Submitted by Cláudia Bueno (claudiamoura18@gmail.com) on 2015-10-20T16:00:07Z No. of bitstreams: 2 Dissertação - Daniel Garcia Silva - 2012.pdf: 2191471 bytes, checksum: 68bc7d63efc7307ce6b62a63489d372d (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-10-21T10:02:07Z (GMT) No. of bitstreams: 2 Dissertação - Daniel Garcia Silva - 2012.pdf: 2191471 bytes, checksum: 68bc7d63efc7307ce6b62a63489d372d (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2015-10-21T10:02:07Z (GMT). No. of bitstreams: 2 Dissertação - Daniel Garcia Silva - 2012.pdf: 2191471 bytes, checksum: 68bc7d63efc7307ce6b62a63489d372d (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2012-06-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Sugarcane is an important crop, cultivated in more than 90 countries, occupying an area of approximately 20 million of hectares. Modern varieties (Saccharum spp.) are highly heterozygous interspecific hybrids, polyploids and often aneuploids, with chromosome numbers between 100 and 130. Such characteristics explain the common opinion that the genome of sugarcane is the most complex among cultivated species, posing a challenge to breeding programs. As a contribution to the understanding of this complex genomic architecture, this study aimed to build the first linkage maps using exclusively DArT markers in sugarcane. The maps were built using a progeny derived from the cross between varieties largely used in the Brazilian breeding program of RIDESA (RB97327 x RB72454). The initial mapping population comprised 186 individuals. Total genomic DNA was extracted from axial buds, following the protocol of Al-Janabi et al. (1999). Using the DArT P/L core facility to generate DArT data, a total of 7680 markers were analyzed, of which 850 were polymorphic. The analysis of segregation patterns in the progeny revealed that 47% of the individuals in the progeny were in fact derived from selfing of the female parent RB97327. These individuals were analyzed as a distinct generation. Linkage analyses were then performed on two populations (from selfing and crossing) separately. The software OneMap was used to construct the maps. The established linkage criteria for linkage analysis were LOD-score ≥ 3.5 and recombination fraction ≤ 0.4. In the first map, built using data from individuals originated from selfing, from 850 polymorphic markers, 392 markers (segregating in a 3:1 manner) were used to create 80 linkage groups related to the variety RB97327. For the population derived from the biparental crossing, four linkage maps were built: an integrated map composed of 98 linkage groups including 632 markers (1:1 and 3:1); an integrated framework map, using a more conservative ordering criteria for the linkage groups, which was composed of 94 linkage groups; and two other linkage maps, one for each parent (RB97327 and RB72454), built to estimate the genome size of the varieties involved in this study. The total length of the linkage map built using data from individuals derived from selfing of the variety RB97327 was 828 cM. The total length of the integrated linkage map was 2848 cM. The lengths of the maps built for each parent, using data from individuals derived from crossing, were 1465 cM (RB97327) and 1976 cM (RB72454). Using the methodology of Hulbert et al. (1988), the estimated genome sizes for these varieties were 2811 cM e 3471 cM, respectively. The maps obtained in these cases covered a low percentage of the estimated genome sizes (52% and 57%). In spite of the low polymorphism, DArT markers showed to be an efficient technique to perform genotyping of sugarcane. Hundreds of polymorphic markers were generated in only one assay, using two methods of genome complexity reduction. These markers represent a new tool for genetic studies in sugarcane, especially if the low cost (USD/marker) involved in data production is considered. / A cana-de-açúcar é uma importante cultura, cultivada em mais de 90 países, ocupando uma área total de aproximadamente 20 milhões de hectares. As variedades modernas (Saccharum spp.) são híbridos interespecíficos altamente heterozigóticos, poliploides e frequentemente aneuploides, com número cromossômico variando de 100 a 130. Tais características proporcionaram ao genoma da cana-de-açúcar o título de mais complexo entre as espécies cultivadas, o que representa um desafio para os programas de melhoramento genético da cultura. No intuito de contribuir com dados que auxiliem na compreensão dessa complexa arquitetura genômica, o presente estudo objetivou a construção dos primeiros mapas de ligação para cana-de-açúcar