Elevated total plasma homocysteine (tHcy) is a risk factor for cardiovascular disease and neurocognitive disease such as dementia. The B vitamins folate and B12 are the main de terminants of tHcy. tHcy concentration can also be affected by mutations in genes coding for receptors, enzymes and transporters important in the metabolism of Hcy. This thesis focuses on mutations in the genes for folate receptor-alpha and methylenetetrahydrofolate reductase (MTHFR) and the effect they have on tHcy concentrations. Six novel mutations in the gene for folate receptor-alpha were described in Paper I. Taken together they exist in a population with a prevalence of approximately 1% and thus are not unusual. There may be an association of –69dupA and –18C>T to tHcy but for the 25-bp deletion, –856C>T, –921T>C and –1043G>A there is probably no association to tHcy. Mutation screening was continued and four additional mutations, 1314G>A, 1816delC, 1841G>A and 1928C>T, were described in Paper II. The prevalences for the heterozygotes were between 0.5% and 13% in an elderly population. There was no significant difference in prevalence between the elderly subjects and patients with dementia. The 1816(–)-allele and the 1841A-allele were in complete linkage and the haplotype 1816(–)-1841A may possibly have a tHcy raising effect. The 1314G>A and 1928C>T mutations had no association to tHcy. The genotype prevalences and haplotype frequencies of the MTHFR 677C>T, 1298A>C and 1793G>A polymorphisms were determined in a population sample of Swedish children and adolescents (Paper III). The MTHFR 677T-allele was associated with increased tHcy concentrations in both children and adolescents. A small elevating effect of the 1298C-allele and a small lowering effect of the 1793A-allele could be shown. In an epidemiological sample of adults from the Canary Islands, Spain, data for serum folate and vitamin B12 were used for a broader study of the nutrigenetic impact on tHcy (Paper IV). The 677T-allele had a significant tHcy increasing effect in men but not in women. The 1298C-allele had a minor elevating effect on tHcy in men with the 677CT genotype. It was not possible to document any effect of the 1793A-allele on tHcy due to its low prevalence. A slightly superior explanatory power for the genetic impact was obtained using the MTHFR haplotypes in the analysis compared to the MTHFR 677C>T genotype-based approach in both the Swedish children and adolescents and in the Spanish adults. Therefore MTHFR haplotypes should be considered when analysing the impact of the MTHFR 677C>T, 1298A>C and 1793G>A polymorphisms on tHcy. Notwithstanding the large geographical distance between our study populations the haplotype composition is quite similar. The MTHFR 677T-allele is slightly more prevalent in Spain compared to Sweden but it has only an effect on tHcy in the Spanish men. Age, gender and factors linked to the ethnicity of the studied subjects, seem to be able to override the nutrigenetic impact of tHcy-raising genotypes or haplotypes in particular settings, such as in the Spanish women in our study. Gene-nutrient interactions on plasma tHcy levels thus may or may not exist in a certain population. The transferability of nutrigenetic findings may therefore be limited, and must be re-evaluated for each particular setting of age-gender-ethnicity.

Avec 67 Mt de fumiers de bovins récupérés chaque année, la France possède un gisement considérable de substrats agricoles mobilisables et valorisables par méthanisation. Le procédé de méthanisation par voie sèche, discontinu, avec recirculation de lixiviat semble être le mieux adapté à la valorisation de ce type de substrats à forte teneur en matière sèche (>20%). A l’heure actuelle, ce procédé est cependant rare sur le territoire. Afin de permettre et de pérenniser le développement de cette technologie, des verrous techniques et scientifiques doivent être levés, notamment ceux qui portent sur la recirculation des lixiviats. L’objectif de cette thèse est d’optimiser le procédé de méthanisation par voie sèche appliquée aux effluents agricoles (principalement fumiers de bovins), afin d’atteindre les conditions les plus favorables à la production d’un maximum de biogaz, de façon constante et en un minimum de temps en considérant les contraintes relatives à un tel procédé. Dans un premier temps, l’objectif a été de comprendre le rôle du lixiviat dans ce procédé de digestion anaérobie discontinu, d’un point de vue biologique. Pour se faire quatre lixiviats ayant différentes origines ont été utilisés. Deux d’entre eux étaient biologiquement actifs (lixiviats provenant de méthaniseurs) et les deux autres stérilisés. Du point de vue abiotique, il a été montré que pour favoriser la digestion anaérobie, le lixiviat devait avoir un pH adéquat, présenter une concentration suffisante de nutriments et un fort pouvoir tampon. D’un point de vue biotique, deux communautés distinctes de microorganismes évoluent dans le lixiviat et dans le fumier, sans aucun transfert entre ces deux environnements, limitant ainsi le rôle d’inoculation souvent attribué au lixiviat. Dans un deuxième temps, la réalisation d’un plan d’expérience a permis d’identifier, au laboratoire sur pilotes instrumentés, des paramètres de recirculation du lixiviat qui influencent les vitesses de production de méthane. Ainsi, le temps entre les recirculations, le volume recirculé et le ratio lixiviat/substrat initialement introduit jouent sur la forme des cinétiques de production. En actionnant l’un ou l’autre de ces leviers, il serait potentiellement possible d’adapter la production de méthane, en fonction des besoins des systèmes de valorisation du biogaz en place sur ces installations. Enfin, la méthode de tomographie de résistivité électrique a été utilisée, à grande échelle, pour suivre la percolation du lixiviat à travers le massif et mettre en évidence les