na planície do Alto Rio Paraná. O primeiro capítulo da tese avaliou o impacto imediato e de médio prazo da depleção no nível hidrométrico sobre os padrões de co-ocorrência das espécies e a estrutura espaço-temporal da assembleia de macrófitas aquáticas em cinco braços do reservatório de Itaipu. O segundo e terceiro capítulos analisaram os padrões de diversidade beta e a contribuição relativa dos seus diferentes componentes (substituição de espécies e aninhamento) para a estruturação das assembleias no reservatório de Itaipu e na planície de inundação do Alto Rio Paraná, respectivamente. Diferentemente do esperado, a assembleia de macrófitas do reservatório de Itaipu revelou um padrão de organização das espécies diferente do acaso no ano em que ocorreu a depleção, provavelmente devido à colonização de novas espécies na margem exposta e à morte de muitos indivíduos pertencentes a diversas espécies do grupo das submersas. Imediatamente após o distúrbio, evidenciamos um padrão tipicamente aleatório de distribuição, devido ao reestabelecimento das espécies submersas, concomitantemente à colonização de espécies emergentes que haviam se estabelecido nas margens durante o distúrbio. Tanto no reservatório de Itaipu como na planície de inundação do Alto Rio Paraná, a substituição de espécies (turnover) revelou-se como principal mecanismo responsável pelos padrões de diversidade beta, o que provavelmente está diretamente associado com as diferenças de dinâmica hidrológica e limnológica entre cada ambiente dentro dos ecossistemas analisados (braços do reservatório e lagoas da planície). / The present thesis evaluated two large-scale disturbances upon the structure of aquatic macrophytes assemblages in distinct Neotropical ecosystems: an historic drawdown occurred in the Itaipu reservoir (Brazil/Paraguay) and the flood and drought pulses in the Upper Paraná River floodplain. The first chapter evaluated the immediate and long term impact of the drawdown over the co-occurrence patterns and the spatio-temporal structure of the aquatic macrophytes assemblage in five arms of the Itaipu reservoir. The second and third chapters analyzed the beta diversity patterns and the relative contribution of its different components (species turnover and nestedness) to the assemblage’s structure in the Itaipu reservoir and the Upper Paraná River floodplain, respectively. Contrary to expected, the macrophytes assemblage in the Itaipu reservoir presented a non-random spatial organization pattern of the macrophyte species in the year of the drawdown probably due to the colonization of the exposed area by new species and by the death of many individuals of submersed species. Immediately after the disturbance, we evidenced a random distribution guided by the reestablishment of the submersed species concomitantly with the emergents, which occupied the shore since the disturbance. Both Itaipu reservoir and the Upper Paraná River floodplain, the species turnover revealed to be the main process reflecting high values of beta diversity, which probably is directly linked with the distinct hydrological and limnological dynamic within the environments in each analyzed environment (reservoir arms and floodplains lagoons).

Submitted by Erika Demachki (erikademachki@gmail.com) on 2018-07-03T18:02:31Z No. of bitstreams: 2 Dissertação - Júlio Cury Hoffmann - 2018.pdf: 1219488 bytes, checksum: 20fea8e1513a899e8a9f32df5739d99a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-07-04T12:29:08Z (GMT) No. of bitstreams: 2 Dissertação - Júlio Cury Hoffmann - 2018.pdf: 1219488 bytes, checksum: 20fea8e1513a899e8a9f32df5739d99a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-07-04T12:29:08Z (GMT). No. of bitstreams: 2 Dissertação - Júlio Cury Hoffmann - 2018.pdf: 1219488 bytes, checksum: 20fea8e1513a899e8a9f32df5739d99a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2018-04-18 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / There are several problems on the analysis of biological communities with sparse data, resulting from gradients with high beta diversity. I used four strategies to solve this problem (Beals smoothing, Swan, Shortest Path and Extended Dissimilarity). I randomly removed from 1% to 50% of the individuals in empirical and simulated matrices. I then performed PCoA and nMDS ordinations and used Procrustes correlation of the original two dimensional ordination with the ordination obtained using the degraded matrices. For the simulated data set, I also correlated the ordenation in two dimensions with the coordinates of the samples in the two-dimensional simulated gradients. Finally, I analyzed how robustness to degradation, quantified as Procrustean correlation, was related to the matrix properties. Different from the expected, in the comparison of the degraded and original ordinations, the uncorrected data with a traditional dissimilarity index (Bray-Curtis) produced higher fit than the four methods evaluated. In relation to the coordinates of the simulated two-dimensional gradients, the evaluated methods were slightly better than the raw data. Overall, the simulated data were more robust to the degradation than the empirical ones and the data of abundance were more robust than matrices of presence and absence. Matrices with small proportion of zeros were more robust to degradation. I conclude that the correction methods evaluated distorted