Existe um relevante interesse em pesquisar a ocorrência de polimorfismos no genoma bovino por diferentes motivos, e mais recentemente, com a finalidade de agregar mais informações ao estudo de características quantitativas visando selecionar animais geneticamente superiores com considerável valor comercial. Os polimorfismos de base única (SNPs) neste estudo foram identificados como RFLP/MboII e RFLP/HpaII sendo que o polimorfismo RFLP/MboII está situado no exon 6 do gene IGF2 (insulin-like growth factor 2), localizado no cromossomo 29 em bovinos, e desempenha um papel importante na proliferação e diferenciação celular para o crescimento e desenvolvimento dos mamíferos. O polimorfismo RFLP/HpaII encontra-se no elemento Bov-A2 (considerado um elemento SINE - Short Interspersed Nucleotide Element) presente na região promotora do gene CYP21 (Steroid 21-hydroxylase gene) no cromossomo 23 em bovinos. Para avaliar a ocorrência dos SNPs utilizou-se a técnica de PCR-RFLP em amostras de DNA a partir de sangue/sêmen de cerca de 300 animais bovinos das raças zebuínas Gir, Guzerá e Nelore. As frequências alélicas mostraram maior incidência do alelo T quando comparado ao C enquanto que as frequências genotípicas apresentaram alta ocorrência do heterozigoto TC em comparação aos homozigotos CC e TT para o polimorfismo IGF2 - RFLP/MboII. Com relação ao polimorfismo CYP21 RFLP/HpaII, a frequência alélica revelou alto valor do alelo T. A população encontrou-se em equilíbrio de Hardy-Weinberg para os SNPs estudados. Ferramentas de bioinformática foram utilizadas para investigações in silico revelando que os sítios polimórficos estão em regiões com potencial regulatório. A associação desses polimorfismos com DEPs das características reprodutivas e produtivas foram investigadas, entretanto mostrou-se significativas apenas para DP550 (IGF2 - RFLP/MboII) e DP450 (CYP21 - RFLP/HpaII). Os resultados obtidos sugerem que protocolos de Biologia Molecular in vitro podem ser usados para identificar novos marcadores moleculares, como SNPs funcionais adicionando informações que certamente contribuirão para estratégias de melhoramento dessas raças bovinas de grande importância para a produção de carne e leite em nosso país. Este foi o primeiro estudo sobre a ocorrência desses polimorfismos em raças zebuínas criadas no Brasil. / There is a considerable interest in researching the occurrence of polymorphisms in the bovine genome for different reasons, and more recently, in order to add more information to the study of quantitative traits to select genetically superior animals with considerable commercial value. The single nucleotide polymorphisms (SNPs) in this study were identified as RFLP/MboII and RFLP/HpaII polymorphisms being the RFLP/MboII is situated in exon 6 of the IGF2 gene (insulin-like growth factor 2), located on chromosome 29 in cattle, perform an important role in cell proliferation, differentiation for growth and in the development of mammals. Polymorphism RFLP/HpaII is the element Bov-A2 (considered an element SINE - Short Interspersed Nucleotide Element) present in the promoter region of CYP21 gene (Steroid 21-hydroxylase gene) on chromosome 23 in cattle. To evaluate the occurrence of SNPs, we used the PCR-RFLP method on DNA samples from blood/semen of about 300 cattle breeds from Zebu Gyr, Guzerat and Nellore. The allele frequencies showed a higher incidence of T allele compared to C while the genotype frequencies showed high incidence of heterozygous CT compared to CC and TT homozygous for the IGF2 polymorphism - RFLP/MboII. On the subject of the CYP21 polymorphism - RFLP/HpaII, the allele frequency showed high value T. The population was found in Hardy-Weinberg equilibrium for the SNPs studied. Bioinformatics tools, used for in silico investigations, revealed that the polymorphic sites are in regions with regulatory potential. The association of these polymorphisms with EPDs of reproductive and productive traits were investigated, but proved to be significant only for DP550 (IGF2 - RFLP/MboII) and DP450 (CYP21 - RFLP/HpaII). The results suggest that protocols of molecular biology in vitro can be used to identify new molecular markers, such as functional SNPs adding information that certainly will contribute to the improvement strategies of these breeds of great importance for the production of meat and milk in our country. It has been the first study on the occurrence of these polymorphisms in Zebu breeds raised in Brazil.