utilizando exclusivamente marcadores DArT, avaliados na progênie derivada do cruzamento de variedades amplamente utilizadas nos programas de melhoramento da RIDESA (RB97327 x RB72454). A população inicial de mapeamento foi composta por 186 indivíduos. O DNA genômico foi extraído de gemas axiais, seguindo o protocolo proposto por Al-Janabi et al. (1999). Após a extração, quantificação e homogeneização da concentração de DNA das amostras, o material foi enviado para a empresa DArT P/L para a geração dos marcadores DArT. Um total de 7680 locos foi analisado, dos quais 850 se apresentaram polimórficos. A análise dos padrões de segregação obtidos na progênie revelou que 47% dos indivíduos da progênie avaliada foram provenientes de autofecundação do genitor feminino RB97327. Os indivíduos identificados como provenientes de autofecundação foram analisados como uma geração distinta. As análises de ligação foram realizadas nas duas populações separadamente. O software OneMap foi utilizado para a construção dos mapas. Os critérios estabelecidos para proceder com as análises de ligação foram LOD-score ≥ 3,5 e fração de recombinação ≤ 0,4. No primeiro mapa, originário da população de autofecundação, dos 850 marcadores polimórficos, 392 marcadores com segregação 3:1 foram utilizados para originar 80 grupos de ligação referentes à variedade RB97327. Para a população derivada do cruzamento biparental foram construídos quatro mapas de ligação: um mapa integrado composto por 98 grupos de ligação a partir da análise de 632 marcadores (com segregações 1:1 e 3:1); um mapa framework integrado, construído a partir de uma ordenação mais refinada dos marcadores dentro de cada um dos grupos de ligação, o qual foi composto por 94 grupos de ligação; e, com o objetivo de se estimar o tamanho do genoma das variedades envolvidas neste estudo, dois mapas de ligação, um para cada genitor (RB97327 e RB72454). O comprimento total do primeiro mapa, referente à variedade RB97327, foi de 828cM. O comprimento total do mapa integrado foi de 2848 cM. Os comprimentos totais dos mapas obtidos para cada um dos genitores, gerados a partir de dados da população de cruzamento biparental, foram de 1465Cm (RB97327) e de 1976 cM (RB72454). Utilizando a metodologia de Hulbert et al. (1988), os tamanhos estimados dos genomas das variedades RB97327 e RB72454 foram 2811 cM e 3471 cM, respectivamente. Assim, pode-se afirmar que os mapas obtidos neste caso apresentaram baixa cobertura (52% e 57%), perante o tamanho estimado dos genomas. Apesar do baixo polimorfismo, os marcadores DArT se mostraram eficientes na genotipagem de progênies de cana-de-açúcar, pois, centenas de marcas polimórficas foram geradas em apenas um ensaio, com dois métodos de redução de complexidade. Estes marcadores representam uma nova ferramenta para o desenvolvimento de estudos genéticos em cana-de-açúcar, principalmente se considerado o baixo custo (R$/marcador) envolvido na obtenção dos genótipos.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2017-04-18T13:21:11Z No. of bitstreams: 2 Dissertação - Ana Paula Simplício Mota - 2015.pdf: 2622408 bytes, checksum: 964fc3216d1a8c8e5e27bc1ef2a5d5be (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-04-18T13:21:34Z (GMT) No. of bitstreams: 2 Dissertação - Ana Paula Simplício Mota - 2015.pdf: 2622408 bytes, checksum: 964fc3216d1a8c8e5e27bc1ef2a5d5be (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-04-18T13:21:34Z (GMT). No. of bitstreams: 2 Dissertação - Ana Paula Simplício Mota - 2015.pdf: 2622408 bytes, checksum: 964fc3216d1a8c8e5e27bc1ef2a5d5be (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2015-10-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The aim of this study was to validate molecular markers specifically associated with alleles of the Co-4 gene that controls the reaction to anthracnose of common bean, in particular the Co- 42 allele, and foment the integration of these markers in breeding programs aimed at developing resistant cultivars. For this, we evaluated 261 individuals F2 and 197 F2:3 progenies coming from crosses between SEL 1308 (carrier of Co-42 allele) and BRS Cometa. The studies confirm that the inheritance of reaction to anthracnose in SEL1308, using race 73 of Colletotrichum lindemuthianum, it is conditioned by an allele with complete dominance. In all, 15 markers were analyzed, ten STS (Sequence-Tagged Sites) and two SSR (Simple Sequence Repeat), recently identified by the Embrapa research group, and three SCAR (Sequence Characterized Amplified Regions) previously reported in the literature. Of these, 13 were polymorphic between