Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Neste estudo foram avaliadas a eficiência técnica e os custos da aplicação do tratamento silvicultural de desbaste de liberação seletivo, com anelamento e aplicação de herbicida (Tordon, 50% de diluição), em uma Floresta Ombrófila Densa no Estado de Roraima, manejada de acordo com os preceitos de exploração de impac o reduzido e legislação vigente. Para analisar o efeito das características das árvores na desvitalização, foi ajustado o modelo logístico binário, indicando uma menor velocidade de desvitalização para espécies secundárias. Foram aneladas 21,6 arv/ha para favorecer a liberação de 12 arv/ha, em uma relação de 1,8 competidores para cada Árvore Comercial potencial para Colheita Futura (ACCF) liberada. O resultado da aplicação do tratamento silvicultural demonstrou uma boa efetividade da técnica, alcançando 100% de mortalidade das árvores competidoras no período de 12 meses após o anelamento, com 69% das árvores desvitalizadas dentro do período de 6 meses. O custo por hectare atingiu valor total de R$ 77,88/ha, sendo o custo por árvore anelada de R$ 3,59 e o custo por árvore liberada de R$ 5,56. Ao analisar a distribuição dos custos, observou-se que 50% deveu-se ao insumo (no caso específico a aquisição do herbicida), 47% decorreu do custo da mão de obra, 2% deveu-se à aquisição de equipamento de proteção individual e 1% de materiais. O rendimento operacional alcançou 0,76 homem/dia.ha-1, abrangendo as atividades de localização das ACCF, identificação das competidoras, corte de cipós, anelamento e aplicação de herbicida. / This study presents the results of the analysis of technical efficiency and costs of silvicultural treatments carried out in a lowland Amazon rainforest logged under reduced impact logging guidelines. The silvicultural treatments consisted in the postharvest girdling and herbicide treatment (using the product Tordon in 50% solution) of remnant trees competing with future crop trees (FCTs). In order to analyze the effect of girdling on tree mortality, a binary logistic model was utilized. The model indicated a slower mortality process for secondary tree species. On average 21,6 competing trees per hectare were girdled in order to benefit 12 FCTs per hectare (on average 1,8 competitors for every FCT). Results demonstrate the high efficiency of the silvicultural treatments tested: mortality of competitors attained 69% within six months after girdling and 100% within twelve months after girdling. The total cost of girdling amounted to BRL 77,88 per ha, BRL 3,59 per girdled tree and BRL 5,56 per FCT. Of the total cost, 50% arose from production factors, especially herbicide acquisition, while 47% were labor costs. Only 2% of the total costs were generated from work safety equipment and 1% of other materials. The operative productivity attained 0,76 man days per hectare which included the activities competitor identification, climber cutting, girdling and herbicide application.

A teca é uma árvore de grande importância comercial pelas características de cor e durabilidade de sua madeira. Devido a sua rusticidade e fácil adaptação ao clima, plantios de teca tornam-se cada vez mais atrativos ao redor do mundo. Contudo, esta espécie apresenta escassez de estudos genéticos moleculares a respeito tanto de sua madeira, quanto de sua tolerância às variações ambientais. Uma vez que o transcriptoma pode apresentar grande quantidade de informação a respeito dos genes expressos por um conjunto celular, neste trabalho foi realizado o primeiro transcriptoma de teca, onde foram sequenciadas flores, folhas, raízes e seedlings pela tecnologia Illumina. A montagem do transcriptoma foi realizada com o programa Trinity acima de 100 milhões de reads e gerou mais de 400 mil contigs, os quais tiveram as anotações funcionais adquiridas com o programa Blas2GO. 51% dos contigs foram anotados, mostrando alta similaridade com as espécies Vitis vinifera e Solanum licopersicum; destes, 78% obtiveram anotações funcionais com o Gene Ontology, totalizando 5.165 termos para Processo Biológico, 2.846 termos para Função Molecular e 742 para Componente Celular. A expressão diferencial foi obtida com o programa edgeR a 5% de probabilidade de erro e mostrou que, para 187.315 contigs montados através da fusão de todas as bibliotecas sequenciadas, 18 mostraram expressão diferencial para flor, 14 para folha, 13 para raiz e 29 para seedling. Após a etapa de caracterização do transcriptoma, foi realizado um experimento de estresse por déficit hídrico em casa-de-vegetação, onde plantas de teca foram submetidas a estresse Moderado (40% de água no substrato por 20 dias), estresse Severo (20 a 40% de água por 30 dias) e tratamento controle (substrato saturado). As medições através de analisador de gases por infravermelho (IRGA) mostraram queda na fotossíntese (até 70% a menos do que o controle), na transpiração (até 77%) e na condutância estomática (até 85%) entre os tratamentos; além disto, o conteúdo relativo de água foliar caiu 13% entre o tratamento severo e o controle, e níveis de prolina livre foram até 3,5 vezes mais altos nos tratamentos de estresse. A temperatura foliar aumentou significativamente com o aumento da irradiância de fótons aplicada. A busca por genes relacionados ao estresse por déficit hídrico na biblioteca de transcritos de Raiz retornou 1.145 sequências, e destas, 4 foram caracterizadas: TgTPS (trealose 6-fosfato sintase), TgPIP (aquaporina, proteína intrínseca de membrana plasmática), TgDREB2 (proteína de ligação a elemento responsivo a desidratação) e TgAREB (proteína de ligação a elemento responsivo a ácido abscísico). Apenas TgTPS, TgPIP e TgDREB2 mostraram alto grau de conservação entre as espécies, podendo ser corretamente amplificadas via PCR e validadas por sequenciamento. Assim, com o banco de dados de transcritos obtido pelo RNA-seq, foi possível identificar genes candidatos ao estudo de características vegetativas e reprodutivas de teca, contribuindo para entender os mecanismos moleculares desta espécie florestal. / Teak is a tree of great commercial importance by the characteristics of color and durability of its wood. Due to its hardiness and easy adaptation to climate, teak plantations become increasingly attractive around the world. However, this species has a lack of molecular genetic studies on both of its wood, as their tolerance to environmental variations. Once the transcriptome can provide lots of information about the genes expressed by a cell group, this work represents the first transcriptome teak, which were sequenced flowers, leaves, roots and seedlings by Illumina technology. The transcriptome assembly was performed with Trinity program above 100 million reads and generated more than 400,000 contigs, which have acquired the functional annotations with Blas2GO program. 