Linhagens de Escherichia coli enterotoxigênica (ETEC) são consideradas como importante agente de diarréia, principalmente entre crianças e turistas em países em desenvolvimento. Entre os fatores de virulência expressos por ETEC, as enterotoxinas termo-lábil (LT) e termo-estável (ST) representam os mais relevantes fenótipos. Evidências preliminares sugerem que a severidade da diarréia associada a linhagens de ETEC deve refletir a diversidade natural de linhagens selvagens quanto à produção de enterotoxinas e/ou à ocorrência de variantes naturais com efeitos tóxicos reduzidos. No presente trabalho, investigamos diversidade genética do óperon etx, que codifica para a toxina LT, e da capacidade de produção e secreção de LT por linhagens de ETEC isoladas de humanos ou suínos em diferentes regiões geográficas. Os resultados mostraram considerável variabilidade na produção de LT com valores variando de 2 a 2.525 ng de toxina por mL de cultura. Secreção de LT foi também variável com valores variando de menos que 0,04% a 49,5% do total de LT produzida pelas diferentes linhagens de ETEC. Adicionalmente, experimentos de alça ligada em coelho mostraram uma boa correlação entre a quantidade de LT secretada sob condições in vitro e a capacidade de causar acúmulo de fluidos in vivo. Nós determinamos ainda diversidade de ETEC pela obtenção das seqüências dos óperons etxAB de 50 linhagens (LT+ or LT+/ST+) pertencentes a diferentes sorotipos com ênfase para as linhagens produtoras apenas de LT e isoladas de crianças assintomáticas. As seqüências de nucleotídeo completas dos genes etxAB revelaram 23 alterações de aminoácidos nas subunidades A (18) e B (5), as quais geraram 16 variantes de LT. Entre estes variantes de LT, um mostrou efeito tóxico reduzido em comparação à toxina de referência LT1. A forma de LT atenuada (LT4) tem atividade enzimática reduzida devido à troca de aminoácido. / Enterotoxigenic Escherichia coli (ETEC) strains represent an important etiological agent of diarrheal disease, particularly among children and travelers in developing countries. Among the virulence factors expressed by ETEC strains the heat-labile (LT) and heat-stable (ST) enterotoxins represent the most revelevant phenotypes. Indirect evidences suggest that the severity of diarrhea associated to ETEC strains might reflect the natural diversity of wild strains to produce enterotoxins and/or the occurrence of variants endowed with reduced toxic effects. In the present study, we investigated both the genetic diversity of the etx operon, encoding the heat-labile toxin, and the capability to produce/secrete LT by ETEC strains isolated from humans or porcine in different geoghrafic areas. The results showed a remarkable variability on the production of LT with values ranging from 2 to 2,525 ng of toxin per ml of culture. LT secretion was also variable with values ranging from less than 0.04% to 49.5% of total LT produced by the different ETEC strains. Additionally, rabbit ileal loop experiments showed a good correlation between the amounts of secreted LT under in vitro conditions and fluid accumulation in vivo. We determined also the diversity of the etxAB operon of 50 ETEC strains (LT+ or LT+/ST+) belonging to different serotypes with emphasis to LT+-only producing strains isolated from asymptomatic children. The complete nucleotide sequences of the etxAB genes revealed 23 amino acid changes at the A (18) or B (5) subunits, which generated 16 variant forms of LT. Among these LT variants, one of them showed reduced toxic effects in comparison to the reference toxin LT1. The attenuated LT form (LT4) had decreased enzymatic activity due to an amino acid replacement (K4R) at the A1 subunit. LT4 retains its immunogenic and adjuvant properties following nasal immunization. Additionaly, the LT4 variant showed altered immune modulatory features and promoted a more biased Th1 response, which favor activation of effector CD8+ T lymphocytes, to co-administred antigen with regard to LT1. Taken together, our results demonstrate that ETEC strains isolated from human subjects express natural genetic variability leading to a remarkable polymorphism of the etx operon as well as production and secretion of LT. Such natural genetic diversity observed in ETEC strains may affect the host-pathogen relationships and, consequently, contribute to the severity of the disease among infected subjects.