Orientador: Regina Maura Bueno Franco / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-23T14:45:55Z (GMT). No. of bitstreams: 1 Rodrigues_RicardoCondeAlves_M.pdf: 3524379 bytes, checksum: 96e6db4afee4c65f60a4ee47a8ee3232 (MD5) Previous issue date: 2013 / Resumo: Cães e gatos são os animais domésticos mais utilizados para interagir e conviver com as pessoas. Estes animais cada vez mais compartilham o mesmo habitat que os seres humanos. Em que pese os benefícios advindos deste íntimo relacionamento, há que se considerar que cães e gatos podem albergar parasitos com potencial zoonótico, dentre os quais Giardia e Cryptosporidium, ambos de grande importância na medicina veterinária e na saúde pública. Giardia é um protozoário entérico cosmopolita responsável por diarreia em grande variedade de hospedeiros, incluindo o ser humano. Cryptosporidium é um parasito emergente e oportunista, que ganhou destaque com o advento da síndrome da deficiência imunológica adquirida, uma vez que este protozoário pode causar quadros graves em indivíduos imunocomprometidos. Do ponto de vista epidemiológico, é importante entender quais são as espécies de Giardia e Cryptosporidium que acometem os seres humanos e os animais, bem como conhecer aquelas que possuem potencial zoonótico. Conhecer a prevalência desses parasitos na população de cães e gatos torna-se ferramenta importante, que possibilita delinear ações que reduzam o risco de transmissão para outros animais, bem como para a população humana. A determinação das assembleias de Giardia duodenalis mais prevalentes nos cães e gatos também é de grande relevância, visto que este protozoário possui grande diversidade genética e os hospedeiros das espécies canina e felina podem albergar tanto assembleias zoonóticas quanto espécie-específicas. O presente estudo teve como objetivo, através do uso de métodos parasitológicos tradicionais, avaliar a prevalência de G. duodenalis e Cryptosporidium sp. em cães (n=299) e gatos (n=38) pertencentes aos estratos errante, comunitário e semidomiciliado e recolhidos ao Centro de Controle de Zoonoses de Campinas (CCZ), no período de março de 2011 a março de 2012. As amostras fecais positivas para G. duodenalis foram caracterizadas molecularmente através do locus tpi. Também se avaliou a eventual associação entre as características epidemiológicas da população em estudo e infecção por Giardia e Cryptosporidium. Os resultados revelaram uma prevalência de 13,3% para G. duodenalis nas amostras fecais de cães. Houve diferença estatisticamente significativa em relação à consistência da amostra fecal, com maior ocorrência nas amostras pastosas ou diarreicas. A prevalência de G. duodenalis em gatos foi de 5,5%. Em relação ao Cryptosporidium, sua prevalência em cães foi de 2,0%. Não foram encontrados oocistos nas amostras de gatos. Os resultados moleculares indicaram em todas as amostras de cães sequenciadas identidade com as assembleias C ou D de G. duodenalis, sugerindo que animais desta espécie pertencentes aos estratos avaliados constituem baixo risco à saúde pública no município de Campinas. A amostra de gato em que foi possível realizar o sequenciamento revelou identidade com a assembleia AI, demonstrando que animais desta espécie pertencentes aos estratos avaliados podem se constituir em preocupação em saúde pública no município de Campinas, podendo os mesmos eliminar cistos com potencial zoonótico / Abstract: Dogs and cats are the most common domestic animals used for interact and live with humans. Even more these animals are sharing the same habitat with the human beings. Despite of the benefits of this intimate relationship, we must consider that dogs and cats can be hosts for zoonotic parasites, including Giardia and Cryptosporidium, both parasites with great relevance in veterinary medicine and public health. Giardia is a cosmopolitan enteric protozoan responsible for diarrhea in a wide variety of hosts, including man. Cryptosporidium is an emergent and opportunist parasite, which attained relevance with the advent of the acquired immune deficiency syndrome, since this parasite can cause severe disease in immunocompromised individuals. From an epidemiological standpoint, it is important to understand which are the Cryptosporidium species and Giardia genotypes which affect humans and animals, as well as know those with zoonotic potential. The prevalence rates knowledge of these parasites in canine and feline populations becomes an important tool that makes possible to delineate actions to reduce risk of transmission to other animals, as