It has been suggested that high protein diets are associated with an increased risk of colorectal cancer due to the higher content of red meat. However, the study of the overall dietary and lifestyle pattern may prove more important than any individual component when assessing colorectal cancer risk. From this, it is proposed that a dietary pattern used for weight loss that is higher in protein but remains low in fat and high in foods rich in fibre and micronutrients that are required for genome stability may not increase the risk of colorectal cancer, thus providing a safe and effective dietary method of weight loss in overweight subjects. This thesis describes the development of a novel in vitro faecal water genotoxicity test using the cytokinesis-block micronucleus (CBMN) cytome assay in the WIL2-NS cell line. This thesis then investigates faecal water genotoxicity and peripheral blood lymphocyte genome stability in overweight men following a weight loss dietary pattern either high in protein, specifically red meat, or high in carbohydrate. Results from this thesis indicate that the genotoxic potential of faecal water can be successfully assessed in vitro using the CBMN cytome assay. A high protein-high red meat weight loss diet did not increase faecal water genotoxicity or peripheral blood lymphocyte DNA damage, measured with the CBMN cytome assay, differently to a high carbohydrate weight loss diet. Faecal water genotoxicity data suggests weight loss and/or caloric restriction following either a high protein or high carbohydrate diet may beneficially modify the carcinogenic load of the colon in the short term, however this needs to be validated in a study that includes a non-weight loss control group. A lack of relationship was seen between faecal water genotoxicity and genome damage in lymphocytes which may suggest that the assessment of both the genome damage potential of the bowel contents and the assessment of the genome stability profile of peripheral blood lymphocytes may be important in comprehensively assessing the impact on genome damage by different dietary patterns. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1316889 / Thesis (Ph.D.) -- University of Adelaide, School of Molecular and Biomedical Science, 2008

Introdução: A gravidez e o parto são frequentemente associados à redução da força dos músculos do assoalho pélvico (FMAP) e à incontinência urinária (IU) e anal (IA), devido às alterações que ocasionam nos mecanismos de controle e suporte das estruturas do assoalho pélvico. Objetivos: O objetivo geral foi analisar a FMAP e a IU e IA no período pós-parto e os específicos foram verificar a associação da FMAP com a IU e a IA após o parto e identificar os fatores associados à FMAP, à IU e à IA após o parto e a interferência da IU na vida da puérpera. Método: Estudo transversal, com 128 mulheres nos primeiros 6 meses após o parto, conduzido em um serviço do setor suplementar de saúde, em Guarulhos, SP. Foram incluídas todas as mulheres integrantes da coorte Cuidado perineal na gestação e após o parto: prevenção e morbidade relacionadas à força muscular perineal, função sexual e continência urinária, que compareceram ao menos a um retorno do pós-parto. Os dados foram coletados por meio de entrevista, a FMAP foi mensurada pela perineometria (Peritron) e o International Consultation on Incontinence Questionnaire-Short Form (ICIQ-SF) foi aplicado às mulheres que referiram IU. Foram realizadas análise descritiva, inferencial e múltipla. O estudo foi aprovado pelo Comitê de Ética em Pesquisa da Escola de Enfermagem da Universidade de São Paulo. Resultados: A média da FMAP foi 33,1 (d.p.=16,0) cmH2O. Não houve redução estatisticamente significante com relação à FMAP na gestação (p=0,088). A prevalência de IU e IA foi de 7,8% e 5,5%, respectivamente. A média do escore do ICIQ-SF foi 9,4 (d.p.=6,0), maior entre as mulheres com parto normal que entre aquelas com cesariana (13,0, d.p.=6,4 e 5,8, d.p.