O palmiteiro (Euterpe edulis Mart.) é uma espécie nativa da Mata Atlântica cujas populações naturais encontram-se degradadas pelo extrativismo. Considerando a escassez de informações relativas às conseqüências genéticas da exploração de palmito, o objetivo deste estudo foi avaliar o impacto do processo de exploração sobre os níveis de diversidade, estrutura genética e tamanho efetivo de populações da espécie. Também foram estudados aspectos genéticos do recrutamento de plantas e o sistema reprodutivo da espécie. O estudo foi realizado em duas localidades do Estado de Santa Catarina, nos municípios de São Pedro de Alcântara e Ibirama. Em cada localidade foram escolhidas duas áreas de ocorrência natural de E. edulis, uma sem influência antrópica e outra que sofreu exploração de palmito, totalizando quatro populações. Os sistemas de exploração foram: (i) extrativismo - onde todos os indivíduos acima de 2 m de altura são cortados, incluindo plantas reprodutivas; and (ii) manejo - onde somente indivíduos acima de 9 cm de DAP são cortados, com a manutenção de 50 plantas reprodutivas por hectare. Em cada população foram examinadas plântulas, jovens e adultos, usando oito locos microssatélites e dez locos alozímicos. Os resultados revelaram que a espécie se reproduz por alogamia ( m tˆ = 0,996 para microssatélites e m tˆ = 1,000 para isoenzimas), porém a ocorrência de cruzamentos entre indivíduos aparentados (até 5%) e cruzamentos biparentais (10%) indica a ocorrência de cruzamentos não aleatórios. Em locos alozímicos, observaram-se as seguintes amplitudes de variação das estimativas de diversidade entre as categorias: Aˆ : 3,05 a 3,15; e Hˆ : 0,416 a 0,431; o Hˆ : 0,378 a 0,403. Em locos microssatélites, a variação observada foi a seguinte: Aˆ : 14,12 a 14,72; e Hˆ : 0,781 a 0,785; o Hˆ : 0,678 a 0,709. Nas populações não exploradas, houve um aumento na freqüência de heterozigotos na direção do estádio adulto, o que sugere a ação da seleção favorecendo o aumento de heterozigotos. Valores altos e significativos do índice de fixação ( fˆ ) foram observados, especialmente nos marcadores microssatélites, indicando desvios do equilíbrio de Hardy-Weinberg. De modo geral, ambos os marcadores revelaram um aumento dos valores de fˆ nas populações exploradas, especialmente entre as plântulas. As estimativas ST Gˆ e ST Rˆ não revelaram alterações na estrutura genética das populações exploradas e demostraram uma divergência genética inferior a 5% na maioria das comparações aos pares, em ambos os marcadores. O tamanho efetivo ( e Nˆ ) dos indivíduos adultos por hectare foi superior a 110 nas populações não pertubadas, enquanto nas populações exploradas, o tamanho efetivo por hectare foi reduzido para 45, sob manejo, e 14, sob extrativismo. Porém, o tamanho efetivo total das populações exploradas ainda é elevado, o que explica a manutenção dos altos níveis de diversidade nessas populações. Finalmente, a informação genética conjunta desses marcadores demonstrou que os efeitos da exploração foram pouco pronunciados até o momento em relação aos níveis de diversidade e estrutura genética das populações de E. edulis. Entretanto, a redução da população de cruzamentos resultou em alterações no comportamento reprodutivo dos indivíduos, promovendo um aumento nos níveis de endogamia nas coortes mais jovens das populações exploradas. Contudo, os resultados obtidos neste estudo indicaram questões adicionais a serem estudadas. Em função do elevado nível de variabilidade dos locos microssatélites observado em E. edulis, recomenda-se aumentar o tamanho das amostras visando otimizar a informação genética proporcionada por esses marcadores. Além disso, novos estudos são necessários sobre os efeitos do manejo tecnificado, uma vez que os resultados obtidos podem ter sido influenciados por outros eventos de exploração ocorridos no passado e pelas populações existentes nas proximidades devido ao elevado fluxo gênico da espécie. / Heart-of-palm tree (Euterpe edulis Mart.; Arecaceae) is a native species of the Atlantic forest whose natural populations are degraded by extractivism. Regarding the relative scarcity of information on the genetic consequences of palm heart exploitation, the aim of this study was to investigate the effects of two exploitation systems - extractivism and management - on the levels of variability, genetic structure and effective size of Euterpe edulis Mart. populations. We also investigated genetic aspects of the plant recruitment and the reproductive system of the species. Four natural populations of E. edulis with different histories of disturbance were surveyed in the districts of São Pedro de Alcântara and Ibirama, Santa Catarina, Brazil. At both sites, we sampled an undisturbed and an exploited population. The exploitation systems were: (i) extractivism - where most individuals