the parents and segregated in the expected proportions to generations analyzed (3:1 or 1:2:1). Among the markers linked in repulsion phase, six STS (P8283-V1, P8284 -V1, P8285-V2, P8286-V1, P8286-V2 and P8286-V3) co-segregated at a distance of 2,64 cM from the allele Co-42 and 0,0 cM apart. As regards the SCAR markers, it was found that all are linked in coupling phase of the Co-42 allele at distances ranging from 2,93 cM (SAS13) at 6,42 cM (SH18). Of codominant markers, the STS P8286-V6 was mapped closest to Co-42 allele at a distance of 2,58 cM. Thus, the STS tested are excellent tools markers for assisted selection of genotypes resistant to anthracnose, since that present the highest selection efficiency estimates (84 - 99%) and the detection of plants carriers of different alleles of the Co-4 gene. However, only the SCAR SH18 possible the specific breakdown of Co- 42 allele, despite having less selection efficiency (85%) compared to the other analyzed markers. Therefore, it is recommend the combined or sequential use of P8286-V6 and SH18 markers for Co-42 selection at the expense of other alleles of the Co-4 gene. As for the selection of resistant genotypes in populations in which only the Co-42 allele is present, it is suggested to use only the P8286-V6 marker, which stands out for being codominant and strongly associated with the resistance allele. From a practical standpoint, the molecular markers validated in this study have shown great potential for use in the development of common bean cultivars resistant to anthracnose, being affordable to laboratories with different levels of infrastructure and highly efficient in monitoring genotypes carriers of resistance alleles of the loco Co-4. / O objetivo desse estudo foi validar marcadores moleculares especificamente associados aos alelos do gene Co-4 que controla a reação à antracnose do feijoeiro-comum, em particular ao alelo Co-42, e fomentar a integração destes marcadores a programas de melhoramento visando ao desenvolvimento de cultivares resistentes. Para isso, foram avaliados 261 indivíduos F2 e 197 progênies F2:3, provenientes de cruzamentos entre SEL 1308 (portadora do alelo Co-42) e BRS Cometa. Os estudos confirmaram que a herança da reação à antracnose em SEL 1308, usando a raça 73 de Colletotrichum lindemuthianum, é condicionada por um alelo com dominância completa. Ao todo, foram analisados 15 marcadores, sendo dez Sequence-Tagged Sites (Sítios Marcados por Sequências) e duas Simple Sequence Repeat (Sequências simples repetidas), identificadas recentemente pelo grupo de pesquisa da Embrapa, e três Sequence Characterized Amplified Regions (Regiões Amplificadas Caracterizadas por Sequências) previamente relatados na literatura. Destes, 13 foram polimórficos entre os genitores e segregaram nas proporções esperadas para as gerações analisadas (3:1 ou 1:2:1). Dentre os marcadores ligados em fase de repulsão, seis STS (P8283-V1, P8284-V1, P8285-V2, P8286-V1, P8286-V2 e P8286-V3) co-segregaram a uma distância de 2,64 cM do alelo Co-42 e a 0,0 cM entre si. No que se refere aos marcadores SCAR, constatou-se que todos estão ligados em fase de acoplamento ao alelo Co-42, a distâncias que variaram de 2,93 cM (SAS13) a 6,42 cM (SH18). Dos marcadores codominantes, o STS P8286-V6 foi mapeado como mais próximo do alelo Co-42, a uma distância de 2,58 cM. Dessa forma, os marcadores STS testados constituem excelentes ferramentas para a seleção assistida de genótipos resistentes à antracnose, visto que apresentaram as maiores estimativas de eficiência de seleção (84 a 99%) e a detecção de plantas portadoras dos diferentes alelos do gene Co-4. Contudo, somente o SCAR SH18 possibilitou a discriminação específica do alelo Co-42, apesar de apresentar menor eficiência de seleção (85%) em comparação aos demais marcadores analisados. Diante disso, recomenda-se a utilização combinada ou sequencial dos marcadores P8286-V6 e SH18 para seleção do Co-42 em detrimento dos demais alelos do gene Co-4. Já para a seleção de genótipos resistentes em populações nas quais somente o alelo Co-42 está presente, sugerese a utilização apenas do marcador P8286-V6, que se destaca por ser codominante e fortemente associado ao alelo de resistência. Do ponto de vista prático, os marcadores moleculares validados neste estudo demonstraram grande potencial para utilização no desenvolvimento de cultivares feijoeiro-comum resistentes à antracnose, por serem acessíveis a laboratórios com diferentes níveis de infraestrutura e altamente eficientes no monitoramento de genótipos portadores de alelos de resistência para o loco Co-4.