well as to the human population. The assemblages of Giardia duodenalis more prevalent in dogs and cats are also an important determination, since this protozoan has great genetic diversity and also the canine and feline's host species can harbor both zoonotic and species-specific assemblages. Through the use of traditional parasitological methods, the present study aimed to evaluate the prevalence of G. duodenalis and Cryptosporidium sp. in dogs (n=299) and cats (n=38) belonging to stray, community and semi-domesticated strata and captured by the Zoonosis Control Center of Campinas (CCZ), from March 2011 to March 2012. The positive samples for G. duodenalis have been molecularly characterized through locus tpi. The possible association among the epidemiological characteristics of the studied population with the infection by Giardia and Cryptosporidium, was also evaluated. The prevalence of G. duodenalis was 13.3% in fecal samples in dogs and statistical significant difference has been observed in relation to the consistency of the fecal sample, with higher prevalence in doughy or diarrheic samples. The prevalence of G. duodenalis in cats was 5.5%. In relation to Cryptosporidium, the prevalence in dogs was 2.0%. Oocysts were not found in fecal samples from cats. All amplified sequences sampled from dogs feces showed identity with C or D assemblage of G. duodenalis, suggesting that dogs belonging to evaluated strata constitute low risk to public health in the city of Campinas. The cat's fecal sample, which were possible to sequence, showed identity with the Assemblage AI, demonstrating that animals of this species belonging to this particular strata can be a concern in public health for the city of Campinas, since they can eliminate cysts with zoonotic potential / Mestrado / Parasitologia / Mestre em Parasitologia

Orientador: Antonio Fernando Ribeiro / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-19T10:15:56Z (GMT). No. of bitstreams: 1 Marsom_FernandoAugustodeLima_M.pdf: 12182231 bytes, checksum: e98655cb1347b5ba1ffbceac13daebb0 (MD5) Previous issue date: 2011 / Resumo: Introdução: A fibrose cística (FC) se manifesta clinicamente com várias formas de gravidade, moduladas por diferentes genótipos e o meio ambiente. Enquanto as classes das mutações no gene CFTR ("Cystic Fibrosis Transmembrane Conductance Regulator") estão bem definidas, como moduladores de gravidade da FC, os polimorfismos continuam controversos. Objetivo: Verificar se polimorfismos em genes modificadores estão associados com a gravidade da FC. Método: Estudo de corte transversal, entre 2009 a 2010. Todos pacientes foram submetidos à análise das principais mutações no gene CFTR, presença dos polimorfismos (por meio de diferentes técnicas moleculares - "nested" PCR, digestão enzimática, PCR "multiplex", genotipagem em sequenciador automático e PCR ARMS) e características clínicas de gravidade da FC. Resultado: As mutações identificadas no gene CFTR foram associadas com variáveis que descrevem o início da doença, atuando como fator de proteção a clínica de maior gravidade [idade (p?0,0001), 1ª manifestação clínica (1MC) (p?0,0001), diagnóstico (p?0,0001), início dos sintomas pulmonares (ISP) (p?0,0001) e digestivos (ISD) (p?0,0001), 1ª bactéria Pseudomonas aeruginosa isolada (1PA) (p?0,0001), insuficiência pancreática (IP) (p?0,0001), P. aeruginosa mucóide (PAM) (p?0,0001), P. aeruginosa não mucóide (PANM) (p?0,0001)]. O gene ACE foi associado a 1MC (p:0,038), ao escore de Bhalla (EB) (p:0,049) e a presença de Bulkolderia cepacia (BC) (p:0,038). O polimorfismo GCLC129C>T foi associado à PAM (p:0,037). O polimorfismo GCLC350 foi associado a 1PA (p:0,049), Achromobacter xylosoxidans (p:0,044) e Staphylococcus aureus (SA) (p:0,037). O gene GSTM1 foi associado ao diagnóstico (p:0,014), índice de massa corpórea (IMC) (0,045), escore de Kanga (EK) (p:0,046), capacidade vital forçada [CVF(%)] (p:0,004) e volume expiratório forçado no primeiro segundo [VEF1(%)] (p:0,004). O gene GSTT1 foi associado ao ISD (p:0.033), osteoporose (p:0.021), EB (p:0,026), escore de Shwachman Kulczycki (SC) (p:0,009), CVF(%) (p:0,015), VEF1(%) (p:0,005), razão entre o VEF1 e a CVF [TIF(%)] (p:0,033), fluxo expiratório forçado entre 25 e 75% da CVF [FEF25- 75%(%)] (p:0,005) e PAM (p:0,038). O agrupamento genotípico dos genes GSTM1 e GSTT1 foi associado com o diagnóstico (p:0,014), BC (p:0,042) e SA (p:0,032). O gene GSTP1 foi associado com o ISP (p:0,026), IP (p:0,011), EB (p:0,015), EK (p:0,028), SC (p:0,039), CVF(%) (p:0,021), VEF1(%) (p:0,021), FEF25-75% (p:0,02) e 