51% of the contigs were annotaded, showing high similarity to Vitis vinifera and Solanum licopersicum; of these, 78% had functional annotations with the Gene Ontology, totaling 5,165 terms for Biological Process, 2846 terms for Molecular Function and 742 for Cell Component. The differential expression was obtained with the edgeR program at 5% probability of error and showed that for 187,315 contigs assembled by merging all sequenced libraries, 18 showed differential expression to flower, 14 to leaf, 13 to root and 29 for seedling. After this step of characterization of the transcriptome, we performed a stress experiment by water deficit at greenhouse, where teak plants were subjected to Moderate stress (40% of water in the substrate for 20 days), Severe stress (20 to 40% water for 30 days) and control treatment (saturated substrate). Measurements by infrared gas analyzer (IRGA) showed a decrease in photosynthesis (up to 70% less than the control), transpiration (up 77%) and stomatal conductance (up 85%) between treatments; furthermore, leaf relative water content dropped 13% between the treatment control and severe, and free proline levels were up to 3.5 fold greater in stress treatments. The leaf temperature increased significantly with increasing irradiance of photons applied. The search for genes related to stress by water deficit in the root transcripts library returned 1,145 sequences, and these, 4 were characterized: TgTPS (trehalose 6-phosphate synthase), TgPIP (aquaporin, protein intrinsic of plasma membrane), TgDREB2 (dehydration responsive element binding protein) and TgAREB (abscisic acid responsive element binding protein). Only TgTPS, TgPIP and TgDREB2 showed a high degree of conservation between species, and can be properly amplified by PCR and validated by sequencing. Thus, with the database of transcripts obtained by RNA-seq, candidate genes were identified for the study of vegetative and reproductive characteristics teak, helping to understand the molecular mechanisms of this forest species.

Os marcadores moleculares têm sido frequentemente utilizados em estudos sobre a diversidade e a estrutura genética populacional. A introdução dos marcadores moleculares revolucionou a genética de populações na década de 50, com a técnica de isoenzimas e recentemente tem conseguido enormes avanços com a aplicação de tecnologias baseadas em DNA. Os marcadores moleculares baseados em DNA permitiram uma ampla cobertura genômica e tornaram-se poderosas ferramentas para estudos de genética de populações. Marcadores codominantes têm sido muito utilizados na genética de populações por serem mais informativos que os marcadores dominantes. O objetivo principal deste trabalho foi utilizar marcadores dominantes com o intuito de contornar o problema da dominância. Para isso, foram utilizadas neste trabalho progênies para genotipagens com RAPD visando inferir o genótipo das plantas matrizes. Foi encontrando um valor de variação entre populações de plantas jovens, igual a ST f ˆ =0,328. E estimativa similar a esta, foi calculada com os dados de freqüências alélicas das plantas matrizes, obtendo-se um valor de ST F ˆ =0,318. O objetivo secundário deste trabalho foi gerar várias estimativas de parâmetros populacionais com a finalidade de comparar os diferentes tipos de marcadores moleculares. Foram comparadas as estimativas relacionadas ao sistema reprodutivo ( tˆ ), heterozigozidade esperada ( e H ˆ ) e observada ( o H ˆ ), estatísticas F de Wrigth, o parâmetro ST f ˆ e dendrogramas obtidos com os diferentes tipos de marcadores (SSR, RAPD e isoenzimas) em diversas abordagens. A taxa de cruzamento ( tˆ ) obtida com os diferentes tipos de marcadores foram congruentes, sendo que a menor foi encontrada com isoenzimas utilizando progênies ( m tˆ =0,835), e a maior obtida com marcadores SSR ( a tˆ =1,07) utilizando indivíduos adultos. Isto levou a concluir que a espécie é alógama ou com tendência para alogamia. Com relação à estrutura genética e o fluxo gênico as estimativas não foram inteiramente concordantes. A menor estimativa de divergência foi obtida com marcadores isoenzimáticos ( p q ˆ =0,154, Nm=1,370) e a maior com RAPD ( ST f ˆ =0,328, Nm=0,512). Porém é importante ressaltar, que estas estimativas não são diretamente comparáveis, pois são obtidas de maneiras diferentes e com dados de progênies ou adultos. Quanto à estruturação da variabilidade visualizada através de agrupamentos, observou-se que os dendrogramas apresentam um padrão concordante sendo que a maior sensibilidade (maior amplitude de distâncias) foi obtida com os dados de SSR. Além disso, foram feitas correlações entre as matrizes de distâncias genéticas e geográficas e entre as matrizes de distâncias genéticas (correlações entre os diferentes marcadores). Estas correlações foram altas indicando que todos os marcadores amostram bem o genoma. Este estudo permitiu comparar dados de duas gerações e uma metodologia diferente para análise de dados com marcadores dominantes, sem impor restrições nos modelos (f =1 ou f =0). Pôde-se concluir que houve congruência entre as estimativas dos parâmetros populacionais obtidas com os diferentes tipos de marcadores, embora tenha ocorrido algumas discrepâncias como foi o caso da estimativa