As distrofias musculares tipo cinturas (DMC) incluem um grupo heterogêneo de doenças genéticas, caracterizadas por degeneração progressiva da musculatura esquelética pélvica e escapular, cuja herança pode ser autossômica dominante (DMC1) ou autossômica recessiva (DMC2). As formas dominantes são relativamente raras, compreendendo menos que 10% dos casos. Até o momento foram mapeados 8 locos para DMC1, (DMC1A-H), onde 3 genes já foram identificados (DMC1A-C) e 17 locos para DMC2 (DMC2A-Q), onde 16 genes já foram identificados. No presente estudo, identificamos uma família uruguaia (família 1) com 11 indivíduos afetados por DMC, distribuídos em 3 gerações, com um padrão de herança autossômico dominante. Os objetivos desse trabalho foram: mapear e refinar o loco gênico associado a uma manifestação familiar de DMC1, verificar se há co-localização da região mapeada com outras formas de DMC1 descritas na literatura e, apontar genes candidatos na região mapeada e triar mutações. Foi realizado estudo de ligação, no qual mapeou-se o loco para essa doença na região 4q13-q24 com Lod score de valor máximo 4.78 para o marcador D4S414. A região foi delimitada entre os marcadores D4S392 e D4S1572. A análise da região redefiniu o loco em 4q21.22-21.23, com uma redução de 33 Mb para 4Mb. Esse loco compreende a DMC1G (família 2), descrita anteriormente pelo nosso grupo. A triagem de mutação, realizada em amostras de afetados das duas famílias, nos permitiu encontrar uma alteração Thr141Iso no exon 5 do gene FAM175A apenas nos pacientes da família 2. Essa mesma alteração foi encontrada em 1 dos 500 controles testados, o que não nos permite excluir esse gene como um candidato para DMC1G já vez que essa frequência foi inferior a 1%. O fato dessa alteração não ter sido vista na família 1 também não nos permite excluí-lo, pois foi sequenciada apenas a região exônica e a metodologia utilizada também não nos permite verificar deleções nem duplicações. Estudos mais detalhados precisam ser realizados a fim de elucidar: (1) se a alteração desse gene é a causadora dessas DMCs ou, (2) se excluído esse gene, poderia ser o responsável. / Limb girdle muscular dystrophy (LGMD) include a heterogeneous group of genetic diseases characterized by progressive degeneration of skeletal muscles of the pelvic and scapular girdles, whose inheritance may be autosomal dominant (LGMD1) or autosomal recessive (LGMD2). The dominant forms are relatively rare, comprising less than 10% of cases. So far eight loci were mapped for LGMD1 (LGMD1A-H), where three genes have been identified (LGMD1A-C) and 17 loci for LGMD2 (LGMD2A-Q), with 16 identified genes. In this study, we analised a family from Uruguay (family 1) with 12 individuals affected by LGMD, with an autosomal dominant pattern distributed in three generations. The objectives of this study were: to map and refine the gene locus associated with a familial DMC1, check for co-location of the mapped region to other forms of DMC1 described in the literature and, to point candidate genes mapped in the region and to screen mutations. A linkage study was conducted, and we mapped the locus for this disease in the region 4q13-q24 with a maximum Lod score of 4.78 for marker D4S414. The region was defined between markers D4S392 and D4S1572. The analysis of the region has redefined the locus to 4q21.22-in 21:23, a reduction from 33 Mb to 4 Mb. This site includes LGMD1G (family 2), previously described by our group. Mutation screening, performed on samples of affected pacients from both families, allowed us to find a modification Thr141Iso in exon 5 on FAM175A gene only in patients of family 2. This same alteration was found in one of the 500 controls tested but does not allow us to exclude this gene as a candidate for LGMD1G since that frequency was less than 1%. The fact that this change was not seen in a family 1 does not allow us to exclude it either because only the exonic region was sequenced and the methodology used does not allow us to detect deletions or duplications. More detailed studies should be conducted to elucidate: (1) whether the alteration found in this gene is the cause of these DMCs, or (2) if not this gene, which could be the one responsible.