=2,6, respectivamente). Na análise múltipla, as variáveis tempo de coabitação (IC 95% 2,29-20,92), cesariana anterior (IC 95% 1,45-,26) e tipo de parto atual (IC 95% -16,71- -1,14) foram associadas à FMAP; peso do recém-nascido atual (OR 1,03; IC 95% 1,0005-1,0517), gestação anterior (OR 13,14; IC 95% 1,63-106,27), IU na gestação (OR20,43; IC 95% 1,70-244,98) e atividade sexual após o parto (OR 0,06; IC 95% 0,01-0,49) foram associadas à IU; apenas a IA prévia (OR 6,26; IC 95% 1,08-36,43) foi associada à IA. Conclusão: Não há associação da FMAP com IU e IA após o parto. O parto vaginal predispõe à redução da FMAP e a cesariana é fator protetor à sua redução. A IU durante a gestação é preditora da IU após o parto e em mulheres com gestação anterior e recém-nascido de maior peso a IU é mais frequente. A interferência da IU na vida da mulher foi moderada. Apenas a IA prévia teve associação com a IA após o parto. Não é possível concluir que há associação direta entre tempo de coabitação com o parceiro e FMAP e IU e atividade sexual após o parto / Introduction: Pregnancy and childbirth are often associated with reduced pelvic floor muscles strength (PFMS), urinary (UI) and anal incontinence (AI) because of the changes in the mechanisms of control and support of the pelvic floor structures. Objectives: To analyse the PFMS, UI and AI during postpartum period. To verify the association of PFMS with UI and AI after birth. To identify factors associated with PFMS, UI and AI after birth and the interference of UI in the quality of life after birth. Methods: Cross-sectional study with 128 women in the first six months after birth, held in an insurance health care facility in Guarulhos, SP. All women participants of the cohort Perineal care during pregnancy and after birth: prevention and morbidity related to PFMS, sexual function and UI who attended at least one postpartum consultation were included. Data were collected through interviews, PFMS was measured by perineometry (Peritron) and the International Consultation on Incontinence Questionnaire-Short Form (ICIQ-SF) was applied to women who reported UI. Descriptive, inferential and multivariate analyses were performed. The research was approved by the Research Ethics Committee of School of Nursing of University of Sao Paulo. Results: The main score of PFMS was 33.1 cmH2O (SD=16.0). There was no statistically significant difference between PFMS during pregnancy and after birth (p=0.088). The prevalence of UI and AI was 7.8% and 5.5%, respectively. The mean ICIQ-SF score was 9.4 (SD=6.0). Higher mean score was verified among women with vaginal birth than among those with caesarean (13.0, SD=6.4 and 5.8, SD=2.6, respectively). In the multivariate analysis, period of cohabitation (95%CI 2.29 to 20.92), previous caesarean (95%CI 1.45 to 19.26) and type of birth (95%CI -16.71 to -1.14) were associated with PFMS; newborn weight (OR=1.03; 95%CI 1.0005 to 1.0517), previous pregnancy (OR=13.14; 95%CI 1.63 to 106.27), UI during pregnancy (OR=20.43; 95%CI 1.70 to 244.98) and sexual activity after birth (OR=0.06; 95%CI 0.01 to 0.49) were associated with UI; just previous AI (OR=6.26; 95%CI 1.08 to 36,43) is associated with AI. Conclusion: There is no association between PFMS and UI or AI after birth. Vaginal birth predisposes a reduction on PFMS and caesarean is a protective factor. UI during pregnancy is predictive of UI after birth and UI is more frequent in women with previous pregnancy and higher weight newborn. UI had moderate interference in women\'s lives. Just previous AI is associated with AI after birth. We can not conclude that there is an association between period of cohabitation and PFMS, UI and sexual activity after childbirth

O veado-mão-curta (Mazama nana) é uma espécie de cervídeo que ocupa a região Sul do Brasil, norte da Argentina e leste do Paraguai, tendo sido severamente afetada pela redução drástica das áreas florestadas. Trata-se, também, da espécie de cervídeo neotropical menos estudada pela ciência. Frente a essa situação, o presente projeto propôs-se a entender como essa espécie se distribui em sua área de ocorrência, propôs áreas prioritárias para sua conservação e estimou a densidade de duas populações. Dada a raridade e a alta elusividade da espécie, propôs-se o uso de metodologias indiretas para se atingir o objetivo proposto. Assim, foram usadas metodologias baseadas na coleta de amostras fecais, extração do DNA e posterior análises molecular e genética. Foram coletadas amostras fecais com o auxílio de um cão farejador em unidades de conservação distribuídas ao longo do Sul do Brasil. Após a identificação da espécie por meio da amplificação de um fragmento do citocromo B e corte com enzimas de restrição (PCR/RFLP) e com os dados de localização das amostras, foram feitas modelagens de distribuição com o software Maxent. Foram escolhidas duas unidades de conservação, onde