higher than 2 m are harvested, including reproductive plants; and (ii) management - where only individuals with more than 9 cm of DBH are harvested, with the maintainance of 50 reproductive plants per ha. Three categories of plants, from seedlings to adults, were examined using eight microsatellite loci and ten allozyme loci. Results demonstrated the preferentially allogamic behaviour of the species ( m tˆ = 0.996 for microsatellites and m tˆ = 1.000 for allozymes), but the occurrence of matings among related individuals (5%) and biparental matings (10%) indicated the existence of non-random matings in this species. For allozymic loci, the following diversity estimates were obtained among the categories: Aˆ : 3.05 to 3.15; e Hˆ : 0.416 to 0.431; o Hˆ : 0.378 to 0.403. For microsatellites, the estimates were as follows: Aˆ : 14.12 to 14.72; e Hˆ : 0.781 to 0.785; o Hˆ : 0.678 to 0.709. In undisturbed populations, there was an increase in heterozygote frequency towards the adult stages, suggesting the action of natural selection favouring such heterozygote increase. Highly significant values of fixation index ( fˆ ) were observed, mainly at microsatellite loci, indicating departures from Hardy-Weinberg expectation. Both markers displayed an increase of fˆ values in the exploited populations, especially for seedlings. The estimates of interpopulation genetic variation ( ST Gˆ ; ST Rˆ ) revealed that more than 95% of the molecular genetic variability of the species is distributed within populations, and there was no evidence of changes in genetic structure of the exploited populations. Effective size ( e Nˆ ) per hectare of the adult individuals was higher than 110 in the two undisturbed populations, while in the exploited populations the effective size per hectare was reduced to 45 under management, and 14 under extractivism. However, the total effective size of the exploited populations was still high, which explains the maintenance of high diversity levels in these populations. Finally, the genetic information from both markers displayed small pronounced effects of the exploitation process on variability and population genetic structure of E. edulis, with the exception of an increase in the inbreeding levels among seedlings and juveniles of the exploited populations. However, our results raised further questions for study. Because of the hypervariability of microssatellite loci used in this work, we would recommend an increase in the sample size (>100) in order to optimize the genetic information provided by these markers. Moreover, new investigations are necessary on the effects of management, since the results from this study could have been influenced by other exploitation events that have occurred in the past and by the existence, due to the high gene flow of the species, of surrounding undisturbed populations.

O presente estudo teve por objetivos caracterizar os vírus Influenza circulantes na cidade de São Paulo e verificar a variabilidade genética do gene da neuraminidase (NA) dos Influenzavírus A. Um total de 3009 amostras de crianças internadas no Hospital Universitário da USP, no período de 1995 a 2006, foram submetidas à duplex RT-PCR para detecção dos Influenzavírus A e B (IA e IB). As amostras positivas para IA foram submetidas à subtipagem pela multiplex RT-PCR. Cento e trinta e três amostras (4,4%) foram positivas, sendo 88,0% (117/133) IA e 12,0% (16/133) IB. Entre as amostras IA, 94 eram H3N2, 7 H1N1 e 16 não foram subtipadas pela multiplex. Um total de 74 amostras (71 H3N2 e 3 H1N1) tiveram o gene da neuraminidase sequenciado (total ou parcialmente). As sequências obtidas foram submetidas à análise filogenética, sendo verificado o agrupamento das cepas circulantes em clusters por ano de isolamento, demonstrando sua evolução temporal. Quando comparadas com as cepas vacinais utilizadas no período, foi verificada uma boa similaridade. / The aim of this study was to characterize Influenza virus circulating in São Paulo city and the neuraminidase (NA) gene sequence of Influenzavirus A in 3009 samples from children hospitalized at USP University Hospital, from 1995 to 2006. Samples underwent duplex RT-PCR for detection and typing of Influenza virus A and B (IA and IB) and also were submitted to multiplex PCR for subtyping of IA. Among 3009 samples, 4.4% were Influenza virus, being 88.0% IA (117/133) and 12.0% IB (16/133). Among samples of IA, 94 were characterized as H3N2, 7 H1N1 and 16 were not subtyped. A total of 74 samples (71 H3N2 and 3 H1N1) had the NA gene sequenced (total or partially). Sequences obtained were compared to sequences of the world and sequences of vaccine strains. Brazilian samples were grouped in clusters with samples isolated in the same year. It was also found a good similarity between circulating strains and vaccine strains.

