Orientador: Erick da Cruz Castelli / Resumo: O gene KIR2DL4 codifica um importante receptor de células Natural Killer (NK). O único ligante de KIR2DL4 conhecido é a molécula HLA-G, expressa principalmente na placenta, modulando a ação das células NK durante a gestação. O gene KIR2DL4 parece ser bastante variável, quando considerado os bancos de dados que armazenam suas sequências conhecidas, porém não está claro o nível de diversidade deste gene em populações reais e heterogêneas. Polimorfismos presentes no gene KIR2DL4 poderiam influenciar a interação entre KIR2DL4 e HLA-G, modificando a ação das células NK. Neste estudo exploramos a variabilidade genética de KIR2DL4 em 157 indivíduos oriundos do Estado de São Paulo/Brasil. Devido à alta similaridade de sequências entre os genes KIR, erros de genotipagem são esperados quando se utiliza sequenciamento de segunda geração. Por este motivo, desenvolvemos uma abordagem para classificar cada leitura com base em sequências KIR conhecidas, endereçando-as ao gene mais provável. Também utilizamos o painel SNPforID 34-plex para avaliar a ancestralidade dessas amostras. Considerando o segmento completo desse gene, indo da região 5’URR até a 3’UTR, com aproximadamente 13kb, o gene KIR2DL4 se mostrou pouco polimórfico, com 152 pontos de variações identificados (MAF 1%). Esses pontos de variação estão organizados em 32 haplótipos estendidos que codificam 13 proteínas diferentes. Foram encontrados 11 haplótipos na região promotora, sendo que 8 possuem MAF maior que 1%. Na região codif... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: KIR2DL4 is the most unusual Killer Cell Immunoglobulin-Like receptor (KIR) family member in terms of structure, expression, and signaling properties. The only known KIR2DL4 ligand is HLA-G, and polymorphisms might disrupt this interaction. KIR2DL4 variability is not well explored in admixed populations. Here we explored KIR2DL4 exon variability in 157 individuals from the State of São Paulo/Brazil. Because of sequence similarity with other KIR genes, it is expected genotyping errors when using secondgeneration sequencing. We developed an approach to score each read based on known KIR sequences, addressing them to the most likely locus. We evaluated the SNPforID 34-plex panel to assess ancestry. The methodology was applied to survey the variability of a very admixed population, such as Brazilian, counting with 157 samples of São Paulo State. Considering a segment of about 13-kb, KIR2DL4 gene was conserved with few different and frequent sequences. Overall, 152 variable sites were detected, arranged in 32 haplotypes codifying 13 protein. We found 11 promoter haplotypes, 8 with a frequency greater than 1%. In the coding region we detected 70 haplotypes, four of which correspond to 50% of the coding sequences (KIR2DL4 * 0080204, * 008105, * 001, * 005). In the 3'UTR region, 14 haplotypes were identified with MAF greater than 1%. The KIR2DL4 coding region was the most variable segment. We observed that KIR2DL4 variability is strongly influenced by the sample ancestry background. K... (Complete abstract click electronic access below) / Mestre

Septic tanks are utilized by many households across North America for wastewater treatment. Despite the economic and environmental importance of septic tanks, there has been limited innovation in septic tank design and research on the microbial communities responsible for wastewater treatment within these systems. InnerTube systems are septic tanks that employ a novel design to reduce solid accumulation in comparison to conventional septic tanks. For this project, 16S metabarcoding was employed to characterize conventional and InnerTube septic tank microbial communities and evaluate relationships between community composition, system design, and treatment efficacy. Wastewater was sampled along the length of InnerTubes to determine patterns of microbial succession and how they may impact InnerTube function. Wastewater was separated into liquid and solid fractions to identify differentially abundant taxa in each fraction. Populations of methylotrophic methanogens increased with distance from the InnerTube inlet. Solid communities were differentially more abundant in methanogens than liquid communities. Higher rates of solid degradation in InnerTubes may be due to longitudinal stratification of substrates and functionally distinct communities and the activity of methanogenic biomass. Septic tanks throughout Ontario were also surveyed to evaluate the effect of system design (conventional vs. InnerTube) and operational flow (single-pass vs. recirculation) on microbial community composition and to identify taxa correlated with chemical oxygen demand (COD) reduction. Single-pass InnerTube communities were more abundant in Pseudomonas which was attributed increased availability of long-chain fatty acid substrates. Recirculating conventional communities were more abundant in Arcobacter and Desulfomicrobium which was attributed to greater resistance to oxidative stress. Desulfovibrio and Brevundimonas were positively correlated with COD reduction. These putative hydrogen producers may facilitate greater COD reduction by forming syntrophic relationships with hydrogenotrophic methanogens. The findings of this project may be used to develop bioaugmentation inoculum, system designs, or operational strategies to optimize septic tank performance. / Thesis / Master of Science (MSc) / Septic systems (anaerobic digesters) are extensively used for on-site wastewater treatment. We evaluated the use of next-generation DNA sequencing to (1) assess the variability of septic system microbial communities and (2) to investigate relationships between communities and septic system type/performance. Microbial communities within septic systems were determined to be heterogeneous. Analyses also indicated that communities were highly variable between septic systems. Despite this variability, specific system types exhibited distinct microbial profiles. System performance was positively correlated with the abundance of hydrogen-producing bacteria. These results demonstrate the potential of next-generation DNA sequencing as a new tool to augment traditional wastewater analyses.