the pattern on the original data. Also, data with low beta diversity (few zeros) are robust to degradation and sufficient to reconstruct the original gradient. / Existem vários problemas nas análises de comunidades em Ecologia decorrentes da grande quantidade de zeros na matriz de espécies por locais (dados esparsos), principalmente em situações em que a diversidade beta é alta. Usando quatro estratégias para resolver estes problemas (Beals, Swan, Menor Caminho e Dissimilaridade estendida) retirei aleatoriamente de 1 ate 50 % dos indivíduos de matrizes empíricas e simuladas (degradação das matizes). Realizei ordenações PCoA e nMDS e, com correlações de Procrustes, relacionei a ordenação original em duas dimensões com a ordenação obtida pelas matrizes degradadas. Com dados simulados relacionei a ordenação em duas dimensões também com as coordenadas das amostras no gradiente bidimensional simulado. Além disso, analisei como a robustez à degradação, medida como correlação Procrustes, está relacionada às características da matriz. Diferente do esperado, na comparação das ordenações de matrizes degradadas com a ordenação da matriz original, os dados utilizados sem correções e com índice de dissimilaridade tradicional (Bray-Curtis) tiveram maior ajuste que os quatro métodos avaliados. Em relação às coordenadas, os métodos aplicados tiveram desempenho um pouco melhor do que os dados sem correções quando a diversidade beta foi maior. Em geral, os dados simulados foram mais robustos à degradação que os empíricos e os dados de abundância foram mais robustos que de presença e ausência. Matrizes com menor proporção de zeros foram mais robustas à degradação. Concluo que os métodos de correção distorceram o padrão dos dados originais. Ainda, dados com baixa diversidade beta (poucos zeros na matrix) são robustos à degradação e são suficientes para reconstruir o gradiente original.

A presente tese avaliou os efeitos de dois distúrbios de larga escala sobre estrutura das assembleias de macrófitas aquáticas em distintos ecossistemas neotropicais: uma grande depleção do nível da água no reservatório de Itaipu (Brasil/Paraguai) e os pulsos de cheia e seca na planície do Alto Rio Paraná. O primeiro capítulo da tese avaliou o impacto imediato e de médio prazo da depleção no nível hidrométrico sobre os padrões de co-ocorrência das espécies e a estrutura espaço-temporal da assembleia de macrófitas aquáticas em cinco braços do reservatório de Itaipu. O segundo e terceiro capítulos analisaram os padrões de diversidade beta e a contribuição relativa dos seus diferentes componentes (substituição de espécies e aninhamento) para a estruturação das assembleias no reservatório de Itaipu e na planície de inundação do Alto Rio Paraná, respectivamente. Diferentemente do esperado, a assembleia de macrófitas do reservatório de Itaipu revelou um padrão de organização das espécies diferente do acaso no ano em que ocorreu a depleção, provavelmente devido à colonização de novas espécies na margem exposta e à morte de muitos indivíduos pertencentes a diversas espécies do grupo das submersas. Imediatamente após o distúrbio, evidenciamos um padrão tipicamente aleatório de distribuição, devido ao reestabelecimento das espécies submersas, concomitantemente à colonização de espécies emergentes que haviam se estabelecido nas margens durante o distúrbio. Tanto no reservatório de Itaipu como na planície de inundação do Alto Rio Paraná, a substituição de espécies (turnover) revelou-se como principal mecanismo responsável pelos padrões de diversidade beta, o que provavelmente está diretamente associado com as diferenças de dinâmica hidrológica e limnológica entre cada ambiente dentro dos ecossistemas analisados (braços do reservatório e lagoas da planície). / The present thesis evaluated two large-scale disturbances upon the structure of aquatic macrophytes assemblages in distinct Neotropical ecosystems: an historic drawdown occurred in the Itaipu reservoir (Brazil/Paraguay) and the flood and drought pulses in the Upper Paraná River floodplain. The first chapter evaluated the immediate and long term impact of the drawdown over the co-occurrence patterns and the spatio-temporal structure of the aquatic macrophytes assemblage in five arms of the Itaipu reservoir. The second and third chapters analyzed the beta diversity patterns and the relative contribution of its different components (species turnover and nestedness) to the assemblage’s structure in the Itaipu reservoir and the Upper Paraná River floodplain, respectively. Contrary to expected, the macrophytes assemblage in the Itaipu reservoir presented a non-random spatial organization pattern of the macrophyte species in the year of the drawdown probably due to the colonization of the exposed area by new species and by the death of many individuals of submersed species. Immediately after the disturbance, we evidenced a random distribution guided by the reestablishment of the submersed species concomitantly with the emergents, which occupied the shore since the disturbance. Both Itaipu reservoir and the Upper Paraná River floodplain, the species turnover revealed to be the main process reflecting high values of beta diversity, which probably is directly linked with the distinct hydrological and limnological dynamic within the environments in each analyzed environment (reservoir arms and floodplains lagoons).