foram realizadas coletas de amostras fecais, baseadas em faixas, para possibilitar a estimativa da densidade de animais nestas populações. Estabeleceu-se a distribuição geográfica potencial de M. nana no Brasil para os Estados do Paraná, Santa Catarina, norte e centro do Rio Grande do Sul, extremo sul de São Paulo e Mato Grosso do Sul. Porção leste do Paraguai e, na Argentina para a província de Missiones. A densidade da espécie para a região norte do Parque Nacional do Iguaçu foi de 1,9 ind/km2 e para o Parque Estadual Vila Rica do Espírito Santo foi de 5,5 ind/km2. A população potencial da espécie foi de 152.991 indivíduos, sendo 15.524 indivíduos a população dentro das áreas protegidas. Sugere-se a manutenção do estado de conservação da espécie como Vulnerável, tanto na lista Brasileira como na lista Internacional de fauna ameaçada de extinção. / The Brazilian dwarf brocket (Mazama nana) is a deer species that occupies the forests of southern Brazil, north of Argentina and east of Paraguay. It has been greatly affected by the drastic reduction of forested areas. It is also the less studied neotropical deer. Considering this situation, this project aimed to shed light on the species distribution along its range, to indicate conservation priority areas and estimate the density of two populations. Given the rarity and high elusiveness of the species, it is proposed the use of indirect methods to achieve this goal. Fecal samples collection based methodologies were used, followed by DNA extraction and subsequent molecular and genetic analysis. Fecal samples were tracked and collected in protected areas spread over south Brazil, with the help of a scat detection dog. After species identification by PCR/RFLP and samples spatialization, species distribution modeling was carried out using Maxent software suit. Two protected areas were chosen for a faecal sampling based on transects, in order to estimate the population density. Potential geographical distribution of M. nana in Brazil was stablished at states of Paraná, Santa Catarina, northern and center Rio Grande do Sul, extreme South of São Paulo and Mato Grosso do Sul. Also at Eastern Paraguay and Missiones province in Argentina. Species density at the northern area of Iguaçu National Park was 1.9 ind/km2 and at the State Park of Vila Rica do Espírito Santo was 5.5 ind/km2. The species potential population was 152,991 individuals, including 15,524 individuals inside protected areas. It is suggested to maintain species conservation status as vulnerable on the Brazilian and on the International red list of threatened species.

O gênero Mazama é composto por cinco espécies no Brasil. São animais de visualização dificultada por causa de comportamentos evasivos, o que torna as capturas e os estudos comportamentais quase impossíveis. Assim, o uso de metodologias não invasivas para estudos ecológicos e genéticos destas espécies se torna necessário. A análise do DNA fecal está dentro das técnicas mais promissoras para esse fim. Este estudo objetivou genotipar amostras fecais, de uma população de veado-mateiro (Mazama americana) para a obtenção de informações genéticas e ecológicas. Para tanto, foram coletadas, com auxílio de um cão farejador, georreferenciadas e estocadas em etanol absoluto, 52 amostras fecais de cervídeos. A coleta realizou-se em um fragmento (21o20S 47o17W) de 600 ha de floresta estacional semidecidual. Dessas amostras coletadas, 31% (n=16) foram classificadas como frescas e 69% (n=36) como não frescas. O DNA foi extraído em torno de 30 dias após a coleta, usando o kit comercial QIAamp® DNA Stool Mini Kit, seguindo o protocolo do fabricante. Das 52 amostras, 45 foram identificadas por PCR/RFLP como pertencentes a M. americana e as demais apresentaram problemas de amplificação e digestão, permanecendo sem identificação. Amplificaram-se por PCR cinco locos microssatélites, e o sucesso de amplificação, visualizado em gel de agarose, variou com o tamanho dos locos e com a classe das amostras. O sucesso de amplificação foi de 65% das amostras da categoria fresca e 35% das amostras da categoria não fresca. Encontrou-se uma correlação negativa (R= -0,82) entre o tamanho dos fragmentos dos locos de microssatélites e o sucesso de amplificação. Foi possível identificar o sexo do animal em 43,7% das amostras fecais, pela amplificação do gene da amelogenina. Os locos microssatélites amplificados foram analisados em