disparités de distribution du lixiviat dans le massif. Cette étude a montré que la géométrie du réseau de recirculation du lixiviat, consistant en un tuyau perforé parcourant la surface du massif dans le sens de la longueur, ne permettait pas un écoulement homogène du lixiviat dans les digesteurs. Certaines zones n’ayant jamais été humidifiées, la production de méthane se trouve réduite et les rendements amoindris. Cette thèse s’articule autour de plusieurs analyses multi-échelles et complémentaires permettant de mieux comprendre le rôle du lixiviat, d’améliorer sa mise en œuvre et son utilisation pour la digestion anaérobie des fumiers de bovins. / With 67 Mt of cattle manure recovered every year, France has a significant source of agricultural waste to be valorised through anaerobic digestion. Batch mode solid state anaerobic digestion (SSAD) process with leachate recirculation seems to be the most suitable technique to valorise that kind of waste, which contains high total solid content (>20%). Currently, this process is rare on French territory. To develop batch mode SSAD, various technical and scientific barriers must be straightened out, and particularly those concerning leachate recirculation. The objective of this work is to optimize SSAD of agricultural was (mostly cattle manure) by pointing out the most favorable settings that allow producing high volumes of biogas, steadily and within a short time, taking into account the particular technical constraints of this process. First of all, the objective was to better understand the biological role of leachate in the batch mode SSAD process. For that purpose, four leachates with different origins were used. Two of them were biologically active (from existing digesters) while the two others were sterilized. It was demonstrated an effective anaerobic digestion was favored by using a leachate gathering the following abiotic characteristics: an adequate pH, a strong buffer capacity and the presence of the right concentration of nutrients. From the biotic point of view, dedicated communities of microbes were in progress in each liquid and solid environment with nested relationship. The role of leachate as inoculum was then limited. In a second part, the influent parameters of leachate recirculation were identified at laboratory scale, by setting up a design of experiment. It was found that the elapsed time between two recirculations, the recirculated volume of leachate and the initial leachate to substrate ratio introduced in the reactor could modify the shape of methane production rate. By changing one or several of those parameters, it would be possible to control and adapt methane production rate to the specific constraints of one SSAD plant. In the last part, the Electrical Resistivity Tomography (ERT) method was used, at full scale, to monitor the leachate percolation through the solid waste and highlight leachate distribution disparities. It was shown the leachate injection system consisting of a perforated pipe laying on the solid top surface was not efficient to evenly moisten the solid waste. From that observation, it was concluded that cumulated methane production could be improved if areas that were not in contact with leachate could be moistened by using another leachate injection system. This manuscript was based on several multi-scale and complementary analyses that allow a better understanding of the role of leachate during SSAD process and an improvement of its utilization for the anaerobic digestion of cattle manure.

Le déoxynivalénol (DON) est une mycotoxine issue du métabolisme secondaire de moisissures, et se retrouve fréquemment comme contaminant naturel de nombreuses denrées d’origine végétale. Les objectifs de nos travaux ont été d’évaluer les propriétés toxiques du DON chez le porc en croissance, sain ou porteur d’agent pathogène, car cette espèce est connue pour sa sensibilité envers la toxine. Nous avons dans un premier temps étudié in vitro les effets du DON sur la réponse immunitaire non spécifique des animaux. Dans un deuxième temps, l’impact de l’ingestion d’un aliment naturellement contaminé sur les performances et la flore intestinale des porcs a été étudié. Enfin, le modèle de portage asymptomatique de salmonelles a été choisi pour caractériser l’effet de l’intoxication sur l’excrétion de ce pathogène. En fonction de la dose de DON utilisée (0,5 - 5µM), la pré-exposition des macrophages à la toxine a entraîné une inhibition de leur activation par l’IFN-? à travers une diminution de l’expression de leurs récepteurs transmembranaires CD14, CD54, CD119 et HLA-DP/DQ/DR, impliqués dans les fonctions de coopération et de signalisation des macrophages. En revanche, le DON n’a pas eu d’effet particulier sur des macrophages préalablement activés par l’IFN-?. L’exposition au DON n’a pas altéré la capacité de phagocytose des neutrophiles. Cependant, le DON (10 - 50 µM) réduit les propriétés de migration de ces cellules, et diminue la production d’IL-8 par les neutrophiles stimulés par du lipopolysaccharide. Nos résultats suggèrent que la diminution de la production d’IL-8 serait due à une inhibition de l’expression de la sous-unité p65 des facteurs de transcription-kB (NF-kB). Dans les études in vivo, nous avons observé une diminution transitoire de la croissance de tous les porcs après une semaine d’ingestion d’un aliment contaminé par le DON (2,7 mg DON/kg d’aliment). Des modifications de profils de flore bactérienne intestinale ont également été mises en évidence par CE-SSCP (Capillary Electrophoresis Single-Stranded Conformation Polymorphism) après 28 jours d’intoxication chronique. Comme attendu, aucun signe clinique ou physiologique important n’a été observé suite à l’inoculation des porcs avec 106 UFC de Salmonella Typhimurium, hormis une augmentation immédiate de la concentration sérique des immunoglobulines A. Une légère accélération de