1PA (p:0,022). O alelo 1 para o polimorfismo de repetição AAT no gene NOS-1 foi associado com a idade (p:0,009) e com o ISD (p:0,001). O alelo 2 com ISP (p:0,031), ISD (p:0,001) e EB (p:0,046). O alelo 1 para o polimorfismo GT-1 no gene NOS-1 não apresentou associação com as variáveis clínicas. O alelo 2 apresentou associação com a saturação de oxigênio transcutânea (p:0,012), EB (p:0,013), CVF(%) (p:0,038), VEF1(%) (p:0,007), TIF(%) (p:0,036) e FEF25-75(%) (p:0,007). O alelo 1 para o polimorfismo de repetição GT-2 no gene NOS1 apresentou associação com a CVF(%) (p:0,032). O alelo 2 apresentou associação com o TIF(%) (p:0,009). O polimorfismo Arg>Gly no gene ADRB2R apresentou associação com a IP (p:0,009), EB (p:0,039), VEF1(%) (p:0,003), FEF25-75(%) (p:0,008), 1PA (p:0,012), PAM (p:0,023) e PANM (p:0,024). O polimorfismo Gln>Glu no gene ADRB2R apresentou associação com o EB (p:0,019) e TIF(%) (p:0,047). A resposta ao broncodilatador inalatório na prova de espirometria apresentou associação com os marcadores de gravidade clínica VEF1(%) (p:0,011) e FEF25-75(%) (p:0,019) apenas para o polimorfismo Arg>Gly no gene ADRB2R. Conclusão: Houve associação entre os polimorfismos analisados e as mutações no gene CFTR com a gravidade clínica da FC / Abstract: Introduction: Cystic fibrosis (CF) is clinically manifested in various forms of gravity, modulated by different genotypes and environment. While the classes of mutations in the CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene are well defined as modulators of severity in CF, polymorphisms remain controversial. Objective: To determine whether polymorphisms in modifier genes are associated with the severity in the CF. Method: Cross-sectional study, between 2009 to 2010. All patients were subjected to analysis of major mutations in CFTR gene, presence of polymorphisms (using different molecular techniques - Nested PCR, enzyme digestion, multiplex PCR, genotyping in automatic sequencer and ARMS PCR) and clinical severity in CF. Results: Mutations were identified in CFTR gene associated with variables that describe the onset of the disease, acting as a protective factor for the clinical severity [age (p?0.0001), first clinical manifestation (1CM) (p?0.0001), diagnosis (p?0.0001) , onset of pulmonary symptoms (OPS) (p?0.0001) and digestive (ODS) (p?0.0001), 1st isolated bacterium Pseudomonas aeruginosa (1PA) (p?0.0001), pancreatic insufficiency (PI) ( p?0.0001), P. aeruginosa mucoid (PAM) (p?0.0001) and P. aeruginosa no mucoid (PANM) (p?0.0001)]. ACE gene was associated with 1CM (p:0.038), Bhalla score (BS) (p:0.049) and presence of Bulkolderia cepacia (BC) (p:0.038). Polymorphism GCLC129C>T was associated with PAM (p:0.037). Polymorphism GCLC350 was associated with 1PA (p:0.049), Achromobacter xylosoxidans (p:0.044) and Staphylococcus aureus (SA) (p:0.037). GSTM1 gene was associated with diagnosis (p:0.014), body mass index (BMI) (0.045), Kanga score (KS) (p:0.046), forced vital capacity [FVC(%)] (p:0.004) and forced expiratory volume in one second [FEV1(%)] (p:0.004). GSTT1 gene was associated with ODS (p:0033), osteoporosis (p:0.021), BS (p:0.026), Shwachman-Kulczycki score (SS) (p:0.009), FVC(%) (p:0.015) , FEV1(%) (p:0.005), ratio between FEV1 and FVC [TIF(%)] (p:0.033), forced expiratory flow between 25 and 75% of FVC [FEF25-75%(%)] (p:0.005) and PAM (p:0.038). The genotypic groupings of genes GSTM1 and GSTT1 was associated with diagnosis (p:0.014), BC (p:0.042) and SA (p:0.032). GSTP1 gene was associated with the OPS (p:0.026), PI (p:0.011), BS (p:0.015), KS (p:0.028), SS (p:0.039), FVC(%) (p:0.021 ), FEV1(%) (p:0.021), FEF25-75% (p:0.02) and 1PA (p:0.022). Allele 1 for AAT repeat polymorphism in NOS-1 gene was associated with age (p:0.009) and ODS (p:0.001). Allele 2 with OPS (p:0.031), ODS (p:0.001) and BS (p:0.046). Allele 1 for repeat polymorphism GT-1 in NOS-1 gene was not associated with clinical variables. Allele 2 was associated with transcutaneous oxygen saturation (p:0.012), BS (p:0.013), FVC(%) (p:0.038), FEV1(%) (p:0.007), TIF(%) (p:0.036) and FEF25-75(%) (p:0.007). The allele 1 for repeat polymorphism GT-2 in NOS1 gene was associated with FVC(%) (p:0.032). The allele 2 was associated with the TIF(%) (p:0.009). Polymorphism Arg>Gly in ADRB2R gene was associated with PI (p:0.009), BS (p:0.039), FEV1(%) (p:0.003), FEF25-75(%) (p:0.008), 1PA ( p:0.012), PAM (p:0.023) and PANM (p:0.024). Polymorphism Gln>Glu in ADRB2R gene was associated with BS (p:0.019) and TIF(%) (p:0.047). The response to inhaled bronchodilator in the spirometry test presented association for the markers of clinical severity FEV1(%) (p:0.011) and FEF25-75(%) (p:0.019) only for the polymorphism Arg>Gly in ADRB2R gene. Conclusion: There was association between the polymorphisms studied and CFTR mutations with the clinical severity in CF / Mestrado / Saude da Criança e do Adolescente / Mestre em Saude da Criança e do Adolescente