de fluxo gênico com marcadores isoenzimáticos. Apesar de os marcadores possuírem diferentes naturezas todos foram igualmente informativos para este estudo populacional, inclusive os dominantes quando foram usados dados de duas gerações. / Molecular markers have frequently been used in studies on diversity and population genetic structure. The introduction of the these markers revolutionized the genetics of populations in the decade of 50 with the isoenzimes technique and recently enormous progresses have been achieved with the application of technologies based on DNA. Molecular markers based on DNA allowed a wide coverage of the genome and therefore became a powerful tool for these studies. Codominant markers, being more informative than the dominant ones are now being widely used. The main objective of this work was to use dominant (RAPD) markers overcomming the problem of dominance through progeny testing. Offspring were genotyped in order to infer the maternal genotype. Using the AMOVA procedure the variation value found among populations of seedlings was equal to ST f ˆ =0.328. The corresponding F statistic, based on allelic frequencies of seed parents, was ST F ˆ =0.318. The second objective of this work was to obtain different estimates of population parameters with the purpose of comparing the different types of molecular markers. In addition to Wright’s F statistics, estimates related to the reproductive system (tˆ ), expected ( e H ˆ ) and observed heterozigozities ( o H ˆ ) and dendrograms obtained with markers SSR, RAPD and isoenzimes were compared. The outcrossing rate ( tˆ ) obtained agreed reasonably well, and the smallest value was found with isozymes using progenies ( m tˆ =0.835), and the largest one, obtained with SSR markers ( a tˆ =1.07) using adult individuals. The results led to a conclusion that the species is allogamic or with tendency to allogamy. Estimates related with the genetic structure and gene flow, however, were not entirely congruent. The smallest divergence estimate was obtained with isozymes ( p q ˆ =0.154, Nm=1.370) and the largest one with RAPD ( ST f ˆ =0.328, Nm=0.512). It is important to point out, that these estimates are not directly comparable, due to the difference in the underlying model and the basic material used (progenies or adults). About the structuring of the variability visualized through groupings, dendrograms presented a congruent pattern and the largest sensibility (larger range of distances) was obtained with SSR data. In addition, correlations were calculated among the matrices of genetic and geographical distances and among the matrices of genetic distances obtained from the different markers. High correlations were verified among these matrices, indicating that all markers sampled well the genome under study. This study allowed to compare data of two generations and a different methodology for data analysis with dominant markers, without imposing restrictions on the model ( f =1 or f =0). It could be concluded that a reasonable consistency was verified among the population parameters obtained with different types of markers, although some discrepancies existed as in the case of estimates of gene flow with isozymes markers. In spite of their different origins, the markers used here were equally informative for this population study, including the dominant one, when data of two generations were used.

O aumento do consumo de agrotóxicos, em geral nos países em desenvolvimento cuja base econômica é a agricultura, como no Brasil (primeiro no ranking mundial), tem sido relacionado à expansão da degradação dos ecossistemas e à perda da biodiversidade, principalmente das espécies não alvo, incluindo ainda os riscos inerentes à saúde humana. Além disso, a ausência de políticas e programas mais efetivos relacionados à regulação e uso de agrotóxicos no Brasil, bem como o estabelecimento de normas restritivas baseadas em resultados gerados em países de clima temperado, tornam-se cada vez mais preocupantes, pois podem subestimar os reais riscos da contaminação ambiental por agrotóxicos em ecossistemas tropicais. Nesse contexto, o presente estudo teve como objetivo avaliar os efeitos diretos e indiretos do agrotóxico pyrimethanil, um fungicida utilizado em diversas culturas de climas temperado e tropical, sobre a comunidade aquática tropical, considerando experimentos laboratoriais e o uso de modelos ecossistêmicos para avaliação destes efeitos. Para atender aos objetivos propostos foram realizados testes de toxicidade com as espécies Pseudokirchneriella subcapitata (alga), Ceriodaphnia silvestrii e Daphnia similis (zooplâncton) e Danio rerio (peixes), além de um experimento em mesocosmos, monitorado em longo prazo (durante 15 dias antes e 366 dias após a contaminação), avaliando as variações físicas e químicas, bem como as respostas das comunidades zooplanctônicas e fitoplanctônicas frente à contaminação por pyrimethanil, em uma concentração média de 1,36 mg.L-1. Nos testes de toxicidade, as CEs obtidas foram de 0,67 mg.L-1 (crônica) e 3,26 mg.L-1 (aguda) para C. silvestrii; de 3,65 mg.L-1 (agudo) para D. similis; de 9,65 mg.L-1 para P. subcapitata e para D. rerio os valores obtidos para imobilidade foram de 10,45 mg.L-1 (96h) e 13,77 mg.L-1(48h) e para a mortalidade foram de 27,45 mg.L-1 (96h) e 32,17 mg.L-1 (48h). Pelos resultados dos experimentos em mesocosmos verificaram-se efeitos negativos diretos sobre o zooplâncton (redução da densidade e alteração na composição de espécies) e indiretos sobre o fitoplâncton, decorrentes da diminuição da pressão de pastagem, além do desaparecimento de algumas espécies mais sensíveis. Os efeitos tóxicos observados foram além do período em que foi observada a degradação completa do pyrimethanil, demonstrando o alto impacto do agrotóxico em ecossistemas aquáticos e a complexidade da dinâmica desse tipo de contaminação em ecossistemas naturais. O design experimental revelou-se adequado, gerando informações importantes sobre os impactos dos agrotóxicos nos ecossistemas aquáticos. A