Submitted by Claudia Rocha (claudia.rocha@udesc.br) on 2018-02-28T15:12:17Z No. of bitstreams: 1 PGPV16MA213.pdf: 884034 bytes, checksum: 7cc478a7cc0d8b7316468ee785e7565f (MD5) / Made available in DSpace on 2018-02-28T15:12:17Z (GMT). No. of bitstreams: 1 PGPV16MA213.pdf: 884034 bytes, checksum: 7cc478a7cc0d8b7316468ee785e7565f (MD5) Previous issue date: 2016-08-26 / Microsatellites or simple sequence repeats (SSR) are co-dominant and highly polymorphic genetic markers used for population genetic studies. Mimosa scabrella Benth., popularly known as ‘‘bracatinga’’, is a pioneer and endemic species of Brazil, occurring in Mixed Ombrophilous Forest associated to Brazilian Atlantic Rainforest biome. It is a fast-growing tree of Fabaceae family which facilitates the dynamics of ecological succession. SSR development when there is no sequence is time and labor intensive, there are no molecular markers for Mimosa scabrella Benth. Due to reduced time, the use of second generation sequencing is a powerful tool for microsatellite development for population genetic studies. This current project proposed to develop and validate the first microsatellite markers for the species, evaluating mother trees and progenies. Using Second Generation Sequencing of Illumina platform, this project identified 290 SSR loci e 211 primer pairs. A subset of 11 primer pairs was synthetized with fluorescence in the Forward primer for PCR and capillary electrophoresis validation with leaf DNA of 33 adult and 411 progeny individuals. Polymorphic loci percentage was 36, four in 11 loci, 3 chloroplast SSR and one nuclear SSR. Allele number of polymorphic loci ranged from two to 11 alleles considering all sampling. Second-generation sequencing has enabled a large number of microsatellite loci identification for bracatinga, resulting in SSR markers development for the species. The assessed and validated SSR markers are suitable and useful for analysis and population genetic studies. Other SSR markers were identified, but still need to be synthesized and evaluated for polymorphism and consistency between mother trees and progenies for validation / Microssatélites ou simple sequence repeats (SSR) são marcadores genéticos codominantes e altamente polimórficos usados para estudos de genética de populações. Mimosa scabrella Benth., popularmente conhecida como bracatinga, é uma espécie pioneira e endêmica do Brasil, ocorrendo na Floresta Ombrófila Mista, associado ao bioma Mata Atlântica. É uma espécie arbórea da família Fabaceae, de rápido crescimento, que facilita a dinâmica de sucessão ecológica. O desenvolvimento de SSR quando não há sequências é demorado e laborioso, e não há marcadores moleculares desenvolvidos para Mimosa scabrella Benth. Devido ao tempo reduzido, o uso de sequenciamento de segunda geração é uma ferramenta poderosa para o desenvolvimento de microssatélites nos estudos de genética de populações. O presente trabalho se propôs a desenvolver e validar os primeiros marcadores microssatélites para a espécie, avaliando matrizes e progênies. Usando o sequenciamento de segunda geração pela plataforma Illumina, este trabalho identificou 290 locos SSR e 211 pares de primers. Um subconjunto de 11 pares de primers foi sintetizado com fluorescência no primer forward para validação por PCR e eletroforese capilar a partir do DNA de folhas de 33 adultos e 411 progênies. A porcentagem de locos polimórficos foi de 36, quatro locos em 11, três SSR cloroplastidiais e um SSR nuclear. O número de alelos por loco polimórfico variou de 2 a 11 considerando toda a amostragem. O sequenciamento de segunda geração possibilitou a identificação de um grande número de locos microssatélites para a bracatinga, resultando no desenvolvimento de marcadores SSR para a espécie. Os marcadores SSR avaliados e validados são aptos e úteis para análises e estudos de genética de populações. Outros marcadores SSR foram identificados, mas ainda precisam ser sintetizados e avaliados quanto ao polimorfismo e consistência entre matrizes e progênies para validação