Orientador: Fernando Roberto Martins / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-24T09:52:26Z (GMT). No. of bitstreams: 1 Zulqarnain_D.pdf: 1175280 bytes, checksum: 54693f874db85bfe334ccd1c36999f30 (MD5) Previous issue date: 2014 / Resumo: Em florestas tropicais, a relação entre lianas e suas árvores-suporte (forófitos) representa uma importante interação antagônica. Em interações antagônicas a capacidade individual de um organismo de usar recursos aumenta, ao passo que a do outro organismo que interage decresce como resultado da interação. Cerca de 69% de todos os sistemas antagonisticos têm sinal filogenético, tendo em vista que interações entre espécies podem ser moldadas pela bagagem filogenética recebida como herança de seus antepassados. Por entretanto interações entre espécies variam de acordo com gradientes ambientais e o padrão de coocorrência de espécies de plantas em pequenas escalas espaciais muda com as condições ambientais. Portanto, o objetivo geral desta tese é avaliar a ocorrência de algum grau de especialização em lianas e forófitos e verificar a probabilidade de coocorrências entre lianas ou entre lianas e forófitos varia com a posição na encosta ou com a variação de variáveis do solo ao longo da encosta. A área focal deste trabalho foi feito em um fragmento da Floresta Estacional Semidecídua no município de Campinas, mas em primeiro capítulo também pesquisou outros três fragmentos, (i) Floresta Ombrófila no município de Ubatuba, (ii) Cerradão no município de Bauru, e (iii) Floresta Estacional Semidecídua no município de Paulo de Faria, em estado de São Paulo, no sudeste do Brasil. No capítulo (1) observou que em florestas ombrófila e estacionais, lianas e forófitos com alta originalidade filogenética tenderam a interagir com um conjuntos de espécies muito distintas. Por outro lado constatou-se que nos bosques de cerrados, lianas e forófitos com altas originalidade filogenética tenderam a interagir com conjuntos comuns de espécies. No segundo capítulo (2), mostramos que lianas coocorrem aleatoriamente no forófito, mas também observamos a existência de uma tendência de que lianas com mecanismos de escalada semelhantes facilitam a escalada de outra liana a escalar a árvore hospedeira. Por contudo não encontramos lianas coocorrência ao longo de gradientes ambientais. No capítulo (3), observamos que as variáveis selecionadas (fatores topoedáficos e diversidade filogenicas dos forófitos) não explicaram a variacão na freqüência de coocorrência das lianas- forófitos. Por constatamos que lianas têm um comportamento oportunista para subir nas árvores e diversidade filogenicas usuando como proxy para atributos de árvores não são importantes para as lianas. Argumentamos que as diferenças ambientais entre florestas e savanas mediaram processos evolutivos distintos nas interações liana-forófito. Os processos estocásticos são o fator dominante gerando padrão de co-ocorrência entre lianas e lianas-forófito / Abstract: Liana and host tree (phorophyte) represent an important antagonistic interaction in tropical forest. In antagonistic interactions the individual ability of using nutrient resources increases whereas the ability of interacting individual decreases as a result of interaction. About 69 % of all antagonistic systems have phylogenetic signal , considering that species interactions can be shaped by phylogenetic baggage that species received as an inheritance from their ancestors. However species interactions vary according to environmental gradients hence the co-occurrence pattern of the plant species in small spatial scales also changes with environmental conditions. Therefore, the aim of this thesis was to evaluate some degree of specialization between lianas and phorophytes and probability of co-occurrences among lianas as well lianas and phorophytes along the slope or the variation of soil variables along the slope. The focal area of this work was carried out in a fragment of tropical semideciduous forest in the muncipality of Campinas, but in the first chapter we also surveyed three other fragments (i) Tropical Rain Forest in the muncipality of Ubatuba, (ii) Woodland Savanna in the municipality of Bauru and (iii) the tropical semideciduous forest in the municipality of Paulo de Faria, in the state of São Paulo, in southeastern Brazil. In chapter (1) we observed that in tropical rain forest and seasonal forests, lianas and phorophyte with high phylogenetic originality tended to interact with a set of very distinct species . Moreover it was found that in the woodland Savanna, lianas and phorophytes with high phylogenetic originality tended