partir dos resultados obtidos sugere-se que a utilização de espécies nativas de regiões tropicais seja ampliada nos testes de toxicidade laboratoriais, sendo fundamental que os mesmos sejam complementados com os experimentos em modelos ecossistêmicos, o que permite uma avaliação dos efeitos diretos e indiretos dos contaminantes em nível de população e comunidade, bem como uma melhor compreensão destes efeitos nas funções e serviços ecossistêmicos. / The increase in the consumption of pesticides, mainly in developing countries whose economic base is agriculture, as Brazil (first in the world ranking), has been associated to the expansion of ecosystem degradation and biodiversity losses, especially of non-target species, also including the risks to human health. In addition, the absence of policies and effective programs related to the regulation and use of pesticides in Brazil, and the establishment of restrictive standards based on results generated in temperate countries, make it becomes increasingly worrisome because it may underestimate the real risks of environmental contamination by pesticides in tropical ecosystems. In this context, the present study aim to evaluate the direct and indirect effects of the pesticide pyrimethanil, a fungicide used in many temperate and tropical crops, upon a tropical aquatic community, considering laboratory experiments and the use of ecosystem models to evaluate these effects. To achieve the proposed objectives toxicity tests were performed with the species Pseudokirchneriella subcapitata (algae), Ceriodaphnia silvestrii and Daphnia similis (zooplankton) and Danio rerio (fish), as well as an experiment in mesocosms, monitored for a long-term (15 days before and 366 days after infection), evaluating the physical and chemical variations, and also the responses of phytoplankton and zooplankton communities across the pyrimethanil contamination in an average concentration of 1.36 mg.L-1. In toxicity tests, the ECs obtained were 0.67 mg.L-1 (chronic) and 3.26 mg L-1 (acute) for C. silvestrii; 3,65 mg.L-1 (acute) for D. similis; 9.65 mg.L-1 for P. subcapitata; and the values obtained for D. rerio immobility were 10.45 mg.L-1 (96h) and 13.77 mg.L-1 (48h) and mortality were 27.45 mg.L-1 (96h) and 32.17 mg.L-1 (48h). The results of the experiments in mesocosms showed direct negative effects on zooplankton (reduced density and change in species composition) and indirect effects on phytoplankton, resulted from the decrease in grazing pressure in addition to the exclusion of some sensitive species. Even after the complete degradation of pyrimethanil, toxic effects were observed, demonstrating the high impact of this pesticide on aquatic ecosystems and the complexity of the dynamics of this type of contamination in natural ecosystems. The design of the experiment revealed to be appropriate for the study, generating important information about the impacts of pesticides on aquatic ecosystems. From the results, it is suggested an increase in the use of native tropical species in the toxicity laboratory tests. Also, this process should be complemented with experiments in ecosystem models, allowing the evaluation of the direct and indirect effects of contaminants in the population and in community level as well as a better understanding of these effects on ecosystem functions and services.

Este trabalho analisa aspectos, em diversas escalas temporais e espaciais, da estrutura e dinâmica da comunidade arbórea na Reserva da Cidade Universitária Armando de Salles Oliveira (CUASO) (23º33\' S, 46º43\' W), em São Paulo, SP. A partir dos dados obtidos são sugeridas ações de manejo para fins de conservação da comunidade arbórea no local. A Reserva é uma mancha de floresta secundária com cerca de 10 ha de área. O histórico (1930-1994) das modificações da paisagem no entorno (330 ha) da Reserva é descrito, e evidencia o processo de urbanização ocorrido no período, com conseqüente diminuição de área coberta por vegetação herbácea e aumento da área coberta por construções. As áreas florestadas sofreram declínio e posterior recuperação parcial. Cerca de 40% da Reserva tem vegetação com mais de 70 anos de idade, e 22% são áreas com menos de 27 anos de idade, localizadas próximo às bordas. Foi realizado o mapeamento, medição de DAP e identificação de todas as 1157 árvores com DAP &gt; 25 cm em 8,58 ha (Área 1, a área total da Reserva com exceção do lago e uma porção de 1,5 ha dominada por Eucalyptus sp.) e de todas as 1270 árvores com DAP &gt; 9,5 cm em 2 ha (Área 2) no interior da Reserva. Na Área 1 foram encontradas 91 espécies (10,9% exóticas) e índice de Shannon H\' = 3,34 nats/ind., com 33,7% das espécies sendo representadas por apenas um indivíduo. Espécies exóticas e nativas introduzidas estão, em geral, restritas às porções próximas à borda, com exceção de Archontophoenix cunninghamiana. Não existem áreas na Reserva a mais de 110 m de distância da borda, devido ao seu tamanho e formato. Análises de correspondência mostram variação importante na comunidade (DAP &gt; 25 cm) com a distância da borda até cerca de 50 m, mas sugerem maior importância da idade da vegetação na determinação da composição da comunidade. Na Área 2, foram encontradas 103 espécies (10,7% exóticas) e H\' = 3,54 nats/ind. Foram descritas as mudanças na estrutura e composição da comunidade arbórea (DAP &#8805; 15,9 cm) ocorridas entre 1992 e 1997 em uma área de 100 x 50 m no interior da Reserva. Densidade e área basal da comunidade total aumentaram consideravelmente no período; diversidade e equabilidade permaneceram praticamente as mesmas, mas diversidade e equabilidade de espécies nativas diminuíram. Entre as árvores com DAP &#8805; 9,5 cm, em uma área de 2,1 ha, A. cunninghamiana foi a espécie com maior densidade, com 305 indivíduos (22,5% do total). A espécie mostra preferência por estabelecimento em locais sombreados. A análise da estrutura de tamanhos indica um aumento futuro da densidade relativa da espécie. Dois levantamentos com 2,5 anos de intervalo (DAP &#8805; 9,5 