Introdução: A variação genética em genes que codificam a absorção, distribuição, metabolismo e excreção (ADME) de medicamentos frequentemente afeta a farmacocinética da droga e resulta na variabilidade da eficácia e segurança do medicamento. No entanto, a frequência da variação genética nos genes ADME diferem entre as populações. O objetivo deste estudo foi analisar as variações genéticas nos genes ADME nos pacientes brasileiros portadores do vírus da hepatite C e comparar com outros bancos de dados (1000 Genomes Project e Exome Aggregation Consortium). Métodos: Um total de 147 genes ADME foram genotipados em 100 amostras por sequenciamento de DNA genômico usando SureSelectXT (Agilent) e MiSeq, NextSeq (Illumina). Resultados: Um total de 2004 SNPs em 147 genes foram analisados, incluindo enzimas de fase I (n=50), enzimas de fase II (n=37) e transportadores (n=60). Uma coleção de variantes genéticas indica que há pelo menos 2 vezes mais variações do que semelhanças entre os pacientes com hepatite C e os principais grupos continentais. Estas diferenças foram observadas em vários genes relevantes, incluindo CYP1A2, CYP3A4, NAT2, ABCB1 e SLCO1B1. Além disso, pacientes auto declarados como branco, pardo, negro e asiático também apresentaram diferenças de frequência alélica quando comparados à europeus, americanos mixos, africanos e asiáticos nos polimorfismos dos genes CYP1A1, CYP2B6, GSTP1 e ABCG2, respectivamente. Conclusão: Concluímos que os pacientes com hepatite C tem uma frequência alélica de genes ADME diferente dos outros bancos de dados. Embora a personalização do tratamento medicamentoso com base no genótipo individual, e não na etnia, possa ser a mais apropriada, as diferenças nas frequências alélicas entre os continentes devem ser consideradas ao projetar ensaios clínicos de novos medicamentos / Background: Genetic variation in genes encoding drug absorption, distribution, metabolism, and excretion (ADME) proteins often affects the drug pharmacokinetics and results in variability in drug efficacy and safety. However, the frequency of genetic variation in the ADME genes differ among populations. The aim of this study was to analyze the genetic variations in the ADME genes in Brazilian patients with hepatitis C and to compare to other databases (1000 Genomes Project e Exome Aggregation Consortium). Methods: A total of 147 ADME were genotyped in 100 samples from Brazil by targeted genomic DNA sequencing using SureSelectXT (Agilent) and MiSeq, NextSeq (Illumina). Results: A total of 2004 SNPs in 147 genes that were analyzed, including phase I enzymes (n=50), phase II enzymes (n=37), drug transporters (n=60). We provide a collection of genetic variants that indicate that there are at least 2-times more variation than similarities between patients with hepatitis C and major continental groups. These differences were observed in several relevant genes including CYP1A2, CYP3A4, NAT2, ABCB1 and SLCO1B1. Moreover, white, brown, black and Asian self-reported patients also showed allele frequency differences when compared to European, mixed American, African and Asian for polymorphisms of the genes CYP1A1, CYP2B6, GSTP1 and ABCG2. respectively. Conclusion: We conclude that the hepatitis C patients has an allele frequency of ADME genes different from other data bases. While personalization of drug treatment based on individual genotype rather than ethnicity may be more appropriate, differences in allelic frequencies across continents should be considered when designing clinical trials of new drugs

O tucumã-do-Amazonas (Astrocaryum aculeatum), da família Arecaceae, é uma espécie com ocorrência na Amazônia Ocidental e Central brasileira. Seu fruto é muito apreciado na região amazônica que consome a polpa na forma fresca. Sua produção é feita pelos agricultores extrativistas. Não existem informações dos parâmetros de diversidade e estrutura genética das populações naturais desta espécie, fundamental para o estabelecimento de estratégias adequadas no uso deste recurso genético, e para aumentar a eficiência da domesticação e seleção para um programa de melhoramento genético. Não é conhecido também como este extrativismo pode estar influenciando a diversidade entre estas populações ao nível dos genitores e progênies, o fluxo gênico e a estrutura genética espacial. Assim, o objetivo desta pesquisa foi caracterizar a estrutura e a diversidade genética de populações de A. aculeatum no Estado do Amazonas, utilizando marcadores microssatélites. Como objetivos específicos o estudo visou desenvolver iniciadores de microssatélites para A. aculeatum; avaliar a diversidade e a estrutura genética; determinar o fluxo gênico, bem como o grau de parentesco, a estrutura genética espacial (EGE) e o coeficiente de coancestria numa população. Os iniciadores de microssatélites foram isolados a partir de uma biblioteca genômica enriquecida e caracterizados usando 40 amostras provenientes de duas populações selvagens. Foram identificados 14 iniciadores de microssatélites, mostrando um alto polimorfismo nas populações avaliadas. Para estimar a diversidade e estrutura genética foram utilizadas amostras de material vegetal de 218 plantas distribuídas em 15 populações, localizadas em 14 municípios do estado de Amazonas. Foram identificados 101 alelos nos iniciadores, com média de 10,1 alelos. As médias das heterozigosidades observadas (HO) foram superiores às esperadas (HE) ao nível de população (HO=0,639, HE=0,557) e locos (HO=0,639; HE=0,594). Os baixos valores de FST (0,07) mostraram uma moderada estrutura populacional e a análise Bayesiana indicou um agrupamento mais adequado de k=4, o que foi confirmado pelas análises de PCoA. Para realizar o fluxo gênico, EGE e coeficiente de coancestria foram utilizadas 244 amostras de material vegetal, distribuídas entre 112 possíveis genitores, 12 matrizes e 120 progênies numa população. Foi detectada EGE significativa para os adultos até a distância de 50 m, indicando dispersão de sementes a curtas distâncias. A análise de paternidade detectou 9,2% de imigração de pólen. Não foram detectadas autofecundações e a distância média de polinização dentro da população foi de 81 m. Os índices de diversidade genética confirmaram a estratégia reprodutiva por alogamia da espécie, com níveis elevados de heterozigotos nas populações, e a estrutura genética sugere que a espécie teria iniciado o processo de formação das subpopulações há pouco tempo, tendo sido influenciada antes e após o início do desmatamento. O fluxo gênico detectado indica que a entrada de alelos na população através da imigração de pólen está contribuindo para manutenção da diversidade genética da população. Com