to interact with common sets of species. In chapter (2) we showed that lianas co-occur randomly on the host tree, but we also observed an existence of a tendency that lianas with similar climbing mechanisms facilitate other liana climbing the host tree. But we did not find role of environmental gradients in lianas co-occurrence. In chapter (3), we observed that selected variables (topoedaphic factors and phylogenetic diversity of phorophyte), also did not explain the variation in the frequency of liana-phorophyte co-occurrence. But we found that lianas have an opportunistic behavior and phylogenetic diversity using as proxy for tree traits are not important to the lianas. We argued that environmental differences in forests and savannas mediated distinct evolutionary processes in structuring liana-phorophyte interactions. The stochastic processes are the dominant factor generating pattern of co-occurrence among lianas and liana and host tree / Doutorado / Biologia Vegetal / Doutor em Biologia Vegetal

The flipped classroom as an educational model is perfectly aligned with the current demands of higher education. Therefore, the objectives of this article were to carry out a bibliometric analysis of the scientific production of the flipped classroom in higher education (2012-2020) and to propose a framework for its implementation in face-to-face, blended or online learning modalities. The records were recovered from the Web of Science Core Collection and Scopus, from which, after a five-phase methodological process, a consolidated dataset of 782 documents was obtained. The results showed the importance of the subject matter as scientific production reflected a continuous growth during the period of study. For their part, the most productive authors come from various institutions worldwide with an H index of over 50. The collaboration indicators show the growth trend of these indexes over the years, which reflects the capacity to generate national and international impact in the documents published in collaboration. The keywords co-occurrence analysis showed that the flipped classroom as a technological and innovative approach is complemented by active learning, blended learning, e-learning, ICT, teaching method, among others. Finally, a framework with five components was proposed as a basic guide for the implementation of the flipped classroom in higher education. / Revisón por pares

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24111号 / 農博第2516号 / 新制||農||1093(附属図書館) / 学位論文||R4||N5402(農学部図書室) / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 北島 薫, 教授 井鷺 裕司, 准教授 東樹 宏和 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

No description available.

Thesis (MScEng)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Hydrocyclones are stationary separating machines that separate materials based on centrifugal separation and are widely used in chemical engineering and mineral processing industries. Their design and operation, compact structure, low running costs and versatility all contribute to their applications in liquid clarification, slurry thickening, solid washing and classification. With any of these operations, the overall profitability of the process relies on the effective control of the process equipment. However, in practice, hydrocyclones are difficult to monitor and control, owing to the complexity and difficulty in measuring internal flows in the equipment. Several studies have indicated that hydrocyclone underflow images can be used to monitor process conditions. The research described in this thesis considers the use of image analysis to monitor particle size and solids concentration in the underflow discharge of a hydrocyclone. The experimental work consisted of laboratory and industrial-based case studies. The laboratory cyclone used was a 76 mm general laboratory cyclone. A Canon EOS 400D digital camera was used for the underflow imaging. Image features such as pixel intensity values, underflow discharge width and grey level co-occurrence matrix (GLCM) were extracted from the images using MATLAB Toolbox software. Linear discriminant analysis (LDA) and neural network (NN) classification models were used to discriminate between different PGM ore types based on features extracted from the underflow of the hydrocyclone. Likewise, multiple linear regression and neural network models were used to estimate the underflow solids content and mean particle size in the hydrocyclone underflow. The LDA model could predict the PGM ore types with 61% reliability, while the NN model could do so with a statistically similar 62% reliability. The multiple