cm) mostraram a morte de três dos 154 indivíduos iniciais e o recrutamento de mais 89, levando a um crescimento populacional de 19,4 %.ano-1, muito elevado. CUAKIA, um gap model derivado de KIAMBRAM, foi parametrizado para simular o estado atual da floresta na Reserva. O modelo previu uma fase sucessional inicial dominada por Piptadenia gonoacantha, seguida por uma fase de dominância de Croton floribundus e Alchornea spp. e, posteriormente, por Ficus insipida e outras espécies de dossel tolerantes à sombra e de grande longevidade. A distribuição espacial de árvores em múltiplas escalas espaciais foi analisada usando a função L (modificação de K de Ripley) e g uni e bivariada. O conjunto de indivíduos com DAP &gt; 25 cm apresentou distribuição regular em pequenas escalas (r < 6 m) e agregada em escalas maiores (17 m < r < 115 m). Quase todas as espécies analisadas apresentaram distribuição agregada em alguma escala espacial. Os resultados sugerem competição em pequena escala e limitação de dispersão de sementes como os principais fatores determinantes dos padrões encontrados. Os dados de mapeamento das árvores com DAP &gt; 25 cm foram usados para a divisão da Reserva em áreas de vegetação relativamente homogênea. Análise de correspondência foi usada como ferramenta de ordenação de parcelas circulares (r = 10 m) dispostas em uma grade regular com espaçamento de 10 m. Os valores de cada parcela foram mapeados e com base nestes mapeamentos foram definidas nove zonas de manejo no interior da Reserva. Uma das zonas é quase exclusivamente ocupada por Eucalyptus sp.. Outras apresentam predominância de espécies exóticas e/ou plantadas na Reserva. Sugere-se a introdução de espécies nativas e o controle de exóticas, especialmente A. cunninghamiana, no interior e no entorno da Reserva. / This work analyses the structure and dynamics, at several spatial and temporal scales, of the arboreal community in the Reserve of the Cidade Universitária Armando de Salles Oliveira (CUASO) (23º33\' S, 46º43\' W), São Paulo, SP. Based on these data, management actions are suggested, aiming at the conservation of the arboreal community at the site. The Reserve is a secondary forest patch with an area of approximately 10 ha. We describe the 1930-1994 changes in landscape structure in the surroundings (330 ha) of the Reserve, showing the urbanization process in the region. As a consequence, the area covered by grasslands was reduced and the area covered by buildings increased. Forested areas declined and recovered partially afterwards. Roughly 40% of the Reserve encompasses vegetation more than 70 years old and 22% are areas less than 27 years old, located near the edges. We mapped, measured the dbh and identified all 1157 trees with dbh &gt; 25 cm in 8.58 ha (Area 1, the total area of the Reserve excluding the lake and a 1.5 ha-area dominated by Eucalyptus sp.) and all 1270 trees with dbh &gt; 9.5 cm in 2 ha (Area 2) in the Reserve. In Area 1 we found 91 species (10.9% being exotic) and a Shannon index H\' of 3,34 nats/ind., with 33.7% of the species being represented by only one individual. Exotic species and introduced natives were generally restricted to the regions near the edge, with the exception of Archontophoenix cunninghamiana. No place inside the Reserve is more than 110 m away from the edge, due to the size and shape of the Reserve. Correspondence analyses showed important variation of the community (dbh &gt; 25 cm) with distance to the edge up to 50 m, but suggest that age of vegetation is more important in defining the composition of the community. In Area 2 we found 103 species (10.7% exotic) and H\' = 3.54 nats/ind. We analysed structural and compositional changes of the arboreal community (dbh &#8805; 15.9 cm) between 1992 and 1997 within a 100 x 50 m plot. Density and basal area of the total community increased considerably in the period; species diversity and evenness remained almost the same, but diversity and evenness of native species decreased. In a 2.1 ha area inside the Reserve, A. cunninghamiana was the species with the highest density among trees with DBH &#8805; 9.5 cm, with 305 individuals (22.5% of total). The species shows preference for establishment in shady sites. The size structure analysis indicates a future increase in the relative density of the species. Two surveys with a 2.5 years interval (DBH &#8805; 9.5 cm) showed the death of three of the initial 154 individuals and the recruitment of 89 more, leading to a population growth of 19.4 %.year-1, a very high rate. CUAKIA, a gap model derived from KIAMBRAM, was parameterized to simulate the present state of the forest in the Reserve The model predicted an initial sucessional phase dominated by Piptadenia gonoacantha, followed by a phase dominated by Croton floribundus and Alchornea spp. and, later, by Ficus insipida and other shade-tolerant and long-living canopy species. The spatial distribution of trees was analysed using the L (modification of Ripley\'s K) and g functions, in their univariate and bivariate forms. The total pool of individuals with dbh > 25 cm showed uniform distribution at small scales (r < 6 m) and clumped distribution at bigger scales (17 m < r < 115 m). Almost all species showed clumped distribution at some scale. The results suggest competition at small scales and seed dispersal limitation as the main determinants of the patterns found. The data from the mapping of trees with dbh &gt; 25 cm were used to divide the Reserve into areas covered with relatively homogeneous vegetation. Correspondence analysis was used to ordinate circular plots (r = 10 m) laid out on a regular 10 m-interval grid. Scores of each plot were mapped and this mapping was used to define nine management zones inside the Reserve. One of the zones is almost exclusively occupied by Eucalyptus sp.. Others are dominated by exotics or trees which were planted in the Reserve. We suggest the introduction of native species and the control of exotics, especially A. cunninghamiana, inside the Reserve and in its surroundings.