la séroconversion des animaux infectés par Salmonella Typhymurium et exposés au DON a été observée, ainsi qu’une perturbation passagère de la population de coliformes thermotolérants des fécès, deux jours après l’infection. Aucun autre effet synergique de l’intoxication et de l’infection n’a été observé sur la persistance et l’excrétion de la bactérie par les porcs infectés. En conclusion, nos résultats montrent qu’in vitro, le DON diminue les fonctions des cellules phagocytaires (neutrophiles et macrophages) et qu’in vivo, aux doses de DON et de salmonelles administrés, cette mycotoxine altère la flore intestinale des porcs, mais ne semble pas être un facteur aggravant du portage asymptomatique de salmonelles. / Deoxynivalenol (DON), is a mycotoxin produced by several Fusarium species. It is a secondary metabolite and can contaminate all the stages of the food chain. DON is commonly detected in cereal grains and pigs remain the most sensitive animal specie. The aim of the present study was to evaluate the toxicological properties of DON in grower pigs using pathogen-free pigs. In the first place, in vitro studies were performed to evaluate DON effects on the no-specific immune response. In the second place, the impact of the ingestion of naturally DON contaminated food on the performance and pig’s microbiota was explored. Finally, a Salmonella asymptomatic model was used to characterize the effect of DON on pathogen excretion. Depending on the DON dose used (0.5 -5 µM) the preliminary exposition of macrophages with increased concentration of DON inhibited their IFN-y activation, through a decrease in the clusters of differentiation CD14, CD54, CD119, and HLA-DP/DQ/DR, which are implicated in cellular cooperation and signalization of macrophages. However, no DON effect was observed on the preliminary IFN-y activated macrophages. High DON dose (10 - 50 µM) did not affect polymorphonuclear cells (PMNs) phagocytosis but reduced significantly the migration capacity and the IL-8 production of LPS-induced PMNs. Results therefore suggested that IL-8 decrease is due to the inhibition of the p65-NFKB subunit expression. In the in vivo study, consumption of DON-contaminated feed (2.8 mg DON/kg of feed) reduced the animal weight gain during the first week of experiment. Changes in the intestinal microflora were observed by Capillary Electrophoresis Single-Stranded Conformation Polymorphism (CE-SSCP) in DON exposed animals, suggesting an impact of this toxin on the dynamics on the intestinal bacterial communities. In pigs inoculated with Salmonella enterica Typhimurium, DON did not increase the asymptomatic pathogenicity of the bacteria when these animals were fed with the contaminated diet. Only a slight increase of the seroconversion was seen, but no synergistic effects on colonization or excretion of the bacteria was observed during the experiment. It was concluded that low doses of DON have a negative impact on different phagocytics cells functions and could modify the gastrointestinal associated microflora. In contrast, this toxin did not seem to increase an asymptomatic infection of Salmonella enterica Typhimurium in pigs.

L’étude des communautés microbiennes de la baie de raisin dans des conditions de production à l’échelle de la parcelle montre une dynamique temporelle des populations cultivables, qui se traduit par une augmentation des niveaux de population à partir des stades de début véraison et début maturité. Concernant la communauté bactérienne cultivable, 44 espèces appartenant à 21 genres ont été identifiées. Parmi les huit genres identifiés pour la population fongique, les espèces appartenant au genre Aureobasidium sont les plus abondantes, contrairement aux espèces fermentaires qui restent minoritaires. L’incidence des facteurs biotiques et abiotiques sur différents paramètres de population microbienne tels que la structure, la densité et l’activité métabolique a été analysée. Nous avons observé que les zones climatiques plus fraîches et humides, favorisent le développement des microorganismes. Ces travaux mettent en évidence l’impact écotoxique du cuivre sur la communauté microbienne, en particulier dans sa fraction bactérienne. Le développement de Botrytis cinerea sur la grappe modifie la communauté microbienne des baies de raisin sain : le nombre d’espèces bactériennes augmente ainsi que leur diversité. La communauté bactérienne de la baie de raisin est proche de celle des feuilles d’un point de vue de sa structure, et mais éloignée de celles des écorces et du sol, avec des indices de diversité et de richesse plus faibles. / The study of microbial communities associated with wine grapes under field conditions revealed changes in the size and structure during the berry ripening process, with levels rising gradually and reaching their highest value when the berries were over ripe. During this work several bacteria and fungi species, including fermentative yeast, have been isolated and identified. From cultured bacteria, over 44 species were identified from 21 genera. Concerning fungi population, among eight genera identified, the genus Aureobasidium was the most abundant. Our study reveals the impact of different abiotic and biotic factors over microbial community structure, density and metabolic activity. Comparing different vineyards in the same region, we observed that areas presenting more humid and colder climate favor the growth of microorganisms. Our results also show that the farming system has a clear impact on the microbial community, especially in the bacterial fraction. One of the reasons is the inhibiting effect of copper-based fungicides, frequently used in both organic and conventional farming systems. The presence of Botrytis cinerea in grape berries without visual symptoms of infection can change the microbial community of the grapes, increasing bacterial population density and diversity.