relação à conservação da espécie, esta deve ser realizada ao nível das bacias hidrográficas, direcionando políticas de manejo para as bacias hidrográficas da Amazônia. Entretanto, dentro da população é importante a renovação com novas progênies selecionadas a partir de um espaçamento mínimo de 50 m entre plantas matrizes para diminuir as probabilidades de coletar sementes de plantas parentes. / The tucum palm (Astrocaryum aculeatum), family Arecaceae, is a species occurring in Western and Central Brazilian Amazon. Its fruit is widely appreciated in the Amazon region that consumes the pulp in fresh form. Its production is made by extractive farmers. There is no information on the genetic diversity and structure of natural populations of this species, fundamental to establishing adequate strategies in the use of this genetic resource, increase the efficiency of domestication and selection for a breeding program. It is also unknown the way this extrativism may be influencing to diversity of these populations at the level of the parents and offspring, as well as gene flow and spatial genetic structure. Therefore, the objective of this research was to characterize the structure and genetic diversity of populations of A. aculeatum in Amazonas State, using microsatellite markers. As specific objectives, the study aimed to develop microsatellite primers for A. aculeatum; evaluate the genetic diversity and structure; determine the gene flow, the degree of relationship or kinship, the spatial genetic structure (SGS) and the coefficient of coancestry in one population. The loci were isolated from a microsatellite-enriched genomic library and were characterized using 40 samples coming from two wild populations. Fourteen microsatellite primers were identified, showing a high polymorphism in the populations evaluated. To estimate the genetic diversity and structure we used samples of plant material from 218 plants distributed in 15 populations located in 14 municipalities of the state of Amazonas. A total of 101 alleles were identified in the primers, with an average of 10.1 alleles. The averages of the observed heterozygosities (HO) were higher than the expected heterozygosities (HE) at the population (HO=0.639; HE=0.557) and loci (HO=0.639; HE=0.594) levels. The low values of FST (0.07) showed a moderate population structure and the Bayesian analysis indicated as the most suitable a cluster of k=4, confirmed by the groups formed in the PCoA. To conduct gene flow, SGS and the coefficient of coancestry, 244 samples of plant material were used, distributed among 112 possible progenitors, 12 matrices and 120 progenies in a population. A significant SGS was detected for adult trees up to the distance of 50 m, indicating seed dispersal over short distances. Paternity analysis indicated 9.2% of pollen immigration. Selfing was not detected and the average distance of pollination within the population was 81 m. The genetic diversity indices confirmed the outcrossing reproductive strategy of the species with high levels of heterozygotes in the populations, and the genetic structure suggests that the species would have started the process of formation of subpopulations a short time ago, being influenced before and after the start of deforestation. The gene flow detected indicates that the entry of alleles in the population through pollen immigration is contributing to the maintenance of genetic diversity of the population. With respect to the conservation of the species, it should be performed at the level of the river basins, directing management policies for the river basins of the Amazon. However, within the population it is important to renew with new progenies selected from a minimum spacing of 50 m between plant matrices to decrease the probability of collecting seeds from plant relatives.

Species conservation is typically founded upon a range of management strategies, which integrate both biological and socioeconomic data. In this thesis, population genetics, acoustic telemetry, spawning aggregation surveys and stakeholder assessments were used to address key knowledge gaps limiting effective conservation management for critically endangered Nassau grouper (Epinephelus striatus) stocks in The Bahamas. A panel of polymorphic microsatellite markers was optimised to assess the genetic population dynamics of more than 400 Nassau grouper sampled throughout the country. Microsatellite data indicate that contemporary Nassau grouper populations in The Bahamas are predominantly genetically diverse and weakly differentiated, but lack geographic population structure. Assessments of changes in effective population size (Ne) show substantive reductions in Ne within The Bahamas compared to historic values that are likely due to natural disturbances. Evidence for recent bottlenecks occurring in three islands as well as an active spawning site, along with higher inbreeding coefficients in two islands were also found, and can be attributed to more recent anthropogenic activities. Collapse of a historically important Nassau grouper fish spawning aggregation (FSA) was supported by both acoustic telemetry and spawning aggregation survey dives. Restriction-site-associated DNA sequencing (RAD-seq) of 94 Nassau grouper was used to explore intraspecific population dynamics, loci under selection and patterns of gene flow in The Bahamas. Genomic assessments of diversity were in accord with microsatellite data and examinations of gene flow support higher levels of connectivity in The Bahamas than was previously suggested. The increased resolution gained from assessments of genomic data support intraspecific population structuring that may be driven by differences in gene flow and putative loci under divergent selection. Telemetry data were successfully used to identify the origins of spawning adults, and support demographic connectivity through migrations between an active FSA in the central Bahamas and home reef habitats within the Exumas and a no-take marine protected area. Stakeholder assessments highlight the complexities of fisheries management within The Bahamas, with key stakeholders often exhibiting conflicting opinions regarding the status of Nassau grouper and the efficacy of management options. However, these groups mutually agree upon the need to better manage remaining Nassau grouper stocks within The Bahamas through science-grounded policies. Synthesis of these studies along with a review of fisheries governance in The Bahamas was used to develop a comprehensive national management plan for Nassau grouper to facilitate better conservation for remaining populations of this ecologically important marine species.