Chez la banane dessert, les saveurs sucrée et acide, caractéristiques importantes pour les consommateurs, sont pilotées par les teneurs en acides citrique et malique. Ce travail a donc porté sur l’étude des processus physiologiques qui pilotent l’accumulation de ces acides dans la pulpe de banane (Musa sp. AA) en combinant analyse expérimentale et modélisation écophysiologique. Nous nous sommes notamment intéressés à l’effet du génotype et des conditions de croissance du fruit en adoptant une approche intégrative liant les phases pré et post récolte.Les effets de la charge en fruit, de la fertilisation potassique, et du stade de récolte sur l’accumulation du citrate et du malate dans la pulpe ont été étudiés expérimentalement. La variabilité génotypique a été prise en compte en choisissant trois génotypes présentant des acidités contrastées à maturité. Des différences d’évolution des teneurs en acides, dues à des modifications métaboliques, ont été observées entre les génotypes pendant les phases pré et post récolte. Le stade de récolte a eu un effet significatif sur les teneurs en acides des fruits pendant la maturation post récolte. La charge en fruit et la fertilisation potassique n’en ont eu aucun. Des modèles écophysiologiques ont été développés pour prédire différents critères d’acidité de la banane en pré et post récolte. Le pH et l’acidité titrable ont été prédits par un modèle d’équilibres acido-basiques, la teneur en malate par un modèle de stockage vacuolaire, et la teneur en citrate par un modèle du cycle de Krebs. Ces modèles ont permis d’identifier les processus physiologiques clés qui pilotent l’acidité de la banane. Des paramètres génotypiques ont été identifiés liés à l’activité de l’enzyme malique mitochondriale et à celle des transporteurs mitochondriaux du malate pour le modèle citrate, et à l’activité des pompes à protons vacuolaire ATPases pour le modèle malate. Ces modèles ont également permis de disséquer l’effet des conditions de croissance du fruit sur l’acidité de la banane. L’intégration des modèles développés dans un modèle d’élaboration de l’acidité et son utilisation potentielle pour l’amélioration variétale sont discutées. / Citric and malic acids determine the sourness and sweetness of banana pulp, which are the two main determinants of consumer preferences. The present work focused on the physiological processes controlling the accumulation of citric and malic acids in banana pulp (Musa sp. AA) using experimental analysis and ecophysiological modeling. We chose an integrative approach linking the pre and post-harvest stages, and focused on the effect of genotype and fruit growing conditions. Experiments were conducted to study the effect of fruit load, potassium fertilization and fruit age at harvest on the accumulation of citrate and malate in banana pulp. To account for genotypic variability, three genotypes with contrasting acidity at the eating stage were studied. Major differences in the pattern of citrate and malate accumulation were found in the three cultivars both during growth and post-harvest ripening and were shown to be the result of metabolic changes. The harvest stage had a significant effect on the concentrations of acids during post-harvest ripening. Fruit load and potassium fertilization had no effect.Ecophysiological models were developed to predict several banana acidity criteria during the pre and post harvest stages. pH and titratable acidity were predicted by a model of acid-base reactions; malate content by a model of vacuolar storage; and citrate content by a model of the TCA cycle. These models led to the identification of the key physiological processes that control banana acidity. Genotypic parameters were identified, which were related to the activity of the mitochondrial malic enzyme and of the malate mitochondrial carriers in the citrate model, as well as to the activity of the vacuolar proton pump, ATPase, in the malate model. The two models were also used to analyze the effects of fruit growth conditions on banana acidity.Combining the three models in a global model of banana acidity, and the possible use of this model for varietal improvement are discussed.