Esta pesquisa teve como objetivo investigar o processo de construção da parentalidade em casais homossexuais masculinos com filhos adotivos, com ênfase nas questões vinculares e geracionais. As transformações nas relações conjugais, parentais e familiares na contemporaneidade, apontam um questionamento da ordem simbólica, desestabilizando a ordem heteronormativa e desmascarando a sacralidade da família tradicional, a qual já não pode mais ser considerada a única base para a construção identitária. Diante do crescente aparecimento e visibilidade das novas configurações familiares, em especial da homoparentalidade, e da movimentação na relação pai/mãe e nas funções materna e paterna torna-se fundamental o estudo de outros funcionamentos familiares igualitários e criativos, em que a norma heterocêntrica não funciona como imperativo. Observa-se que nos encontramos em um momento de experimentação dessas novas famílias, o que traz consigo questionamentos e preocupações concernentes às especificidades no processo de vinculação entre pais homossexuais e seus filhos, por exemplo, o relacionado com o Complexo de Édipo. O referencial teórico utilizado nesta tese é o da psicanálise vincular aliada à teoria queer de gênero. O método utilizado é o clínico qualitativo com entrevistas semidirigidas e a aplicação da técnica projetiva do genograma. Com estes instrumentos, o objetivo pretendido foi compreender a construção da parentalidade lançando um olhar às transformações dos continentes psíquicos no contexto da adoção - considerada em sua complexidade. Para tanto, foram entrevistados cinco casais de homens com filho/s adotado/s conjuntamente. Os encontros ocorreram na casa dos colaboradores e a análise dos resultados foi feita em três categorias criadas a posteriori das entrevistas. Tendo como eixo central a questão vincular, as categorias elaboradas foram as seguintes: 1) Vínculo conjugal e a escolha pela parentalidade; 2) O vínculo parental e; 3) O vínculo familiar, o legado geracional e a família atual. A discussão dos achados da pesquisa compreendeu uma visão ampliada dos resultados, os quais foram tratados a partir de três eixos relacionados às categorias de análise: 1) Assunção homossexual e o não dito; 2) Adoção como uma forma de parentalizar e reparar e; 3) Família e norma, a nomeação dos membros como indicativo relacional. Os resultados encontrados remontam alguns diferenciais no exercício da parentalidade homossexual, a partir dos quais se destacam três que marcam a especificidade dessa experiência: 1) Os efeitos da falta de modelos parentais alternativos e a construção do vínculo parental; 2) O desejo de fazer família como forma de recuperar algo perdido e; 3) A presença da alteridade na família homoparental como potência para a subjetivação dos filhos. Para finalizar, as considerações finais retomam as reflexões sobre o conceito de família, seu significado e os modos como a dinâmica relacional e seus vínculos afetam a saúde psíquica de seus membros. Nesses termos, defendem-se a premissa da alteridade, em substituição à diferença sexual como garantia de subjetivação para as crianças provenientes desses novos arranjos / This research aimed to investigate the process of parenthood construction in homosexual couples with adoptive children, emphasizing on the linkage and generational issues. The transformation on couple, parental and familiar relations on contemporaneity, points to a questioning of the symbolic order, destabilizing the heteronormative order and unmasking the sacrality of the traditional family, which can no longer be considered the only basis for the identitary construction. Before the growing emergence and visibility of the new familiar configurations, specially homoparenthood, and the motion on relation father/mother and on maternal and paternal functions it becomes fundamental to study other familiar functions more even and creative, in which the heterocentric norm does not work as an imperative. It can be noticed that we are at a moment of experimenting for these new families, what brings questionings and worries concerning to the specificities on the process of linkage between homosexual parents and their children, for example related to the Oedipal Complex. The theoretical reference used in this thesis is the Linkage Psychoanalysis, associated