sequenciador automático. Os eletroferogramas gerados pelo seqüenciador impossibilitaram a genotipagem da maioria dos locos e amostras, tornando inviável qualquer análise genética e ecológica com confiabilidade. Fica evidente a dificuldade de se trabalhar com a metodologia do DNA fecal para a identificação individual e sexagem de amostras obtidas de Cervídeos florestais em vida livre. Algumas melhorias metodológicas (coleta de amostras fecais frescas, seleção de iniciadores para locos menores e quantificação do DNA extraído por PCR em tempo real) são sugeridas para o aumento nos índices de sucesso na genotipgem em estudos futuros. / Mazama genus is composed by five species in Brazil. All of them are difficult to observe due to their evasive behaviors, what makes the captures and behavioral studies almost impossible. Thus, the use of non invasive methodologies is necessary to study the ecology and genetics of these species. The fecal DNA analysis is one of the most promising techniques for this purpose. This study aimed to genotype a Mazama americana population faecal samples for obtaining genetics and ecological information. For this, 52 deer faecal samples were collected in a 600ha seasonal semideciduos forest fragment (21o20S 47o17W), with the help of a detection dog, stored in ethanol and georeferenced. Of these samples 31% (n=16) was classified as fresh and 69% (n=36) as not fresh. About thirty days after the collection the DNA was extracted using the QIAamp® DNA Stool Mini Kit following the manufacturers instructions. From the 52 samples collected and extracted, 45 were identified by PCR/RFLP as M. americana and the others showed amplification and digestion problems, remaining without identification. Five microsatellite loci were amplified by PCR and the amplification success, visualized in agarose gel, varied with the loco size and age class. The amplifications success occurred in 65% of the fresh samples and in 35% of the non-fresh samples and a negative correlation (R= -0.82) was found between amplification success and loci sizes. It was possible to identify the animal sex in 43% of the samples by the amelogenin gene. The microsatellite loci amplifications were analyzed in an automatic sequencer. The majority of the samples and loci were impossible to genotype because of the quality of the elestroferograms, what made impossible any reliable genetic and ecological analysis. It is evident the difficulty to work with the faecal DNA methodology using field collected forests deer samples for individual and sexual identifications. Some methodological improvements (collect fresh samples, select primers for shorter loci and quantify the extracted DNA by real time PCR) are suggested to increase the genotyping success indexes in future studies

A presente tese foi elaborada em três capítulos, correspondente às seções 2, 3 e 4. No primeiro objetivou-se avaliar a associação de quitosana com grão de soja integral nas dietas sobre o consumo, fermentação ruminal, digestibilidade e metabolismo de nutrientes e seus efeitos sobre a produção de leite, perfil de ácidos graxos do leite e a eficiência produtiva de vacas em lactação. Para tal, 24 vacas multíparas da raça Holandesa, oito dessas com cânula ruminal, foram distribuídas em quadrados latinos 4×4 replicados. Os tratamentos foram obtidos por esquema fatorial 2×2 pela combinação de quitosana e grão de soja integral nas dietas. De modo geral, a associação de quitosana com grão de soja aumentou a eficiência de fermentação ruminal, reduziu as populações bacterianas ligadas à biohidrogenação e aumentou o teor de ácidos graxos insaturados na gordura do leite, mas houve significativa redução do consumo e digestibilidade dos nutrientes, da síntese de proteína microbiana e da produção de leite. No entanto, a adição de quitosana em dietas sem suplementação lipídica pode ser uma boa estratégia nutricional para aumentar a retenção de N e a eficiência alimentar de vacas em lactação, e adicionalmente, aumentar o teor de ácidos graxos insaturados e de cis-9, trans-11 CLA no leite. No segundo capítulo, o objetivo geral foi avaliar os indicadores externos Cr2O3 e TiO2 e os internos MSi, FDNi e FDAi, estes analisados em diferentes sacos de incubação in situ, a partir da acurácia, precisão e robustez das estimativas de excreção fecal em ensaio de digestão com vacas leiteiras consumindo diferentes dietas. Foram utilizadas oito vacas canuladas no