A cultura do maracujazeiro tem sido afetada por um grande número de pragas e doenças, que exigem dedicação e esforços urgentes, no sentido de minimizar as perdas e evitar sua disseminação. O vírus da pinta verde do maracujazeiro (PVM) (Passion fruit green spot virus PFGSV) caracteriza-se por induzir a formação de pequenas manchas verdes em frutos e em folhas, e lesões necróticas em ramos. Exames de secções ultrafinas de tecidos infectados ao microscópio eletrônico de transmissão consistentemente revelam a presença de partículas baciliformes em cisternas do retículo endoplasmático e viroplasma denso no citoplasma. Os efeitos citopáticos encontrados, a relação com o ácaro vetor, Brevipalpus phoenicis, e a comparação com outros vírus transmitidos por Brevipalpus (VTB), como o da leprose dos citros, classifica o vírus como sendo do tipo citoplasmático. Seu relato inicial deu-se há cerca de 10 anos em Vera Cruz-SP, mas em 1994 foi relatada uma doença no Estado da Bahia chamada de definhamento precoce do maracujazeiro (DPM), que apresenta sintomas, efeitos citopáticos e vetor semelhantes ao da pinta verde, tendo sido sugerida a possibilidade de serem duas denominações para uma mesma doença. Atualmente a PVM/DPM encontra-se em vários outros Estados como Minas Gerais, Rio de Janeiro, Sergipe, Rondônia, Maranhão, Rio Grande do Norte, Paraíba e Pará, além do Distrito Federal. Sua diagnose ainda depende dos sintomas observados, infestação por ácaros Brevipalpus e microscopia eletrônica. Para se desenvolver um método de diagnose molecular, que permita detectar o vírus causador da PVM/DPM de maneira rápida e confiável, em grande número de amostras, foi feita uma Biblioteca de cDNA a partir do RNA dupla fita do vírus, extraído de tecidos sintomáticos de maracujazeiros infectados com um isolado do PFGSV encontrado em Limeira-SP. Com o sequenciamento parcial do genoma viral, foram desenhados primers específicos que amplificam partes dos genes putativos da p24 e aqueles que codificam a proteína de movimento (MP) e a Replicase (Rep) de diferentes isolados do PFGSV. Primers do PFGSV e de dois outros VTBs do tipo citoplasmático (VTB-C) para os quais se dispõe de primers para sua detecção por RT-PCR (vírus da leprose dos citros C - CiLV-C; mancha anelar de Solanum violaefolium - SvRSV) foram testados em reações homólogas e heterólogas. Ocorreram amplificações por RT-PCR gerando fragmentos de tamanho esperados apenas para os vírus homológos, mas não nas reações heterólogas, indicando que PFGSV deve diferir do CiLV-C e SvRSV. Assim, tem-se agora uma ferramenta molecular que detecta especificamente o PFGSV. Um estudo inicial sobre a variabilidade genética do PFGSV foi feito a partir da extração do RNA total, seguido de RT-PCR utilizando os primers específicos, purificação dos fragmentos obtidos e uso da técnica de Single Strand Conformational Polymorphism (SSCP). Foram analisados isolados procedentes de diferentes regiões brasileiras e em geral a variabilidade foi maior para as amostras do Estado de São Paulo. Logrou-se transmitir experimentalmente o PFGSV com ácaros para uma espécie silvestre de maracujá (Passiflora morifolia). / In Brazil, passion fruits are affected by several diseases and pests which affect their yield. Among them, a recently recognized viral disease, caused by Passion fruit green spot virus (PFGSV), is characterized by the presence of green spots on fruits and senescent leaves, and necrotic lesions on branches. When the infection is early, stem lesions may coalesce, girdling the branch resulting in the subsequent death of the plant. Electron microscopic examination of the thin sections of infected tissues revealed the presence of short, bacilliform particles in the cistern of the endoplasmic reticulum and dense, vacuolated viroplasma in the cytoplasm. The disease was shown to be transmitted by the mite Brevipalpus phoenicis (Acari: Tenuipalpidae). The localized symptoms, transmission by Brevipalpus mite and the observed cytopathic effect are considered evidences to demonstrate the viral nature of the disease and place it among the socalled cytoplasmic type of Brevipalpus-transmitted viruses (C-BTV), whose prototype is the Citrus leprosis virus C (CiLV-C). Though the first report of the disease occurred more than 10 years ago at Vera Cruz-SP, little is known about PFGSV, though it has been found in several passion flower growing areas in Brazil. In 1994 was report a disease named of DPM (definhamento precoce do maracujazeiro) was reported state of Bahia, with characteristics similar to that of the PVM and it has been suggested that DPM and PVM are the same disease. Subsequently the PVM/DPM has been found in several others Brazilian States as Minas Gerais, Rio de Janeiro, Sergipe, Rondônia, Maranhão, Rio Grande do Norte, Paraíba, Pará and Distrito Federal. Diagnosis has been made by symptoms, association with Brevipalpus mites and the time consuming transmission electron microscopy. This work reports the results of efforts to generate a quick and precise method to detect the virus for the diagnosis of the disease, evaluate the variability of the PFGSV isolates from different regions of the country and determine the taxonomic position of this virus. From the dsRNA present in extracts of the PFGSV-infected passion flower plant tissues, a cDNA library was obtained and its sequencing permitted to identify part of the viral genome. Based on these sequences, particularly of p24 and the putative genes that code for the movement protein (MP) and replicase (Rep), specific primers were designed which specifically detected PFGSV by RT-PCR in extracts of PFGSV-infected tissues. Evaluation of the variability of different isolates of PFGSV was made by single strand conformational polymorphism (SSCP) of the amplified fragments of the viral genome. In general, it a larger variation was found in isolates from São Paulo state. PFGSV seems to differ from two other C-BTV with available primers, CiLV-C and the Solanum violaefolium ringspot virus (SvRSV), since RT-PCR assays do not cross amplify their genomes. Experimental transmission of PFGSV by mites to woodland passion flower (Passiflora morifolia) was achieved.