linear regression models could explain 56% and 40% of variance in the mean particle size and solids content respectively. In contrast, the neural network model could explain 67% and 45% of the variance of the mean particle size and solids content respectively. For the industrial system, a 100% correct classification was achieved with all methods. However, these results are regarded as unreliable, owing to the insufficient data used in the models. / AFRIKAANSE OPSOMMING: Hidrosiklone is stasionêre skeidingsmasjiene wat materiale skei op grond van sentrifugale skeiding en word algemeen gebruik in die chemiese ingenieurswese en mineraalprosessering industrieë. Hul ontwerp en werking, kompakte struktuur, lae bedryfskoste en veelsydigheid dra by tot hul gebruik vir toepassings in vloeistofsuiwering, slykverdikking, vastestof wassing en klassifikasie. In enige van hierdie prosesse hang die oorhoofse winsgewendheid van die proses af van die effektiewe beheer van die prosestoerusting. In die praktyk is hidrosiklone egter moeilik om te monitor en beheer weens die kompleksiteit en moeilikheidsgraad daarvan om die interne vloei in die apparaat te meet. Verskeie studies het aangedui dat hidrosikloon ondervloeibeelde gebruik kan word om die proseskondisies te monitor. Die navorsing beskryf in hierdie tesis maak gebruik van beeldanalise moniteringstegnieke om die ertstipes en grootte- verspreidingsgebiede/ klasse van die ondervloei afvoerpartikels te bepaal. Sodoende word ‘n grondslag gelê vir verbeterde sikloon monitering en beheer. Die eksperimentele werk het bestaan uit beide laboratorium en industrieel-gebaseerde studies. Die laboratorium sikloon wat gebruik is, was ‘n 76 mm algemene laboratorium sikloon. ‘n Canon EOS 400D digitale kamera is gebruik om die hidrosikloon ondervloei beelde vas te vang. Beeldeienskappe soos beeldelement intensiteitswaardes, ondervloei afvoerwydte en grysvlak mede-voorkoms matriks is onttrek uit die beelde deur gebruik te maak van MATLAB Toolbox sagteware. Lineêre diskriminantanalise (LDA) en neural netwerk (NN) klassifikasiemodelle is gebou om te onderskei tussen die verskillende PGM ertse en gebaseer op veranderlikes wat afgelei is uit beelde van die ondervloei van die sikloon. Net so is daar ook gebruik gemaak van lineêre regressie- en neural netwerkmodelle om die vasestofkonsentrasie en gemiddelde partikelgrootte in die ondervloei van die sikloon te beraam. Die LDA model kon die PGM ertstipes met 61% betroubaarheid voorspel, terwyl die neural netwerkmodel dit kon doen met statisties dieselfde betroubaarheid van 62%. Die lineêre regressiemodelle kon onderskeidelik 56% en 40% van die variansie in die gemiddelde partikelgrootte en vastestofkonsentrasie verduidelik. In teenstelling iermee, kon die neurale netwerkmodel 67% en 45% van die variansie in die gemiddelde partikelgrootte en vastestofkonsentrasie verduidelik. In die nywerheidstelsel kon beide tipe modelle perfekte onderskeid tref tussen die partikelgroottes wat gemeet is op opeenvolgende dae van die bedryf van die siklone. Hierdie resultate is egter nie betroubaar nie, a.g.v. die beperkte hoeveelheid data wat beskikbaar was vir modellering.

Vector-borne diseases are an increasing global threat to humans due to climate changes, elevating the risk of infections transmitted by mosquitos, ticks, and other arthropod vectors. Ixodes ricinus, a common tick in Europe, transmits dangerous tick-borne pathogens to humans. Tick-borne encephalitis (TBE) is a vector-borne disease caused by TBE virus (TBEV). Climate change has contributed to increased tick abundance and incidence of tick-borne diseases, and between 10,000 and 15,000 human TBE cases are reported annually in Europe and Asia. TBEV shows a patchy geographical distribution pattern where each patch represents a natural focus. In nature, TBEV is maintained within the tick-rodent enzootic cycle. Co-feeding is the main route for TBEV transmission from infected to uninfected ticks and for maintenance within the natural foci. The increasing number of TBE cases in Scandinavia highlights the importance of characterizing additional TBEV sequences and of identifying novel natural foci, and in this work we sequenced and phylogenetically characterized four TBEV strains: Saringe-2009 (from a blood-fed nymph), JP-296 (from a questing adult male), JP-554 (from a questing adult male), and Mandal-2009 (from a pool of questing nymphs, n = 10). Mandal-2009 represents a TBEV genome from a natural focus in southern Norway. Saringe-2009 is from a natural endemic focus in northern Stockholm, Sweden, and JP-296 and JP-554 originate from a natural focus “Torö” in