Toxoplasma gondii est un parasite intracellulaire obligatoire. L'infection par T. gondii est largement répandue dans le monde entier. Néanmoins, elle est peu étudiée dans les pays d'Asie du Sud-est dont la Thaïlande.Nous avons réalisé 3 travaux sur le terrain en Thaïlande pour essayer de comprendre la circulation de ce parasite à travers une étude de séroprévalence chez des poulets en zone rurale et des essais d’isolement de souches chez les animaux en vue d’un génotypage. Lors des deux premières missions de terrain dans deux villages de la province de Kanchanaburi, nous avons cherché à déterminer la séroprévalence de l’infection chez des poulets (Gallus domesticus) en utilisant 2 tests sérologiques, Modified-Agglutination Test (MAT et immunofluorescence indirecte (IFAT) puis à isoler des souches de T.gondii à partir des animaux séropositifs. Lors de la troisième mission réalisée dans 3 autres provinces thaïlandaises(Nakhonratchasima, Lopburi et Saraburi), nous avons essayé d’isoler directement le parasite à partir de carcasses de poulets vendues sur les marchés ou d’autres animaux trouvés morts.La séroprévalence globale pour les 2 premières misions sur 600 poulets du Kanchanaburi était de 17,7% (IC 95% :14,6-20,7) et 33,0% (IC 95% : 29,2-36,8), par MAT et IFAT respectivement. Le calcul du coefficient κ montre une absence de concordance entre les deux tests.Au total, 162 essais d'isolement ont été effectués par inoculation à des souris, mais aucune souche viable de T. gondii n'a été isolée pendant ces 3 travaux sur le terrain. Cependant, nous avons détecté la présence d’ADN toxoplasmique en qPCR ciblant le gène 529 bp dans 13 culots de digestion d’organes de poulets, pigeon, caille et dans des cerveaux ou coeurs de souris inoculés par 16 autres poulets. Les Ct observés en qPCR étaient ≥33 indiquant une faible quantité d’ADN parasitaire dans nos échantillons qui n’a pas permis une caractérisation génétique par marqueurs microsatellites.Ce travail a démontré l'importance et les difficultés du travail de terrain pour l'étude de séroprévalence ainsi que l'étude d'isolement. L'isolement des souches de T. gondii a demandé un travail d'échantillonnage intensif, complexe dans l’environnement tropical et humide de la Thaïlande. Les différents paramètres ayant pu avoir un impact négatif sur nos résultats sont discutés. Ils expliquent l’absence d’isolement de souches chez des animaux séropositifs. / Toxoplasma gondii is an obligate intracellular parasite. Toxoplasma gondii infection is widespread throughout the world. Nevertheless, it is poorly studied in Southeast Asian countries including Thailand. We carried out 3 field works in Thailand to try to understand the circulation of T. gondii through a seroprevalence study in chickens in rural areas and strain isolation attempts in animals. During the two first field works, performed in Kanchanaburi province, we determined the seroprevalence in chickens (Gallus domesticus) using 2 serological tests, a Modified-Agglutination-Test (MAT) and an immunofluorescence assay (IFAT) and subsequently tried to isolate the strains of T. gondii from seropositive animals. During the third field work carried out in 3 other Thai provinces (Nakhonratchasima,Lopburi and Saraburi), we attempted to isolate strains directly from chicken carcasses sold in different markets or other dead animals.The overall seroprevalence for 600 chickens sampled over the two field works in Kanchanaburi was 17.7% (95%CI: 14.6% -20.7) and 33.0% (95% CI: 29.2-36.8), by MAT, and IFAT, respectively. The κ coefficient indicated an absence of concordance between the 2 serological tests.A total of 162 isolation attempts were performed by mouse bioassays, but no viable strain of T. gondii was isolated during these 3 field works. However, a qPCR targeting 529 bp T. gondii gene was positive for 13 digestion pellets of organs of chickens, pigeon, quail and in brains or hearts of mice inoculated with 16 other chickens. These qPCR were weaklly positive (Ct ≥33) indicating a low amount of parasite DNA in our samples that did not allow genotyping T. gondii with microsatellite markers.This work demonstrated the importance and difficulties of field work for the seroprevalence study as well as strain isolation. The isolation of T. gondii strains required intensive and complex sampling in the tropical and humid environment of Thailand. The diverse factors that could have a negative impact on our results are discussed. They might explain the absence of strain isolation from seropositive animals.