Forests are among the most important repositories of terrestrial biodiversity and provide a broad range of ecosystem services. During millennia, forests have changed, adapted and evolved under changing conditions. However, in the present century, forests are facing environmental changes at rates with no precedents. A major concern is the risk of declining forest genetic diversity, since genetic variation as the raw material underpinning adaptation is key in maintaining the resilience of forest ecosystems against environmental changes. Understanding the different processes responsible for developing and maintaining the genetic diversity of tree species is essential to better predict tree responses under new conditions. Therefore, this thesis aimed to determine how different forces interact to shape and maintain within and among population genetic diversity of Scots pine and what the implications are for conservation and management under forthcoming environmental conditions. From local to continental scales, I followed a multilevel approach, and found that (i) historic climate changes and geographical barriers have played an important role in shaping the extent and spatial distribution of current genetic diversity of Scots pine. Despite contemporary habitat reduction and fragmentation we found that (ii) high levels of neutral genetic diversity remain in the Scottish populations of Scots pine, with gene flow and specifically wind-driven gene flow dominating over genetic drift and preventing differentiation among the Scottish populations. However, (iii) considerable impacts in the spatial distribution of genetic variation have occurred as a consequence of intensive historical forest management practices. Furthermore, we found that (iv) substantial levels of adaptive genetic variation are present in the Scottish populations of Scots pine, likely a result of selective processes resulting from the different environments they live in, with highly heritable traits, although similar capacity for response through phenotypic plasticity to warming. The results of this thesis help to further disentangle the forces maintaining genetic diversity in one of most widespread conifers in the world, and improving predictions of likely range shifts and adaptation of the species in response to contemporary changes. The thesis provides some recommendations to conservation and management practices.

Mycoplasma agalactiae est responsable de l'agalactie contagieuse, maladie des petits ruminants difficilement contrôlée et figurant sur la liste de l’OIE. Afin d’évaluer la diversité génétique de ce pathogène, 101 isolats ont été comparés par trois techniques (VNTR, RFLP, répertoire vpma). Les résultats révèlent une grande homogénéité génétique dont la souche type PG2 est représentative. Quelques isolats font exception telle la souche 5632 que nous avons séquencée et analysée ici. La comparaison des génomes et des protéomes entre 5632 et PG2 indiquent que la plasticité de ces génomes est liée à d’importants échanges d'ADN et à la présence de nombreux éléments génétiques mobiles (10% du génome). Ces analyses révèlent également une forte dynamique au sein de répertoires de gènes codant des protéines de surfaces. Pour les mycoplasmes, bactéries minimales dépourvues de paroi, ces évènements ont certainement joués un rôle dans leur survie et leur adaptation à des hôtes complexes. / Mycoplasma agalactiae is responsible of contagious agalactia, a disease of small ruminants that is still difficult to control and is listed by the OIE. In order to evaluate the genetic diversity of this pathogen, 101 isolates were compared using three techniques (VNTR, RFLP, vpma repertoire). Results revealed a high genetic homogeneity with the PG2 type strain as representative. Some isolates however diverged such as the 5632 which was sequenced and analysed here. Whole comparative genomic and proteomic analyses of the 5632 and PG2 strains indicate that their genomic plasticity resides in important genes flux and in the presence of several mobile genetic elements (10% of the genome). These analyses also revealed that specific loci encoding repertoire of surface proteins are highly dynamic. For these minimal bacteria that lack a cell-wall, these events have most likely played a major role in their survival and adaptation to complex hosts.