southern Stockholm. In addition, we have studied the effect of different biotic and abiotic factors on population dynamics of I. ricinus in southern Stockholm and observed significant spatiotemporal variations in tick activity patterns. Seasonal synchrony of immature stages and total tick abundance are important factors for the probability of horizontal transmission of TBEV among co-feeding ticks. We found that the probability of co-occurrence of larvae, nymphs, and female adults was highest during early summer whereas increasing vegetation height and increasing amounts of forest and open water around the study sites had a significant negative effect on co-occurrence of larvae, nymphs, and female adults. The proximal part of the 3 ́non-coding region (3 ́NCR) of TBEV contains an internal poly(A) tract, and genomic analysis of Saringe-2009 revealed variability in the poly(A) tract indicating the existence of different variants within the TBEV pool of Saringe-2009. Like other RNA viruses, TBEV exists as swarms of unique variants called quasispecies. Because Saringe-2009 came from an engorged nymph that had been feeding on blood for >60 h, we propose that Saringe-2009 represents a putative shift in the TBEV pool when the virus switches from ectothermic/tick to endothermic/mammalian environments. We investigated the role of poly(A) tract variability in replication and virulence of TBEV by generating two infectious clones of the TBEV strain Toro-2003, one with a short/wild-type (A)3C(A)6 poly(A) tract and one with a long (A)3C(A)38 poly(A) tract. The infectious clone with the long poly(A) tract showed poor replication in cell culture but was more virulent in C57BL/6 mice than the wild-type clone. RNA folding predictions of the TBEV genomes suggested that insertion of a long poly(A) tract abolishes a stem loop structure at the beginning of the 3 ́NCR. Next generation sequencing (NGS) analysis of the TBEV genomes after passaging in cell culture and/or mouse brain revealed molecular determinants and quasispecies structure that might contribute to the observed differences in virulence. Our findings suggest that the long poly(A) tract imparts instability to the TBEV genome resulting in higher quasispecies diversity that in turn contributes to TBEV virulence. Phylogenetic analysis of Saringe-2009, JP-296, JP-554, and Mandal-2009 predicted a strong evolutionary relationship among the four strains. They clustered with Toro-2003, the first TBEV strain from Torö, demonstrating a Scandinavian clade. Except for the proximal part of the 3 ́NCR, TBEV is highly conserved in its genomic structure. Genomic analysis revealed that Mandal-2009 contains a truncated 3 ́NCR similar to the highly virulent strain Hypr, whereas JP-296 and JP-554 have a genomic organization identical to Toro-2003, the prototypic TBEV strain from the same natural focus. NGS revealed significantly higher quasispecies diversity for JP-296 and JP-554 compared to Mandal-2009. In addition, single nucleotide polymerphism (SNP) analysis showed that 40% of the SNPs were common between quasispecies populations of JP-296 and JP-554, indicating the persistence and maintenance of TBEV quasispecies within the natural focus. Taken together, these findings indicate the importance of environmental factors for the occurrence pattern of the different life-stages of the tick vector, which are important for the persistence of TBEV in nature. Our findings also show that the selection pressure exerted by specific host also affects the population structure of the TBEV quasispecies. In addition, our results further demonstrate that the evolution of quasispecies has effect on TBEV virulence in mice. / Vektorburna sjukdomar är ett växande globalt hot mot både människor och djur. De pågående klimatförändringarna kan leda till förhöjda risker för infektioner överförda av myggor, fästingar och andra leddjursvektorer. Ixodes ricinus är en vanlig fästing i Europa som överför fästingburna patogener som är farliga för människor. Fästingburen encefalit (TBE) är en vektorburen sjukdom som orsakas av TBE-virus (TBEV). De pågående klimatförändringarna har bidragit till en ökning både av vektorn och sjukdomsfrekvensen. Mellan 10 000 och 15 000 mänskliga TBE-fall rapporteras årligen i Europa och Asien. Den geografiska fördelningen av TBEV visar ett ojämnt fördelningsmönster där viruset är koncentrerat till vissa fokusområden. TBEV återfinns i naturen i en livscykel där viruset hela tiden överförs mellan fästingar och däggdjur. Spridningen sker dels från en infekterad fästing till ett ryggradsdjur när fästingen äter på värddjuret. Spridning mellan fästingar