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.

La cryptococcose neuroméningée (CNM) est la seconde infection opportuniste chez les patients infectés par le VIH. Il s’agit de la 4ème cause de décès dus aux maladies infectieuses en Afrique avec une mortalité annuelle de 600.000 cas. Les levures responsables appartiennent au complexe d’espèces Cryptococcus neoformans / C. gattii. Notre étude décrit, l’épidémiologie et la résistance aux antifongiques de souches environnementales et cliniques de cryptocoques en Côte d’Ivoire. Les isolats sont issus d’une file active de 1750 PVVIH et de 667 prélèvements réalisés dans l’environnement de vie des patients. Nous démontrons une grande diversité génotypique au sein de notre cohorte, la présence de plusieurs espèces de cryptocoques dans un seul prélèvement chez un même patient ainsi que dans des prélèvements issus de suivi de patients, ce qui n’avait jamais été démontré en Afrique de l’Ouest. Nous avons constaté que la récurrence de la CNM est due à des infections multiples par des souches différentes au cours du temps. Nos résultats décrivent également pour la première fois, l’isolement de cryptocoques à partir de fientes de pigeons à Abidjan. Et nous constatons que les génotypes des isolats environnementaux et cliniques sont très différents, ce qui exclut les fientes de pigeons comme source de contamination des patients dans notre échantillon. Enfin, la majorité des isolats est sensible aux antifongiques de référence mais un patient peut être contaminé par des isolats de sensibilité différente. / Cryptococcal meningitis (CM) is the second opportunistic infection in HIV infected patients. It is the fourth cause of death due to infectious diseases in Africa with an annual mortality of 600,000. The yeasts responsible belong to the C. neoformans / Cryptococcus gattii species complex. Our study describes epidemiology and resistance to antifungal of environmental and clinical strains of Cryptococcus in Ivory Coast. The isolates are from an active list of 1,750 patients VIH positive and 667 samples taken in the living environment of patients. We demonstrate a high genotypic diversity within our cohort and the presence of several species of Cryptococcus in one sample from the same patient as well as in samples from patients follow up, which had never been shown in West Africa. We found that the recurrent cryptococcosis is caused by multiple infections by different strains over time. Our results describe also, for the first time, the isolation of Cryptococcus from pigeon droppings from Abidjan. And we notice that, as the genotypes of environmental and clinical isolates are very different, that excludes contamination of patients by pigeon droppings. Finally, most of the isolates were susceptible to reference antifungal but a patient might be contaminated by isolates with different susceptibility.