rúmen para a realização de coletas totais de fezes com 24, 48 e 72 h de duração. De modo geral, o Cr2O3 gerou estimativas acuradas e precisas, no entanto a recuperação fecal e a robustez foram afetadas pelo consumo de extrato etéreo das vacas. O indicador TiO2 apresentou incompleta recuperação fecal, baixa acurácia, precisão e robustez. Dentre as combinações avaliadas para os indicadores internos, a FDNi em sacos de poliéster teve completa recuperação fecal e gerou as estimativas mais acuradas, precisas e robustas. A falta de acurácia e precisão dos indicadores têm grande impacto final sobre as estimativas de digestibilidade. No terceiro capítulo, o objetivo foi avaliar o uso da creatinina como indicador do volume urinário para estimativas de excreção total de derivados de purinas como técnica de avaliação da produção microbiana ruminal em vacas leiteiras alimentadas com diferentes dietas. Também foram utilizadas as oito vacas canuladas no rúmen para a realização de coletas totais de urina com 24, 48 e 72 h de duração. De modo geral, a creatinina foi afetada pelas condições experimentais do estudo, incluindo efeito de dieta e variações conforme o período experimental e animais. Apesar da relação entre excreção observada e estimada de derivados de purinas, essa deve ser vista com cautela, em razão de que o volume urinário foi subestimado e que as estimativas não identificaram corretas diferenças entre as dietas, comprometendo as avaliações sobre a produção microbiana ruminal. / The present thesis was elaborated in three chapters, corresponding to sections 2, 3 and 4. In the first one, the aim was to evaluate the association of chitosan (C) and whole raw soybean (WRS) in diets, evaluating the intake, ruminal fermentation, digestibility and nutrient metabolism and its effects on milk production, milk fatty acids profile and the productive efficiency of lactating cows. Twenty four multiparous Holstein cows, eight of them fitted with ruminal cannula, were distributed in a replicated 4 × 4 Latin squares. The treatments were a combination of C and WRS diets arranged in a 2 × 2 factorial design. This association increased the efficiency of ruminal fermentation, reducing the bacterial population responsible for the biohydrogenation and increased the unsaturated fatty acids in milk. The C and WRS diets caused a significant reduction in DMI and nutrient digestibility, in microbial protein synthesis and milk yield. However, the addition of C in diets without a lipid supplementation may be a good nutritional strategy to increase the N retention and increase the food efficiency of lactating cows, and, indeed, to increase the unsaturated fatty acids content, mainly cis-9, trans-11 CLA. In the second chapter, the objective was to evaluate the external indicators Cr2O3 and TiO2 and the indigestible internal DM, NDF and ADF that were determined in in situ different incubation bags from the accuracy, precision and robustness of the fecal excretion estimates in a digestion assay with different dairy cow diets. Eight cows fitted with ruminal cannula were used to perform total fecal collection over 24, 48 and 72 hours. The Cr2O3 generated accurate estimates, however, the fecal recovery and robustness were affected by the ether extract intake. The TiO2 indicator showed incomplete fecal recovery, low accuracy, precision and robustness. Among the combinations for the internal indicators, the iNDF in polyester bags had a complete recovery and generated the most accurate and robust estimates. The lack of accuracy and precision of the indicators have a big impact on the digestibility estimates. In the third chapter, the aim was to evaluate the use of creatinine as an indicator of urinary volume. It would be possible to estimate the total excretion of purine derivatives to evaluate the ruminal microbial protein synthesis in different cow diets. Also, eight multiparous cows fitted with ruminal cannula were used to make total urine collection over 24, 48 and 72 hours. The creatinine was affected by the study experimental conditions, including dietary effect and variations according to period and animals. The relationship between observed and estimated excretion of purine derivatives should be viewed with caution, because the urinary volume was underestimated and the estimates did not identify the correct differences between diets, that could compromise the evaluations of ruminal microbial production.