sker troligen främst genom så kallad “co-feeding”, det vill säga att flera fästingar suger blod samtidigt från samma värddjur. Viruset kan då passera från en infekterad fästing, genom värddjuret till oinfekterade fästingar. Virus kan identifieras och studeras med genetiska metoder. Det ökande antalet TBE-fall i Skandinavien styrker vikten av att hitta och karakterisera ytterligare TBEV-stammar och identifiera nya naturliga fokusområden. Vi har sekvenserat och fylogenetiskt beskrivit fyra TBEV-stammar: Saringe-2009 (blodfylld nymf), JP-296 (födosökande vuxen hane), JP-554 (födosökande vuxen hane) och Mandal-2009 (födosökande nymfer, n = 10). Mandal-2009 är ett TBEV från ett naturligt fokusområde i södra Norge. Saringe-2009 kommer från ett naturligt fokusområde i norra Stockholms län, Sverige. JP-296 och JP-554 härstammar från Torö som är ett naturligt fokusområde i södra Stockholms län, Sverige. Förutom den genetiska sekvenseringen av TBEV har vi också studerat effekten av olika biotiska och abiotiska faktorer på populationsdynamik av I. ricinus i södra Stockholm och observerade variation i fästingsaktivitetsmönster både temporalt och spatialt. Förekomstmönster av fästinglarver, nymfer och vuxna honor, och det totala antalet fästingar är viktiga faktorer för sannolikheten för horisontell överföring av TBEV mellan fästingar. Vi fann att sannolikheten för synkron förekomst av larver, nymfer och honor var högst under försommaren. Vegetationshöjd, mängden skog och mängd öppet vatten runt undersökningsområden hade signifikanta negativa effekter på sannolikheten för att larver, nymfer och honor skulle förekomma samtidigt. Den variabla delen av den icke-kodande 3 ́regionen (3'NCR) av TBEV-genomet innehåller ofta en intern poly(A)-sekvens. Liksom andra RNA-virus, förekommer TBEV som så kallade ”quasispecies” vilka definieras som grupper av olika genetiska varianter av virus. Genom analysen av TBEV-stam Saringe-2009 avslöjades variation i poly(A)-sekvensen vilket indikerar förekomst av ”quasispecies”. Eftersom Saringe-2009 kom från en blodfylld nymf som hade sugit blod i > 60 timmar, föreslår vi att Saringe-2009 visar en förändring i ”quasispecies”-poolen när viruset överförs från exoterm fästingmiljö till endoterm däggdjursmiljö. Vi undersökte poly(A)-ekvensens variabilitet och dess roll vid replikering och för virulens hos TBEV, genom att skapa två infektiösa kloner av Torö-2003 stammen; en med en kort/vild-typ (A)3C(A)6 poly(A)-sekkvens, och en med en lång (A)3C(A)38 poly(A)-sekvens. Den infektiösa klonen med lång poly(A)-sekvens replikerade sämre än vildtypklonen i cellkultur, men (A)3C(A)38 poly(A) var mer virulent i C57BL/6-möss än (A)3C(A)6 poly(A). Datasimulering av TBEV-genomets sekundär-RNA-struktur visade att de längre poly(A)-sekvenserna påverkar veckningen av en specifik sekundärstruktur (SL14) i början av 3 ́NCR. Djupsekvenseringsanalys av TBEV-gnomen avslöjade skillnader för specifika gener och ”quasispecies”-strukturen efter passering i cellkultur och/eller mushjärna. Dessa förändringar föreslås bidra till de observerade skillnaderna i virulens. Våra resultat indikerar att den långa poly(A)-sekvensen ger instabilitet i TBEV-genomet, vilket resulterar i ökad mångfald av ”quasispecies”-populationen som i sin tur kan bidra till TBEV-virulens. Fylogenetisk analys av Saringe-2009, JP-296, JP-554 och Mandal-2009 visade på ett nära släktskap mellan de fyra skandinaviska TBEV-stammarna. De nya stammarna formerade ett kluster med en tidigare TBEV-stam identifierad på Torö (Toro-2003), vilket skapade ett skandinaviskt klad. Genetisk analys visade att Mandal-2009 innehåller en trunkerad 3 ́NCR som liknar den högvirulenta stammen HYPR. JP-296 och JP-554 hade däremot samma genetiska struktur som den längre Torö-2003 stammen från samma fokusområde. Djupsekvensering visade höge mångfald av ”quasispecies”-populationen för JP-296 och JP- 554 jämfört med Mandal-2009. Analys av enkel nukleotid polymorfism (SNP) visade att 40 % av alla SNP var gemensamma mellan ”quasispecies”-populationen för JP-296 och JP-554. Detta indikerar att TBEV-”quasispecies”-strukturen kan vara konserverad för närbesläktade virus vilken kan leda till att den bevaras inom specifika fokusområden. Sammantaget så visar dessa studier att miljöfaktorer påverkar förekomsten av fästingvektorn och dess olika livsstadier, vilket är en bakomliggande faktor för utbredning av TBEV i naturliga fokusområden. Det visar även på att värdmiljön påverkar strukturen för ”quasispecies”-populationen. Dessutom visar våra studier att evolution och utveckling av ”quasispecies”-strukturen kan påverka virulensen för TBEV i möss.