This thesis is the first study to provide a detailed characterization of Acropora cervicornis transplants and donor colony survival on southeast Florida coral reefs. Since May 2006 this species has been listed as a threatened species under the Endangered Species Act. As populations continue to decline restoration efforts need to be evaluated to determine if there is an effort that could facilitate a population rebound. The overall goal of this project was to examine potential Acropora cervicornis restoration techniques along the entire Florida reef tract including Broward County, Miami Dade County, and Monroe County. For my thesis I used a portion of the data collected from the Broward County region nursery. I analyzed data on the donor colonies and the nursery fragments. The goals were to determine if fragments generated from clippings removed from donor colonies can 1) be transplanted to a nursery site, 2) have acceptable survivorship and 3) increase in complexity (branching). Beyond survival and growth, I also examined genotypic differences in fragment survival and growth rates. Twelve A. cervicornis donor colonies separated by as much as 26 km were identified, and monitored quarterly for 19 months. From each donor colony three 10 cm clippings were removed for transplantation to the nursery habitat and one 1 cm clipping was taken for genetic analysis. Prior to transplantation, each 10 cm clipping was cut into 3 cm fragments. Transplantation occurred in September, October, and December 2007, transplanting 1/3 of the fragments horizontal and 2/3 vertical in orientation. Fragments in the nursery were monitored monthly through November 2008. During each monthly monitoring, images were taken, fragments were measured, branches were counted, and condition (partial mortality, disease, predation, etc.) was assessed. Each donor colony sampled with in Broward County for this project was determined to be a unique genotype using microsatellites. Significant differences in survival, growth, and number of branches were determined among fragment genotypes. Vertically orientated fragments had higher survivorship, but horizontal fragments had higher mean growth rates and number of branches per fragment. This coral restoration project has the real possibility of providing important information on the effectiveness of utilizing the asexual, fragmentation, capacity of A. cervicornis to facilitate A. cervicornis population conservation. My effort could contribute to a quantitative comparison of Acropora genotypic variation in survivorship and growth, which will provide information on intra- and inter-regional potential for large-scale restoration within the Florida reef tract.

Duvenhage virus (DUVV) belongs to genotype (gt) 4 of the lyssavirus genus, in the family Rhabdoviridae, order Mononegavirales. This virus causes fatal rabies encephalitis and has only been reported from the African continent. To date there have been only five isolations of DUVV, three of which were from human fatalities and all of which were associated with insectivorous bat species. Genotype 4 lyssaviruses have not been well studied and as such little is known about them. The aim of this study was to determine the full genome sequence and investigate the epidemiology of this uniquely African lyssavirus. Standard methods of PCR and sequencing were used to determine the coding and non coding regions of various DUVV isolates. In order to determine the full genome sequence, an RNA circularization technique was used to obtain the genomic terminal sequences. Using various molecular techniques we then analyzed the sequence data, at both phylogenetic and evolutionary levels. Our analysis showed the evolutionary forces acting against DUVV, to be similar to that which has been found for its closest relative, European bat lyssavirus type 1 (EBLV1) (gt 5). Both these viruses have strong constraints against amino acid change, with no evidence of positive selection. Phylogenetic studies showed that not all Lyssavirus genes are equal for phylogenetic or lyssavirus classification analysis. High intergenotypic values at the nucleoprotein amino acid level emphasize that there is a need to reinvestigate the criteria for lyssavirus genotype classification. The strong support observed in our full genome studies suggests that full genomes may in fact be best for Lyssavirus analysis, so as to avoid the potential bias of individual gene analyses. Analysis of DUVV indicates that it is an older virus within the lyssavirus genus and as shown by the discovery of the most recent isolate, the genetic diversity and incidence of this virus is greatly underestimated. Poor surveillance of rabies-related lyssaviruses as well as the poor diagnostic capabilities through most of Africa are large contributors to our lack of information. Improved surveillance of the African rabies-related lyssaviruses will extend our knowledge on the geographic distribution, host species associations and epidemiology of these viruses. / Dissertation (MSc)--University of Pretoria, 2011. / Microbiology and Plant Pathology / unrestricted