Espera-se que a água esteja dentro de um padrão de qualidade após passar pelos processos de tratamento, que deve ser mantido durante a distribuição chegando aos pontos de consumo em condições de jamais prejudicar a saúde humana e animal. Contudo, há vários problemas de saúde que mundialmente vêm sendo associados ao suprimento público de água, fato que tem exigido um controle de qualidade cada vez mais rigoroso. Apesar dos recursos analíticos disponíveis, que facilitam a detecção e quantificação de agentes físicos, químicos e microbiológicos potencialmente perigosos à saúde, há grande dificuldade em estabelecer parâmetros de qualidade e definir índices toleráveis daquilo que se consideram como agentes potencialmente perigosos à saúde. Muitas doenças veiculadas pela água são causadas por bactérias principalmente do grupo entérico, cuja presença é determinada através de indicadores como os coliformes totais e termotolerantes. Outros microrganismos patogênicos podem estar presentes e não serem detectados por não estarem associados a estes indicadores. Como somente uma pequena quantidade de bactérias pode ser cultivada, como demonstrado pela avaliação direta de fragmentos de genomas, tornou-se evidente que em várias situações muitas espécies microbianas embora presentes deixem de ser detectadas. Como ainda não se dispõe de informações suficientes a este respeito, este trabalho teve o objetivo de comparar métodos de identificação de bactérias cultiváveis e incultiváveis que possam comprometer a qualidade da água, analisando-se amostras coletadas ao longo do sistema de abastecimento da cidade de Piracicaba, desde a captação e processo de tratamento, distribuição e estocagem residencial da água de abastecimento, o que permitiria avaliar possíveis fontes de contaminação ao longo do trajeto nas redes de distribuição até os pontos de consumo. Amostras foram coletadas nas épocas de chuvas e seca para avaliar a qualidade da água de abastecimento e os resultados mostram que as bactérias presentes no sistema de abastecimento da cidade é 61,29% maior como estimado por SSCP em relação aos métodos de cultivo testados, sendo que o cultivo em meio R2A apresentou contagens medias superiores ao cultivo em meio TSA. Bactérias patogênicas potenciais como Shigela flexneri e Sphingomonas sp. mostraram resistência aos processos de tratamento e purificação da água, sendo identificadas em muitos pontos no sistema de abastecimento de água da cidade e nas amostras dos reservatórios domiciliares. Bactérias como Salmonella typhi, Salmonella sp. e Staphylococcus aureus foram identificadas apenas em amostras coletadas na rede, ou seja, não detectadas na amostra do ponto de captação, indicando uma provável contaminação no trajeto de distribuição da água tratada. Contudo uma maior preocupação é voltada aos reservatórios domiciliares, pois algumas amostras apresentaram uma concentração de cloro abaixo do limite mínimo exigido em Portaria e, também, a presença de microrganismos patogênicos potenciais como os pertencentes ao Grupo Entérico. Estes dados revelam que apesar do eficiente sistema de tratamento da cidade, existem microrganismos que resistem aos processos de tratamento disseminando-se pela rede e que há possíveis focos de contaminação na rede de distribuição da água, podendo comprometer a qualidade da água disponível ao consumo publico. / It is expected that the water be within the quality standards after being through the treatment processes, which must be maintained along its distribution system up to the consumption points under the same conditions. However, there are several health problems worldwide associated to the public water supply. This fact has required a more and more rigorous quality control. It is difficult to set quality parameters and to define tolerant levels of what is considered as agents potentially dangerous to health, even if the analytical resources used to detect and quantify these chemical, physical, and microbiological agents are available. Bacteria, mainly from the enteric group, cause many diseases disseminated through water. Its presence is determined by using indicators, such as, total and thermo-tolerant coliforms. Other pathogenic microorganisms can be present in water without being detected, because they are not associated to those indicators. Just a small amount of bacteria can be cultivated, as demonstrated by direct evaluation of genome fragments. It is evident that in several situations many microbial species are not detected, even being present in the environment. As there is not enough information available, this work aimed to compare the identification methods of cultivated and non-cultivated bacteria that can damage the water quality. The samples were collected along the water supply system from Piracicaba, São Paulo, from the collection site, treatment process, and distribution to domestic reservoirs in order to check possible sources of contamination throughout the distribution system up to the consumption points. Samples were collected in the rainy and dry seasons to evaluate the quality of water supply. The results demonstrated that the population of bacteria present in the supply system from the city is 61.29% higher than that estimated by SSCP. In relation to the cultivation methods under testing, R2A medium presented higher average counting when compared to TSA medium. Potentially pathogenic bacteria, such as, Shigela flexneri and Sphingomonas sp., demonstrated resistance to water treatment and purification processes. These microorganisms were identified in several points along the city water supply system and in the samples collected from the domestic reservoirs. Bacteria, such as, Salmonella typhi, Salmonella sp. and Staphylococcus aureus were identified only in some samples collected along the distribution system, that is, they were not detected in the samples from the collecting point. This fact indicates that there might have been a contamination along the distribution of treated water. However, an important concern is towards the domestic reservoirs, because some samples presented a lower concentration of Chlorine than the minimum amount required by law, and the presence of potentially pathogenic microorganisms from the enteric group. These data reveal that, despite the efficiency of the water treatment system in the city, there are microorganisms resistant to the treatment processes, and they are disseminated through the distribution pipes. There might be possible contamination focuses along the distribution pipes that can damage the quality of water available to the public consumption.