The field of conservation genetics, in combination with non-invasive sampling, provides a powerful set of tools for investigating the conservation status and natural history of rare species that are otherwise difficult to study. A systematic literature review demonstrated that this is certainly the case for many forest associated antelope species, which are poorly studied and yet constitute some of the most heavily hunted wildlife in Africa. The aim of the present study was to use non-invasive sampling to investigate genetic patterns in forest antelope populations in the high-biodiversity Udzungwa Mountains, Tanzania, within the context of the conservation of these species and the wider ecosystem. Genetic information was derived from faecal samples collected across the Udzungwa landscape and assigned to five antelope species (N = 618, collected 2006-09). Faecal pellet length was measured for a subset of samples but statistical assignment to species by this method proved unreliable. Phylogenetic analysis using mitochondrial control region sequences unexpectedly revealed that Harvey’s duiker within the Udzungwas are paraphyletic with respect to sequences from a putative sister species from southern Africa. However, there was no corresponding pattern in the microsatellite dataset suggesting that these mitochondrial lineages do not represent contemporary genetic isolation. Instead, Harvey’s duiker nuclear variation is shaped both by isolation by distance, due to positive spatial autocorrelation at short distances, and clustering of distinct genotypes from western outlying forests. These forests also harbour the endangered Abbott’s duiker and therefore require effective conservation management. Despite being detected throughout the Udzungwas, genetic diversity in Abbott’s duiker was very low in comparison to other species. These results suggest several promising research directions but also have significant conservation implications that will be disseminated to the Tanzanian wildlife authorities and the wider conservation community.

This study focuses on emerging E. coil serotypes and has developed methods for the isolation and identification of non-0157 STEC and EPEC. A basal medium for the isolation of these pathogens was developed as well as a serogroup specific PCR assay for the detection of the 02 serogroup. These culture and molecular based techniques have proven to be valuable in the detection, identification, and epidemiological investigation of these groups of emerging pathogens. These methods were applied to 1) a farm study, whereby samples (faecal and soil) and 2) an abattoir study, whereby samples (hide and carcass) were analysed for the presence of non-0157 STEC and EPEC. Isolates were subsequently characterised in terms of serotype/serogroup and virulence markers. The data generated by this work has illustrated the extent of non-0157 STEC and EPEC contamination in the farm and abattoir environments, thus providing scientific background upon which control strategies may be based.

L’objectif général de cette thèse est de caractériser la dynamique des transferts des bactéries fécales à l’aide d’une modélisation spatio-temporelle, à l’échelle du bassin versant (BV) dans une région agricole et à l’échelle événementielle. Ce projet vise à mieux comprendre l'influence des processus hydrologiques, les facteurs environnementaux et temporels impliqués dans l’explication des épisodes de contamination microbienne des eaux récréatives. Premièrement, un modèle bayésien hiérarchique a été développé pour quantifier et cartographier les niveaux de probabilité des eaux à être contaminées par des effluents agricoles, sur la base des données spectrales et des variables géomorphologiques. Par cette méthode, nous avons pu calculer les relations pondérées entre les concentrations d’Escherichia coli et la distribution de l’ensemble des paramètres agro-pédo-climatiques qui régissent sa propagation. Les résultats ont montré que le modèle bayésien développé peut être utilisé en mode prédictif de la contamination microbienne des eaux récréatives. Ce modèle avec un taux de succès de 71 % a mis en évidence le rôle significatif joué par la pluie qui est la cause principale du transport des polluants. Deuxièmement, le modèle bayésien a fait l’objet d'une analyse de sensibilité liée aux paramètres spatiaux, en utilisant les indices de Sobol. Cette démarche a permis (i) la quantification des incertitudes sur les variables pédologiques, d’occupation du sol et de la distance et (2) la propagation de ces incertitudes dans le modèle probabiliste c'est-à-dire le calcul de l’erreur induite dans la sortie par les incertitudes des entrées spatiales. Enfin, une analyse de sensibilité des simulations aux différentes sources d’incertitude a été effectuée pour évaluer la contribution de chaque facteur sur l’incertitude globale en prenant