When provided with spatial niches by growth in static nutrient medium, Pseudomonas fluorescens diversifies through adaptive radiation into several well-defined phenotype classes. One of these classes, named wrinkly spreader (WS) for its morphology on agar medium, forms a biofilm at the air-liquid interface through mutations in one of several loci including the genes wspF and awsX. These genes code for negative regulators of di-guanylate cyclases (DGCs). These DGCs catalyse synthesis of cyclic-di-GMP, a second messenger, overproduction of which effects physiological changes leading to overproduction of a cellulose polymer and the WS phenotype. Intriguingly, a diverse range of wspF mutations leads to diversity both in colony morphology and strain fitness.In this study, I investigate genetic and fitness diversity in wrinkly spreaders with the aim of identifying the causal factors that link genetic diversity and physiological factors with diversity in fitness. I approach the subject from several directions, examining the historical context of genetic diversity in wspF and awsX, distribution of control over output in the Wsp pathway and overall fitness effects of different causal factors. I investigate the genetic basis of wrinkly spreader evolution through generation of a large number of novel WS strains and exploration of the distribution of mutations in the wspF and awsX genes. In combination with this I calculate estimates of the past rates of mutation in these genes, derived from a phylogenetic investigation of a group of orthologues. I examine the response of the Wsp pathway to change in WspF function through a novel computational analysis that is capable of revealing valuable information on control in a biological system based purely on model structure. In addition I show how this analysis can be refined through specification of broad estimates of system parameters, thereby avoiding issues related to over-reliance on specific parameter values. Finally, I investigate the fitness implications of these factors, as well as a variety of others, through assays of fitness in a group of WS strains combined with machine learning analyses of predictive relationships between protein and mutation characteristics and experimentally measured strain fitness, and consider the implications of this analysis in the context of intermediate physiological effects.I find that mutations in the WspF protein that lead to the WS phenotype tend to be located in regions of historically strong conservation, the first time that any such pattern to WS mutations has been identified. Mutations in AwsX, on the other hand, do not fit such a pattern. Computational analysis of the Wsp pathway shows that, regardless of model parameters, pathway output is always more sensitive to changes in methylesterase activity by WspF than to changes in phosphorylation of WspF, which may explain the greater frequency of mutations fixed in vivo seen in the methylesterase domain. Despite these patterns, none of a wide range of mutation and sequence-based biochemical characteristics, including local rates of past evolution and size and position of mutations, exhibited any predictive power over WS fitness. Overall, the findings in this study point towards an essential role for complex pleiotropic effects in strongly modulating the fitness effect of different mutations in wspF.

Les antigènes de groupes sanguins érythrocytaires peuvent être responsables d’une allo-immunisation anti-érythrocytaire et d’accidents immuno-hémolytiques lors de transfusion ou de grossesse. La transfusion des populations d’Afrique sub-saharienne est complexifiée par l’absence d’expression d’antigènes publics, l’expression d’antigènes privés et l’expression d’antigènes partiels en particulier pour le système RH. L’étude des systèmes de groupes sanguins d’intérêt transfusionnel chez les donneurs de Bamako a confirmé l’efficacité de la stratégie du génotypage multiplex incluant des polymorphismes d’appels pour identifier des donneurs rares, qui permet d’accéder aux phénotypes déduits des prélèvements. L’exploration du système RH réalisée par séquençage chez les Dogons et les Peulhs de Mopti met clairement en évidence que la diversité allélique et la fréquence de certains allèles RH sont fonction de l’ethnicité. Un nouvel haplotype associant un allèle RHD*DIVa codant pour un antigène D partiel, des antigènes ce potentiellement partiels, et une réactivité partielle anti-C, a été identifié chez les Dogons. L’exploration des allèles codant pour les antigènes de haute et basse fréquence en Afrique subsaharienne d’Est en Ouest constitue un exemple d’étude qui distingue clairement les populations d’Afrique subsaharienne de celles d’Europe par des différences de fréquences des allèles définissant la diversité génétique d’une population par rapport à une autre. Des orientations stratégiques en fonction du contexte local ont été identifiées pour l’évolution de la transfusion au Mali dans les prochaines années. / Blood group antigens may be responsible for alloimmunization and immuno-hemolytic accidents during transfusion or pregnancy. The transfusion of of sub-Saharan Africa populations is complex due to absence of high antigens expression, low antigens expression and partial antigens expression particularly for RH system.The study of blood group for transfusion of interest among donors in Bamako confirmed the effectiveness of multiplex genotyping strategy including polymorphisms calls to identify the rare donors, which permit access to phenotypes derived samples. In a second phase, the exploration of RH blood group system by sequencing among Dogon and Fulani in Mopti clearly shows that the allelic diversity and the frequency of some alleles RH depend on the ethnicity. A new haplotype RHD*DIVa/RHCE*ceTI(D2) combining an RHD*DIVa allele encoding a partial D antigen, potentially partial ce antigens, and a partial reactivity with anti-C, was identified among Dogon. In a third phase, the exploration of alleles encoding of the high and low frequency antigens in sub-Saharan Africa from East to West is an example of a study that clearly makes a difference between the populations of sub-Saharan African and those of Europe in terms of frequencies of alleles that define genetic diversity of one population compared to another. Thus, knowledge of ethnicity is more relevant than knowing the geographical origin in order to optimize transfusion in Saharan Africa and in European countries where some of these populations live. Guidelines strategic in relation with the local context have been identified for development of transfusion for next years in Mali.