Espera-se que a água esteja dentro de um padrão de qualidade após passar pelos processos de tratamento, que deve ser mantido durante a distribuição chegando aos pontos de consumo em condições de jamais prejudicar a saúde humana e animal. Contudo, há vários problemas de saúde que mundialmente vêm sendo associados ao suprimento público de água, fato que tem exigido um controle de qualidade cada vez mais rigoroso. Apesar dos recursos analíticos disponíveis, que facilitam a detecção e quantificação de agentes físicos, químicos e microbiológicos potencialmente perigosos à saúde, há grande dificuldade em estabelecer parâmetros de qualidade e definir índices toleráveis daquilo que se consideram como agentes potencialmente perigosos à saúde. Muitas doenças veiculadas pela água são causadas por bactérias principalmente do grupo entérico, cuja presença é determinada através de indicadores como os coliformes totais e termotolerantes. Outros microrganismos patogênicos podem estar presentes e não serem detectados por não estarem associados a estes indicadores. Como somente uma pequena quantidade de bactérias pode ser cultivada, como demonstrado pela avaliação direta de fragmentos de genomas, tornou-se evidente que em várias situações muitas espécies microbianas embora presentes deixem de ser detectadas. Como ainda não se dispõe de informações suficientes a este respeito, este trabalho teve o objetivo de comparar métodos de identificação de bactérias cultiváveis e incultiváveis que possam comprometer a qualidade da água, analisando-se amostras coletadas ao longo do sistema de abastecimento da cidade de Piracicaba, desde a captação e processo de tratamento, distribuição e estocagem residencial da água de abastecimento, o que permitiria avaliar possíveis fontes de contaminação ao longo do trajeto nas redes de distribuição até os pontos de consumo. Amostras foram coletadas nas épocas de chuvas e seca para avaliar a qualidade da água de abastecimento e os resultados mostram que as bactérias presentes no sistema de abastecimento da cidade é 61,29% maior como estimado por SSCP em relação aos métodos de cultivo testados, sendo que o cultivo em meio R2A apresentou contagens medias superiores ao cultivo em meio TSA. Bactérias patogênicas potenciais como Shigela flexneri e Sphingomonas sp. mostraram resistência aos processos de tratamento e purificação da água, sendo identificadas em muitos pontos no sistema de abastecimento de água da cidade e nas amostras dos reservatórios domiciliares. Bactérias como Salmonella typhi, Salmonella sp. e Staphylococcus aureus foram identificadas apenas em amostras coletadas na rede, ou seja, não detectadas na amostra do ponto de captação, indicando uma provável contaminação no trajeto de distribuição da água tratada. Contudo uma maior preocupação é voltada aos reservatórios domiciliares, pois algumas amostras apresentaram uma concentração de cloro abaixo do limite mínimo exigido em Portaria e, também, a presença de microrganismos patogênicos potenciais como os pertencentes ao Grupo Entérico. Estes dados revelam que apesar do eficiente sistema de tratamento da cidade, existem microrganismos que resistem aos processos de tratamento disseminando-se pela rede e que há possíveis focos de contaminação na rede de distribuição da água, podendo comprometer a qualidade da água disponível ao consumo publico. / It is expected that the water be within the quality standards after being through the treatment processes, which must be maintained along its distribution system up to the consumption points under the same conditions. However, there are several health problems worldwide associated to the public water supply. This fact has required a more and more rigorous quality control. It is difficult to set quality parameters and to define tolerant levels of what is considered as agents potentially dangerous to health, even if the analytical resources used to detect and quantify these chemical, physical, and microbiological agents are available. Bacteria, mainly from the enteric group, cause many diseases disseminated through water. Its presence is determined by using indicators, such as, total and thermo-tolerant coliforms. Other pathogenic microorganisms can be present in water without being detected, because they are not associated to those indicators. Just a small amount of bacteria can be cultivated, as demonstrated by direct evaluation of genome fragments. It is evident that in several situations many microbial species are not detected, even being present in the environment. As there is not enough information available, this work aimed to compare the identification methods of cultivated and non-cultivated bacteria that can damage the water quality. The samples were collected along the water supply system from Piracicaba, São Paulo, from the collection site, treatment process, and distribution to domestic reservoirs in order to check possible sources of contamination throughout the distribution system up to the consumption points. Samples were collected in the rainy and dry seasons to evaluate the quality of water supply. The results demonstrated that the population of bacteria present in the supply system from the city is 61.29% higher than that estimated