L’objectif des travaux de cette thèse concerne la caractérisation du germoplasme marocain du cactus Opuntia. Les études réalisées pour atteindre cet objectif ont portées sur le comportement phénologique, les caractéristiques génétiques et la composition physicochimique du cactus, ainsi que sur les molécules à fort potentiel thérapeutique, susceptibles d’avoir des effets bénéfiques pour les cellules du système nerveux central, dans les extraits de cactus (fruit, fleur, graine, huile, raquette et épine) et ceci en comparaison avec l’huile d’Argan. Les travaux ont été réalisés dans quatre laboratoires partenaires partageant des compétences dans les domaines d’analyses agronomique, biochimique et moléculaire. Les résultats de nos travaux sont présentés dans trois volets : (i) la caractérisation agronomique du cactus, (ii) la purification et la caractérisation des extraits et des molécules naturelles et (iii) l’évaluation des effets biologiques de ces molécules sur un modèle cellulaire. L’étude phénologique sur des écotypes âgées de 4 ans, issus du site expérimental de l’INRA d’Ain Nezagh, nous a permis de les classer selon le taux de fructification ou la production de biomasse de manière à mieux orienter leur utilisation en fonction de l’origine géographique et de l’espèce. L’étude de la diversité génétique, basée sur les traits morphologiques et les marqueurs moléculaires, a permis d’identifier sur le site d’Ain Nezagh sept espèces de cactus dont deux n’avait jamais été décrites au Maroc, O. leucotricha et O. inermis. Les analyses morpho-anatomique et physico-chimique de la fleur, du jus, du fruit et de la raquette d’écotypes âgées de 10 ans provenant du site de l’INRA de Jemâat Riah ont démontré la présence de deux espèces différentes de cactus du genre Opuntia, comportant quatre variétés non identifiées auparavant sur ce site. Nos travaux montrent donc l’existence d’une grande diversité génétique intra-espèces (variétés) et inter-espèces chez le cactus au Maroc. Paralèllement à ces études, les compositions chimiques des huiles essentielles de raquette et de graine de cactus ainsi que celle d’huile d’argan ont été déterminées. A partir de ces analyses, nous avons choisi d’étudier les effets de deux stérols, le spinastérol et le schotténol, ainsi que d’extraits de stérols sur l’activation du récepteur nucléaire LXR (Liver X receptor, impliqué dans la régulation du métabolisme du cholestérol) dans les cellules cérébrales de la microglie (lignée murine BV-2). Nos résultats montrent que le spinastérol et le schotténol, sans être cytotoxiques, peuvent moduler les expressions des deux isoformes de LXR, LXR-α et LXR-β, ainsi que de leurs gènes cibles ABCA1 et ABCG1. De plus, le schotténol provoque une activation spécifique de LXR-β. Ces résultats suggèrent que ces deux phytostérols pourraient avoir un rôle protecteur dans la modulation du métabolisme du cholestérol dans la microglie. / The objective of this PhD thesis is to characterize the Moroccan germplasm of the cactus Opuntia collected from different regions in Morocco, by studying the phenologic behavior, the genetic features and physicochemical composition, along with the molecules of high therapeutic potential which may have beneficial effects on the central nervous system cells from cactus extracts (fruit, flower, seed, oil, cladodes and spine) and compared to Argan oil. This work has been conducted in fours different laboratories sharing complementary analyses skills at agronomic, biochemistry, molecular levels. Our results are presented in three parts : (i) cactus agronomic characteristics, (ii) purification and characterization of natural extracts and molecules and (iii) the evalution of biological effects of these molecules using a cell model. Initially, the first experimental INRA site of cactus culture, located in Ain Nezagh and containing ecotypes older than 4 years, allowed us to achieve a phenological study with the classification of the ecotypes according to fruiting rate and to the biomass production in order to better guide their use according to geographical origin and species. The genetic diversity study based on morphological traits and molecular markers permited the identification, on the site of Ain Nezagh, of the presence of seven species of cactus among which two have never been described in Morocco: O. leucotricha and O. inermis. The morpho-anatomical and physicochemical analyses of cactus flower, juice, fruit and cladodes of 10 years old ecotypes issued from the Jemâat Riah INRA site, demonstrated the presence of two different species of the genus Opuntia including four varieties not previously identified on this site. Thus, our work indicates the existence of a large intra-species (varieties) and inter-species genetic diversity. Secondly, the chemical compositions of cladode essential oils or cactus seeds as well as argan oil were determined. From these analyzes, we have chosen to study the effects of two sterols, spinasterol and schottenol and also sterol extracts on the activation of the nuclear receptor LXR (Liver X receptor, involved in the regulation of cholesterol metabolism) in microglia brain cells (BV-2 murine cell line). Our results show that spinasterol and schottenol, without being cytotoxics, can modulate the expression of the two isoforms of LXR, LXR-α and LXR-β, as well as of their target genes ABCA1 and ABCG1. In addition, the schottenol causes LXR-β specific activation. These results suggest that these two phytosterols could have a protective role in the modulation of cholesterol metabolism in microglia.