Predadores de topo desempenham um papel importante na manutenção dos sistemas em que eles ocorrem porque influenciam diretamente a estrutura e a dinâmica de comunidades. Desta forma, este estudo descreveu alguns mecanismos de co-ocorrência espaço-temporal entre a onça-pintada (Panthera onca) e duas espécies de mesopredadores (Puma concolor e Leopardus pardalis), o seu controle top-down na comunidade de mamíferos e os requerimentos ambientais que determinam a sua distribuição no bioma Amazônia. Para as análises de co-ocorrência espaço-temporal foram utilizados o modelo de ocupação e a densidade de Kernel utilizando os registros de armadilhamento fotográfico (2008-2011). Para descrever o controle top-down foi elaborada uma rede trófica utilizando os itens alimentares consumidos pelas espécies e disponíveis na literatura (1983-2014). Para indicar quais as áreas mais adequadas foi utilizado o modelo de distribuição de espécies utilizando as localizações geográficas de ocorrência da espécie que foram compiladas de três diferentes bases de dados (2000-2013). A ocorrência das duas espécies de mesopredadores não foi diferente nos sítios com e sem a onça-pintada nas quatro temporadas de amostragem. A probabilidade de detecção da jaguatirica foi maior nos sítios com a presença da onça-pintada em apenas uma temporada de amostragem. A sobreposição no período de atividade das espécies de mesopredadores com a onça-pintada foi baixa, com cerca de 55% de sobreposição. Também ocorreu uma mudança razoável no período de atividade das espécies entre as temporadas de amostragem, com mínima de 32% e máxima de 56% de sobreposição. As maiores diferenças na detecção e na sobreposição temporal ocorreram na terceira temporada quando teve o maior número de capturas e recapturas da onça-pintada. A rede trófica apresentou seis níveis e grande riqueza de espécies e densidade de interações. Após a remoção da onça-pintada, houve a perda de um nível trófico e de aproximadamente 20% de interações. Quando comparada a distribuição atual da onça-pintada com a histórica, foi possível constatar a perda de espaço ambiental em áreas mais frias (< 6,3 °C), mais secas (< 288 mm), mais úmidas (> 7517 mm) e com maior elevação (> 3597 m). O modelo de distribuição também indicou que muitas áreas potenciais estão disponíveis à ocorrência da onça-pintada e que algumas merecem atenção, especialmente, nas porções leste e sul da Amazônia onde a espécie corre maior risco de desaparecimento local devido à antropização acelerada. Este estudo forneceu significativa contribuição para a compreensão da população de onça-pintada na Amazônia, bioma que ainda possui a maior lacuna de conhecimento sobre a biologia e ecologia da espécie. Demonstrou o efeito da sua presença na detectabilidade e no período de atividade de outras espécies. Também demonstrou seu papel ecológico como predador de topo exclusivo porque foi a única espécie que predou todas as outras de níveis tróficos inferiores. Descreveu o espaço ambiental originalmente ocupado (distribuição histórica) e o perdido (distribuição atual). Indicou as áreas mais adequadas à sua ocorrência e aquelas potenciais ao seu desaparecimento. / Apex predators play an important role in the maintenance of systems in which occur because they directly influence the structure and dynamics of communities Thus, this thesis aims to describe some of the mechanisms of spatio-temporal co-occurrence between the jaguar (Panthera onca) and mesopredators (Puma concolor and Leopardus pardalis), their top-down control on the community and environmental requirements that determine their distribution. To the analyses of spatio-temporal co-occurrence were used the occupancy model and the Kernel density with records derived from camera trapping (2008-2011). To the analysis of trophic networks was used a foodweb model with prey spectra of felids compiled from the available literature (1983-2014). To indicate the most suitable areas to its occurrence was used a species distribution model with geographic location of the species compiled from three different databases. The occupation of the two species of mesopredators was not different among sites with and without jaguar. The probability of detection was different for ocelot, with higher detection on sites with than without jaguar. The overlap in the activity pattern among jaguar and mesopredators was low, with approximately 55% of overlapping. Also there was a reasonable change in the overlap between sampling seasons, with a minimum of 32% and maximum of 56% of the difference in the activity pattern. The differences in the detection and temporal overlap occurred in the third season when occurred the highest number of jaguar captures and recaptures. The trophic network presented six levels and, a high species richness and links density. After removal of the jaguar, a trophic level and approximately 20% of links were lost. When compared historical and current distributions, the loss of environmental space occurred in areas colder (< 6.3 ° C), drier (< 288 mm), wetter (> 7517 mm) and at higher elevation (> 3597 m). The distribution model also indicated that there is many potential suitable areas available to the jaguar occurrence and, some of them deserve attention, particularly, in eastern and southern portions of Amazonia where the species is most at risk of local extinction. This study provided a significant contribution to the knowledge of the population of jaguar in the Amazon biome which still has the largest gap of information on the biology and ecology of the species. It demonstrated the effect of the presence of the species in the detectability and the activity pattern of others. Also, it demonstrated their ecological role as an apex predator exclusive because it was the only one that ate all other species of lower trophic levels. It described the environmental space originally occupied (historical distribution) and lost (current distribution). It indicated potential suitable areas to its occurrence and threatened areas to its disappearance.