Une stratégie pour améliorer durablement la fertilité des sols dégradés par érosion au Nord du Vietnam consiste à apporter des amendements organiques exogènes (AOEs). L'application du lisier de buffle, son compost et lombricompost, ainsi que le biochar permettraient à faible coût d’améliorer la qualité des sols et la croissance des plantes en réduisant l'utilisation d'engrais, mais également de séquestrer du carbone. L’objective de cette thèse est d’évaluer (1) l’utilité des quatre AOEs seuls ou en association pour séquestrer du carbone, et (2) l’effet de l’apport des quatre substrats organiques seuls ou en association sur la quantité et qualité des matières organiques d’un sol agricole tropical dégradé typique du Nord du Vietnam. Pour répondre à cet objectif, nous avons effectué des incubations au laboratoire, en sachet de litière dans des conditions de terrain et suivi pendant trois ans une expérience en mesocosme avec ajouts des AOEs au sol cultivé en conditions de terrain.Nos résultats montrent que le compostage en présence de vers de terre conduit à une plus forte transformation de la matière organique issue du lisier de buffle par rapport au compostage traditionel. Le lombricompost était enrichi en composés azotés et appauvri en polysaccharides, et se caractérisait par une altération plus importante des lignines en comparaison avec le compost. La stabilité biologique de ces AOEs a été liée à leur teneur en carbone soluble, diminuant suivant l’ordre : lisier de buffle > compost > lombricompost, alors que leur réactivité chimique était similaire. Le biochar, constitué de carbone aromatique, se caractérisait par une très forte stabilité biologique et chimique. L’association du biochar avec les autres AOEs a influencé leur stabilité chimique et biologique, en protégeant la matière organique labile contre l'oxydation chimique et la dégradation biologique.Notre expérience de trois ans en mésocosmes en conditions naturelles a montré que tous les AOEs ont un effet positif sur le stockage du carbone dans le sol ainsi que sur la qualité de la matière organique de sol. L’association de biochar et de lombricompost en augmenttant l’abondance des composés dérivés de la lignine ainsi que la teneur en sucre provenant des plantes et des microorganismes, semble montrer un effet synergique de cette association sur la fertilité des sols (activité microbienne, prospection racinaire). Comparé aux résultats d’incubation en sachet de litières, ces résultats indiquent un effet significatif et contrasté des AOEs sur la croissance des plantes en particulier sur l’apport racinaire. En conclusion, l’association de biochar et de lombricompost semble la meilleure solution pour améliorer la qualité de sol dégradé par l'érosion dans le Nord du Vietnam. Ces résultats devront être confirmés par des études à long terme, tant du point de vue de la qualité physicochimique que biologique des sols amendés par ces AOEs. / Intensification of agricultural use of tropical soils in Northern Vietnam leads to acidification associated with organic matter loss, rapid decline of their fertility and high erosion rates. Such negative effects may be counteracted by exogenous organic amendments (EOMs). The application of buffalo manure, its compost and vermicompost and biochar alone or in mixture with other EOMs is promising to improve at low cost soil quality, plant growth and carbon sequestration. The aims of this study were to evaluate (1) the usefulness of the four EOM alone or in mixture to sequester carbon and (2) the effect of these amendments on quantity and quality of soil organic matter of a tropical soil degraded by erosion. To anwer to this objective we carried out incubations in the laboratory, in litterbags under field conditions and we monitored a mesocom experiment, where the EOM were added and subjected during three years to cultivation and natural rainfall conditions. Our results showed that composting in the presence of earthworms led to stronger transformation of buffalo manure than regular composting. Vermicompost was enriched in N-containing compounds and depleted in polysaccharides. It further contained stronger modified lignin compared to regular compost. Biological reactivity of these AOEs was related to their soluble organic matter content, which decreased in the order buffalo manure > compost > vermicompost, whereas their chemical reactivity was similar. Bamboo biochar was enriched in aromatic carbon and characterized by a high biological and chemical recalcitrance. The presence of biochar influenced the biological as well as chemical reactivity of the other organic amendments. It led to a protection of organic matter against chemical oxidation and changed their susceptibility to biological degradation. Our experience with mesocosmes during 3 year under the natural conditions showed that all organic amendments had a positive effect on soil carbon storage and significantly influences soil organic matter quality. Biochar could increase the soil carbon sequestration potential, when applied in mixture with vermicompost. The presence of biochar increased lignin derived compounds abundance as well as both plant and microbial sugar content of soil amended with vermicompost but it had no effect in the case of control soil. Compared to our litterbag experiment these results show that EOM have a strong contrasting effect on plant growth, in particular root litter input. In conclusion, the incorporation of biochar and vermicompost seems to be the best solution to improuve the quality of degraded soil in Northem Vietnam. More studies about the impacts of this amendment on soil physico-chemical and biological properties in long-term are needed to comfirm these results.

Master of Science / Department of Mathematics / Ilia Zharkov / When considering an unramified double cover π: C’→ C of nonsingular algebraic curves, the Prym variety (P; θ) of the cover arises from the sheet exchange involution of C’ via extension to the Jacobian J(C’). The Prym is defined to be the anti-invariant (odd) part of this induced map on J(C’), and it carries twice a principal polarization of J(C’). The pair (P; θ), where θ is a representative of a theta divisor of J(C’) on P, makes the Prym a candidate for the Jacobian of another curve. In 1974, David Mumford proved that for an unramified double cover π : C’η →C of a plane quintic curve, where η is a point of order two in J(C), then the Prym (P; θ) is not a Jacobian if the theta characteristic L(η) is odd, L the hyperplane section. We sought to find an analog of Mumford's result in the tropical geometry setting. We consider the Prym variety of certain unramified double covers of three types of tropical plane quintics. Applying the theory of lattice dicings, which give affine invariants of the Prym lattice, we found that when the parity α(H3) is even, H3 the cycle associated to the hyperplane section and the analog to η in the classical setting, then the Prym is not a Jacobian, and is a Jacobian when the parity is odd.