La bactériose vasculaire du riz (BLB) et à stries foliaires (BLS) causées respectivement par Xanthomonas oryzae pv. oryzae (Xoo) et X. oryzae pv. oryzicola (Xoc) sont deux maladies émergentes en Afrique de l'Ouest, suite à l'expansion de la culture du riz et à l'introduction de variétés à haut rendement au cours de ces dernières décennies. Trois nouvelles races de Xoo ont été caractérisées en Afrique dont on a montré, sur la base d'une analyse génétique, leur spécificité africaine. En revanche, une étude réalisée sur une dizaine de souches de Xoc isolées au Mali en 2003, démontre qu'elles sont apparentées à des souches de Xoc asiatiques. En Asie, plusieurs gènes de résistance à Xoo ont été identifiés et déployés dans les programmes de lutte contre BLB. Cependant aucun gène de résistance à Xoc n'a été encore identifié chez le riz. Les objectifs de notre étude étaient (i): d'implémenter les collections de souches de Xoo et Xoc Africaines disponibles mais incomplètes, à l'aide de nouvelles campagnes d'échantillonage réalisées de 2009 à 2012 dans différentes zones agroécologiques du Burkina Faso et du Mali, (ii) de déterminer la diversité génétique de ces souches, (iii) d'identifier et caractériser de nouvelles sources de résistance contre BLB et BLS au sein d'accessions de riz cultivées au Burkina Faso. Nos résultats ont montré que les souches africaines de Xoc sont hautement variables tant d'un point de vue génétique que du pouvoir pathogène. L'analyse par PCR de deux effecteurs de types III conservés (xopAJ et xopW) permet de différencier les souches de Xoc en deux groupes, xopAJ étant absent dans la majorité des souches et une insertion de 1050 bp étant détectée dans la séquence codante de xopW de certaines souches. Néanmoins, il apparait que la forte diversité génétique des Xoc n'est pas corrélée à leur origine géographique, ni à la période de collecte, ou à la nature de l'hôte. Les souches de Xoo caractérisées appartiennent toutes à la race A1 qui n'avait pas encore été signalée au Mali. Au regard de la diversité des souches et de leur évolution, il est important d'envisager un plan de surveillance épidémiologique à plus large échelle des populations de Xo dans les régions concernées en Afrique de l'Ouest. Enfin, nous avons montré que certaines variétés de riz cultivées au Burkina Faso présentent un phénotype de résistance spécifique des souches africaines de Xoo et ce, à tous les stades de développement de la plante. Ces données originales contrastent par rapport au phénotype des lignées de riz résistantes de référence (Xa4, xa5 et Xa7 efficaces uniquement au stade de tallage maximum). Eu égard à l'absence de gènes de résistance dans le riz efficaces contre Xoc, ces variétés qui constituent également une source de résistance efficaces contre la diversité des souches de Xoc africaines, offrent potentiellement un nouveau moyen pour assurer le contrôle du BLS au Burkina Faso et éventuellement dans d'autres pays Africains. / Bacterial Leaf Blight (BLB) and Bacterial Leaf Streak (BLS) diseases respectively caused by Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae. pv oryzicola (Xoc) are two emerging diseases of rice in West Africa, due to the recent expansion of rice cultivation and introduction of improved rice varieties over the last decade. Three news Xoo races were characterized based on genetic analysis, demonstrating their african specificity. In contrast, a study achevied on about ten Xoc strains isolated in Mali in 2003, show that they are related to asian Xoc strains. In Asia, several R genes against Xoo have been identified and deployed in breeding program to control BLB. In contrast, no R gene against Xoc has been identified in rice. The objectives of this PhD thesis are to (i) complete the Xo collections of African isolates upon annual sampling operated from 2009 to 2012 in various agroecological areas of Burkina Faso and Mali, (ii) determine the genetic diversity of these strains , (iii) identify and characterize news sources of resistance genes to BLB and BLS within rice accessions cultivated in Burkina Faso.Our results showed that african Xoc are highly diverse genetically and phenotypically. PCR-based analyse of two conserved type III effector gene (xopAJ and xopW) differentiated two groups of Xoc strains, with xopAJ not detected in a majority of African Xoc strains and 1050 bp insertion detected in xopW gene for few strains. However, the high genetic diversity observed among the Xoc strains is not correlated to geographical origin, sampling data or host plant species. Xoo strains characterized belong all to race A1 previously reported by Gonzalez et al. (2007) in Burkina Faso. Given the diversity of X. oryzae strains and their evolution, it is essential to establish a large scale epidemiological monitoring of Xo populations in concerned regions in west Africa.At last, some accessions cultivated in Burkina Faso showed specific resistance to african Xoo strains at all plant development stages. These original data contrast with rice lines carring Xa4, xa5 and Xa7 resistance genes against BLB, which are only effective at maximun tillering stage.Given no sources of effective resistance genes against BLS is available in rice, these accessions which were also efficient against a set of Xoc strains representative of the diversity in Africa, represent a huge potential source for the control of BLS in Burkina Faso, and eventually in others african countries.