en compte leurs interactions. Il apparaît que sur l’ensemble des scénarios, l’incertitude de la contamination microbienne dépend directement de la variabilité des sols argileux. Les indices de premier ordre de l’analyse de Sobol ont montré que parmi les facteurs les plus susceptibles d’influer la contamination microbienne, la superficie des zones agricoles est le premier facteur important dans l'évaluation du taux de coliformes. C’est donc sur ce paramètre que l’attention devra se porter dans le contexte de prévision d'une contamination microbienne. Ensuite, la deuxième variable la plus importante est la zone urbaine avec des parts de sensibilité d’environ 30 %. Par ailleurs, les estimations des indices totaux sont meilleures que celles des indices de premier ordre, ce qui signifie que l’impact des interactions paramétriques est nettement significatif pour la modélisation de la contamination microbienne Enfin, troisièmement, nous proposons de mettre en œuvre une modélisation de la variabilité temporelle de la contamination microbiologique du bassin versant du lac Massawippi, à partir du modèle AVSWAT. Il s'agit d'une modélisation couplant les composantes temporelles et spatiales qui caractérisent la dynamique des coliformes. La synthèse des principaux résultats démontrent que les concentrations de coliformes dans différents sous-bassins versants se révèlent influencées par l’intensité de pluie. La recherche a également permis de conclure que les meilleures performances en calage sont obtenues au niveau de l'optimisation multi-objective. Les résultats de ces travaux ouvrent des perspectives encourageantes sur le plan opérationnel en fournissant une compréhension globale de la dynamique de la contamination microbienne des eaux de surface. / Abstract : The aim of this study was to predict water faecal contamination from a bayesian probabilistic model, on a watershed scale in a farming area and on a factual scale. This project aims to better understand the influence of hydrological, environmental and temporal factors involved in the explanation of microbial contamination episodes of recreational waters. First, a bayesian probabilistic model: Weight of Evidence was developed to identify and map the probability of water levels to be contaminated by agricultural effluents, on the basis of spectrals data and geomorphologic variables. By this method, we were able to calculate weighted relationships between concentrations of Escherichia coli and distribution of key agronomic, pedologic and climatic parameters that influence the spread of these microorganisms. The results showed that the Bayesian model that was developed can be used as a prediction of microbial contamination of recreational waters. This model, with a success rate of 71%, highlighted the significant role played by the rain, which is the main cause of pollution transport. Secondly, the Bayesian probabilistic model has been the subject of a sensitivity analysis related to spatial parameters, using Sobol indications. This allowed (1) quantification of uncertainties on soil variables, land use and distance and (2) the spread of these uncertainties in the probabilistic model that is to say, the calculation of induced error in the output by the uncertainties of spatial inputs. Lastly, simulation sensitivity analysis to the various sources of uncertainty was performed to assess the contribution of each factor on the overall uncertainty taking into account their interactions. It appears that of all the scenarios, the uncertainty of the microbial contamination is directly dependent on the variability of clay soils. Sobol prime indications analysis showed that among the most likely to influence the microbial factors, the area of farmland is the first important factor in assessing the coliforms. Importance must be given on this parameter in the context of preparation for microbial contamination. Then, the second most important variable is the urban area with sensitivity shares of approximately 30%. Furthermore, estimates of the total indications are better than those of the first order, which means that the impact of parametric interaction is clearly significant for the modeling of microbial contamination. Thirdly, we propose to implement a temporal variability model of microbiological contamination on the watershed of Lake Massawippi, based on the AVSWAT model. This is a model that couples the temporal and spatial components that characterize the dynamics of coliforms. The synthesis of the main results shows that concentrations of Escherichia coli in different sub-watersheds are influenced by rain intensity. Research also concluded that best performance is obtained by multi-objective optimization. The results of these studies show the prospective of operationally providing a comprehensive understanding of the dynamics of microbial contamination of surface water.