Citrus is grown in almost all countries with a sub-tropical or tropical climate. Africa produces about 7% of global citrus production representing 67 362 564 tonnes in the 2003-04 season. Of these countries, South Africa is the most important citrus producer with the bulk of its fruit being exported to mainly European countries. Although South Africa is the world’s fourteenth biggest producer, it is currently ranked third in terms of global export volumes. An increase in the number of foodborne disease outbreaks over the past few decades has been related to the shift towards consumption of fresh produce and growing world trade. Other factors include changing demographic profiles, changing farm practises, extensive distribution and handling networks, increased consumption of unprocessed products, emergence of new pathogens and more effective detection methods. Shigella spp., Listeria monocytogenes, Hepatitis virus, Caliciviridae virus, Salmonella spp., Escherichia coli and Vibrio cholera are some of the microorganisms implicated in disease outbreaks caused by the consumption of fresh produce. This dissertation focuses on citrus fruit safety and a selected foodborne pathogen, Salmonella enterica serovar Typhimurium. Salmonella has been implicated in several outbreaks associated with the consumption of unpasteurized orange juice, mangoes, cantaloupes, sprouts and tomatoes. S. enterica sv. Typhimurium is also a water-borne pathogen, and its importance in agricultural irrigation and packhouse wash water was also studied. The presence of S. enterica sv. Typhimurium in biofilms in packhouse water and on fruit was finally investigated since biofilms are known to harbour a number of these pathogens. Biofilm formation was monitored in the warm water dip tank using a photo acoustic monitoring device and confirmed by scanning electron microscopy and enumeration. Water sources, i.e. bathroom, handwash stations, irrigation water and warm water baths had high total viable bacterial counts and faecalassociated contamination. Biofilms also formed within the packhouse dip tank at an increased rate. The Polymerase Chain Reaction (PCR) was used to investigate the presence of Salmonella in the citrus export chain. No Salmonella spp. could be detected. S. enterica sv. Typhimurium survived for up to four weeks on the surface of citrus fruit under simulated export conditions. However, Salmonella is not able to survive uninterrupted cold storage conditions for a period longer than two or three weeks. Scanning Electron Micrographs showed that Salmonella is capable of attaching to and colonizing the citrus fruit surface and is able to be incorporated into existing biofilms in warm water tanks of packhouses. This study showed that Salmonella can thrive in packhouse water and potentially be a continuous source of contamination for fruit moving through the infected warm water dip tank. Everyone participating in fruit production, storage and post-harvest handling of fresh fruit should be involved in ensuring quality and safety, since events in the orchard can affect storage life, and incorrect handling during marketing may nullify all previous efforts of quality maintenance. To minimize the occurrence of these pathogens in the fruit chain from production to consumption, several basic good agricultural practices and food safety systems needs to be incorporated and managed correctly. / Dissertation (MSc)--University of Pretoria, 2009. / Microbiology and Plant Pathology / unrestricted

Le changement climatique et le phénomène d'Ilot de Chaleur Urbain - ICU sont quelques effets de l'action humaine sur le milieu. Les conséquences de ce phénomène sont perçus non seulement en termes d'économie - consommation énergétique, mais aussi directement sur le confort des habitants. Dans le contexte des villes tropicales, où les citoyens sont exposés à une forte chaleur, le confort thermique devrait être considéré comme une priorité dans l'élaboration des politiques d'aménagement et conception des espaces extérieurs. Nous avons étudié ce phénomène à travers un cas concret, la ville de Barranquilla, qui répond non seulement à la condition tropicale, mais qui exprime la réalité et les conflits de l'Amérique Latine et de la Colombie. A travers notre étude, nous avons confirmé la relation entre le microclimat et la forme urbaine ; nous avons aussi caractérisé cette relation et fait une contribution à l'enrichissement de l'état de l'art. Mais nous avons également mis en évidence le lien qui peut exister entre les conditions de confort dans les espaces extérieurs et les conditions socio-économiques de la population dans les villes, qui comme Barranquilla, sont marquées par la ségrégation sociale et la fragmentation spatiale. Enfin, nous avons conclu que la meilleure façon d'intégrer des aspects climatiques à la conception urbaine, c'est d'inclure ces connaissances sous forme de principes dans la formation du concepteur urbain. Dans cette optique, nous proposons d'orienter la réflexion vers la création d'une pédagogie plus active basée sur la sensibilité des acteurs et sur le travail collectif et collaboratif. / Climate change and Urban Heat Island (UHI) phenomena are some of the effects of human activity. The consequences of UHI are perceived not only in terms of economic (energy) costs, but also in terms of thermal comfort for inhabitants. In the context of tropical cities, where citizens are exposed to extreme heat, thermal comfort should be considered a policy priority in the design of public space.We have studied the phenomenon of thermal comfort through the case of Barranquilla, a city which not only meets the tropical conditions but also shows us the peculiar conflict and reality of Latin America and Colombia. In our study, we confirmed the relationship between microclimate and urban form; we also characterized this relationship and contributed to enrich the state of the art. In this study we put into evidence the connection between thermal comfort conditions in outdoor public spaces and socio-economic conditions of people in cities marked by social segregation and spatial fragmentation, such as Barranquilla.Finally, this study concludes that the best way to incorporate thermal comfort into urban design and planning is not through design strategies but through the assimilation of principles. Thus, we propose a new pedagogy based on sensitivity to the thermal environment and on collective efforts to enrich the practice of urban design and to develop a symbiosis with climate considerations that seems to have faded at some point in the history of urban development.