by SSCP. In relation to the cultivation methods under testing, R2A medium presented higher average counting when compared to TSA medium. Potentially pathogenic bacteria, such as, Shigela flexneri and Sphingomonas sp., demonstrated resistance to water treatment and purification processes. These microorganisms were identified in several points along the city water supply system and in the samples collected from the domestic reservoirs. Bacteria, such as, Salmonella typhi, Salmonella sp. and Staphylococcus aureus were identified only in some samples collected along the distribution system, that is, they were not detected in the samples from the collecting point. This fact indicates that there might have been a contamination along the distribution of treated water. However, an important concern is towards the domestic reservoirs, because some samples presented a lower concentration of Chlorine than the minimum amount required by law, and the presence of potentially pathogenic microorganisms from the enteric group. These data reveal that, despite the efficiency of the water treatment system in the city, there are microorganisms resistant to the treatment processes, and they are disseminated through the distribution pipes. There might be possible contamination focuses along the distribution pipes that can damage the quality of water available to the public consumption.

In the present study, haplogroup composition of five native Turkish sheep breeds, (Karayaka, Akkaraman, G&ouml / k&ccedil / eada, Dagli&ccedil / , Morkaraman) and two sheep breeds from neighboring countries (Herik from Iran, samples from Azerbaijan) were determined by single strand length polymorphism (SSCP) analysis of mitochondrial DNA (mtDNA) NADH dehydrogenase subunit 4 (ND4) region and restriction fragment length polymorphism (RFLP) analysis of mtDNA control (CR) region. Results of the SSCP and RFLP approaches were found to be 96,82% consistent. Most of the 3,18% inconsistency was due to unidentified band patterns of 9 individuals. SSCP method could identify haplogroups A, B and C, but not D and E. Similarly RFLP method could identify haplogroup A, B and possibly D, but not E and C. Data of the present study were compared with those of the previous studies to test the robustness of results under different samplings and were found to be homogenous with a previous study with similar sampling strategy. Neighbor joining tree, principal component analysis (PCA), Delaunay network analysis and analysis of molecular variance (AMOVA) were employed to analyze the haplogroup frequencies and breeds were separated in four groups according to the genetic barriers between breeds from different geographical locations. Strongest differentiation was present between two groups which were eastern breeds (Morkaraman, Herik-Iran and Azerbaijan) and western breeds (G&ouml / k&ccedil / eada, Akkaraman, Karayaka and Dagli&ccedil / ). Additionally, Azerbaijan was proposed as the entrance point of the haplogroup A and the Iran was proposed as the entrance point of haplogroup C to Anatolia with the Spearman rank correlation test.

A cultura do maracujazeiro tem sido afetada por um grande número de pragas e doenças, que exigem dedicação e esforços urgentes, no sentido de minimizar as perdas e evitar sua disseminação. O vírus da pinta verde do maracujazeiro (PVM) (Passion fruit green spot virus PFGSV) caracteriza-se por induzir a formação de pequenas manchas verdes em frutos e em folhas, e lesões necróticas em ramos. Exames de secções ultrafinas de tecidos infectados ao microscópio eletrônico de transmissão consistentemente revelam a presença de partículas baciliformes em cisternas do retículo endoplasmático e viroplasma denso no citoplasma. Os efeitos citopáticos encontrados, a relação com o ácaro vetor, Brevipalpus phoenicis, e a comparação com outros vírus transmitidos por Brevipalpus (VTB), como o da leprose dos citros, classifica o vírus como sendo do tipo citoplasmático. Seu relato inicial deu-se há cerca de 10 anos em Vera Cruz-SP, mas em 1994 foi relatada uma doença no Estado da Bahia chamada de definhamento precoce do maracujazeiro (DPM), que apresenta sintomas, efeitos citopáticos e vetor semelhantes ao da pinta verde, tendo sido sugerida a possibilidade de serem duas denominações para uma mesma doença. Atualmente a PVM/DPM encontra-se em vários outros Estados como Minas Gerais, Rio de Janeiro, Sergipe, Rondônia, Maranhão, Rio Grande do Norte, Paraíba e Pará, além do Distrito Federal. Sua diagnose ainda depende dos sintomas observados, infestação por ácaros Brevipalpus e microscopia eletrônica. Para se desenvolver um método de diagnose molecular, que permita detectar o vírus causador da PVM/DPM de maneira rápida e confiável, em grande número de amostras, foi feita uma Biblioteca de cDNA a partir do RNA dupla fita do vírus, extraído de tecidos sintomáticos de maracujazeiros infectados com um isolado do PFGSV encontrado em Limeira-SP. Com o sequenciamento parcial do genoma viral, foram desenhados primers específicos que amplificam partes dos genes putativos da p24 e aqueles que codificam a proteína de movimento (MP) e a Replicase (Rep) de diferentes isolados do PFGSV. Primers do PFGSV e de dois outros VTBs do