Thesis (MPA.) -- University of Limpopo, 2017 / The World Health Organisation (WHO) and World Bank (WB) state that worldwide access to sanitation has improved with countries in the north having 100% access to sanitation. However, only 64% of the world's population has access to improved sanitation. Sub-Saharan Africa has a noticeable improvement with South Africa improving from 73% in 2010 to 74% in 2014. They further estimate that $260 billion is lost globally each year due to lack of adequate water supply and sanitation. Universal access to water and sanitation would result in an estimated $32 billion in economic benefits per year globally from reductions in health care costs and increased productivity from reduced illness. Sub-Saharan Africa loses an estimated 4.3% ($US694 billion) of its Gross Domestic Product (GDP) each year due to lack of adequate water supply and sanitation. Furthermore, the UNDP (2015) indicates that sanitation is one of the Millennium Development Goals (MDG), however many regions are performing poorly in attaining their declared sanitation targets. South African has not reached its target but it is maintaining its commitment to the provision of sanitation as a basic human right. However, it has left the responsibility to local government to work out how this should be done with no legislation. Currently there is no policy on sanitation and municipalities only develop by-laws that serve as guidelines in managing waste and providing the service. The available literature on this subject speaks very little about the knowledge and understanding that the communities have with regard to faecal sludge management and no study at all deals with the perceptions of people on this issue, particularly around Polokwane Municipality. It is for these reasons that the study was aimed at investigating the perceptions of Polokwane residents regarding alternative faecal sludge management. Methodologically the study used qualitative research approach where in face-to-face interviews and focus group interviews were conducted around Polokwane Municipality. Among the participants interviewed were Ward Councillors, Community Development Workers, Ward Committees and Traditional Authorities. These stakeholders were intentionally chosen as they are at the coalface of service delivery on a daily basis and they are part of the forums that interact with the Municipality on basic services and other related community matters. Data for this study were analysed using thematic data analysis approach. vi  The findings of this study suggest that the “concerned residents” under Polokwane Municipality see themselves being victims and vulnerable to controllable health threats. In addition, the study discovered that the majority of participants were aware of the delegated sewage maintenance duties on the Polokwane Municipality. This study findings further indicated that there is a growing concern among municipal authorities and communities‟ especially in Africa and South Africa in particular, to improve the inadequate faecal management. The objectives of the study were among others to determine the perceptions and awareness of the Polokwane Local Municipality residents regarding alternative faecal sludge management methods. Indeed, it has been discovered that some of the residents are aware of various management methods but expect authority to develop policies and improve the inadequate methods that are currently used in managing faecal sludge. The study among others discovered that this study should be used as a point of reference for municipal projects administration, i.e. for the development of Integrated Development Plan (IDP) on the water and sanitation and faecal sludge management in future. The Ministry of environmental health and management at Polokwane Local Municipality should organise solid and integrated awareness with the community to ensure a healthy environment for all. The study further realised that there is a need to equip most of residents in Polokwane Local Municipality with knowledge on how best man can improve environmental health, as well as how worse can a person destroy the environment. It should be an important task for the Polokwane Local Municipality to ensure that residents understand the faecal sludge management enterprise developments in the area to reduce the incompleteness of the perceptions among the residents. Various faecal sludge methods should be adopted and encouraged among the Polokwane Local Municipality residents in order to promote the preference for the sanitation methods. Key words: Sanitation, Faecal sludge, Faeces, Health hazards and Sub-Saharan Africa

<p>The time bound agenda of the Millennium Development Goals (MDG&rsquo / s) aims at reducing poverty, extending gender equality and advancing opportunities for health and education by addressing current and future water resource and sanitation needs. In many rural areas of South Africa, the cost implication of routing surface water supplies and providing water borne sewerage may far exceed the budgets of local water service authorities. This has resulted in a major thrust in service provision via localised sources, mainly boreholes and springs as well as on site sanitation options. Whilst the National Water Act (Act 36 of 1998) mandates the South African government to provide potable water to all citizens in an equitable manner, this needs to be balanced against the preservation of the country&rsquo / s water resources both quantitatively and qualitatively to ensure sustainability. It is imperative that this fine balance between protection and effecting societal demands and economic development through large-scale water provision be maintained, as successful strategising will be resultant of integrated social, economic and environmental issues especially in economically developing countries. In order to fulfil the mandate of the NWA, policies and strategies for effective protection and use of groundwater resources have been drawn up and are in the process of being drawn up by the national Department of Water Affairs and Forestry (DWAF). The major scope of research in this thesis stems from feasibility studies commissioned by the DWAF for the implementation of a groundwater protection zoning policy for the management and protection of groundwater resource quality. The research work focuses on specifically the microbiological zone of protection and attempts to determine the fate of various pathogens that emanate from on site sanitation facilities as they move through the subsurface. The research was predominantly proposed as a desktop collation and analysis of existing published data however / it was later decided to include a local case study site.</p>