tipo citoplasmático (VTB-C) para os quais se dispõe de primers para sua detecção por RT-PCR (vírus da leprose dos citros C - CiLV-C; mancha anelar de Solanum violaefolium - SvRSV) foram testados em reações homólogas e heterólogas. Ocorreram amplificações por RT-PCR gerando fragmentos de tamanho esperados apenas para os vírus homológos, mas não nas reações heterólogas, indicando que PFGSV deve diferir do CiLV-C e SvRSV. Assim, tem-se agora uma ferramenta molecular que detecta especificamente o PFGSV. Um estudo inicial sobre a variabilidade genética do PFGSV foi feito a partir da extração do RNA total, seguido de RT-PCR utilizando os primers específicos, purificação dos fragmentos obtidos e uso da técnica de Single Strand Conformational Polymorphism (SSCP). Foram analisados isolados procedentes de diferentes regiões brasileiras e em geral a variabilidade foi maior para as amostras do Estado de São Paulo. Logrou-se transmitir experimentalmente o PFGSV com ácaros para uma espécie silvestre de maracujá (Passiflora morifolia). / In Brazil, passion fruits are affected by several diseases and pests which affect their yield. Among them, a recently recognized viral disease, caused by Passion fruit green spot virus (PFGSV), is characterized by the presence of green spots on fruits and senescent leaves, and necrotic lesions on branches. When the infection is early, stem lesions may coalesce, girdling the branch resulting in the subsequent death of the plant. Electron microscopic examination of the thin sections of infected tissues revealed the presence of short, bacilliform particles in the cistern of the endoplasmic reticulum and dense, vacuolated viroplasma in the cytoplasm. The disease was shown to be transmitted by the mite Brevipalpus phoenicis (Acari: Tenuipalpidae). The localized symptoms, transmission by Brevipalpus mite and the observed cytopathic effect are considered evidences to demonstrate the viral nature of the disease and place it among the socalled cytoplasmic type of Brevipalpus-transmitted viruses (C-BTV), whose prototype is the Citrus leprosis virus C (CiLV-C). Though the first report of the disease occurred more than 10 years ago at Vera Cruz-SP, little is known about PFGSV, though it has been found in several passion flower growing areas in Brazil. In 1994 was report a disease named of DPM (definhamento precoce do maracujazeiro) was reported state of Bahia, with characteristics similar to that of the PVM and it has been suggested that DPM and PVM are the same disease. Subsequently the PVM/DPM has been found in several others Brazilian States as Minas Gerais, Rio de Janeiro, Sergipe, Rondônia, Maranhão, Rio Grande do Norte, Paraíba, Pará and Distrito Federal. Diagnosis has been made by symptoms, association with Brevipalpus mites and the time consuming transmission electron microscopy. This work reports the results of efforts to generate a quick and precise method to detect the virus for the diagnosis of the disease, evaluate the variability of the PFGSV isolates from different regions of the country and determine the taxonomic position of this virus. From the dsRNA present in extracts of the PFGSV-infected passion flower plant tissues, a cDNA library was obtained and its sequencing permitted to identify part of the viral genome. Based on these sequences, particularly of p24 and the putative genes that code for the movement protein (MP) and replicase (Rep), specific primers were designed which specifically detected PFGSV by RT-PCR in extracts of PFGSV-infected tissues. Evaluation of the variability of different isolates of PFGSV was made by single strand conformational polymorphism (SSCP) of the amplified fragments of the viral genome. In general, it a larger variation was found in isolates from São Paulo state. PFGSV seems to differ from two other C-BTV with available primers, CiLV-C and the Solanum violaefolium ringspot virus (SvRSV), since RT-PCR assays do not cross amplify their genomes. Experimental transmission of PFGSV by mites to woodland passion flower (Passiflora morifolia) was achieved.

La microcouche de surface (SML) correspond au premier millimètre de la colonne d'eau. Située à l'interface air-eau, la SML est un environnement unique, riche en microorganismes, en matières organiques, en hydrocarbures et présentant des conditions extrêmes par l'impact des radiations UV et les fortes concentrations de polluants. Les échantillons ont été prélevés dans la SML et dans l'eau sous-jacente (UW) à 7 stations de la Baie de Guanabara, Brésil. Cette étude a permis de caractériser l'abondance et la diversité des bactéries et des hydrocarbures présents dans la SML de la baie. L'origine des hydrocarbures a été analysée par des marqueurs chimiques par chromatographie en phase gazeuse. Sur le plan microbiologique, 43 souches bactériennes ont été isolées et identifiées. Leur résistance aux radiations UV a été évaluée à l'aide d'un simulateur solaire. La SML de la baie est bien définie par rapport à l'UW et enrichie en hydrocarbures et en bactéries. Le bactérioneuston est plus diversifié que le bactérioplancton. La plupart des souches testées sont très résistantes aux UV et sont des espèces potentiellement intéressantes sur le plan biotechnologique.