to the queer theory of gender. The method employed is the clinical qualitative clinical with semi directed interviews and the application of a projective technic of genogram. The purpose was to comprehend the construction of the parenthood - observing the transformation of the psychic continents in the context of adoption considered in its complexity. This way, five couples of men with children adopted together were interviewed. The meeting occurred in the house of the participants and the analysis of the results was made in three categories created after the interviews. The categories are: 1) Conjugal bond and the choice for parenthood, 2) The parental bond and 3) The familiar bond, the generational legacy and the actual family. The discussion of the findings from the research understands an amplified vision of the results, treated in three themes related to the categories of analysis: 1) Homosexual assumption and the Non-spoken, 2) Adoption as a way of parenting and reparing and 3) Family and norm, Naming the members as a relational indicative. The results point to some differentials in the homosexual parenthood, from which we point out three of these for marking the specificity of these experience: 1) The effects of the lack of alternative parental models and the construction of the parental bond, 2) The desire of making family as a way of recovering something lost and 3) The presence of otherness in homoparental family as a might to the childrens subjectivation. The final considerations retake the reflections about the concept of family, its meaning and the ways how the relational dynamics and its bonds affect the psychic health of its members. In these terms, we defend the premise of otherness, in replacement to the sexual difference as a guarantee to the subjectivation for the children from these new arrangements

A seleção genômica (Genomic Selection - GS) permite identificar indivíduos superiores com base no seu método genômico e apresenta a possibilidade de incorporação do melhoramento quantitativo à genética molecular. O melhor preditor linear não viesado (Best Linear Unbiased Prediction - BLUP) é um método de predição dos efeitos aleatórios do modelo com base nos componentes de variância obtidos por meio do método máxima verossimilhança restrita (Restricted maximum likelihood - REML). A eficiência do REML\\BLUP pode ser incrementada por meio da incorporação de matrizes de parentesco genômico nos modelos de seleção genômica, uma vez que os efeitos genéticos genômicos aditivos dos indivíduos avaliados constituem os componentes aleatórios dos modelos mistos abordados. Dentre os algoritmos disponíveis para estimá-las, a partir de dados de polimorfismo de nucleotídeo único (Single-nucleotide polymorphism - SNP\'s) há as matrizes de Vanraden (2008) Astle e Balding (2009) e as de Yang et al. (2010) (matriz de parentesco unificado e matriz de parentesco unificado ajustado). Adicionalmente ao método de estimação da matriz de parentesco, a acurácia da GS depende da densidade de marcadores e da extensão e padrão de desequilíbrio de ligação (Linkage desequilibrium - LD) que existe no painel. Com isto, os objetivos foram: i) investigar o efeito da redução nas densidades de marcadores SNP\'s, por meio do LD, na estimativa do parentesco genético dos indivíduos e, consequentemente, na acurácia preditiva da GS; ii) estudar o efeito do uso de diferentes tipos de matrizes de parentesco genômico na acurácia da seleção genômica para linhagens e híbridos de milho tropical. Para isso, foram considerados dois painéis distintos de milho tropical: uma composta por 64 linhagens endogâmicas e a outra, por 452 híbridos. Estas foram avaliadas para o caráter produtividade de grãos, em oito e cinco ambientes, respectivamente. As linhagens e os híbridos foram genotipados com a plataforma Affymetrix® Axiom® Maize Genotyping Array, com cerca de 600 mil marcadores. Foram construídos diferentes cenários de GS quanto ao tipo de painel (linhagens e híbridos), densidade de marcadores (400k, 60k, 9586 e 1304 para linhagens e 50k, 4458 e 495, para híbridos) e tipos de matrizes de parentesco (citadas acima). Em cada um destes cenários foi estimada a herdabilidade, acurácia, capacidade preditiva e a coincidência de seleção. A partir dos resultados conclui-se que: tanto para híbridos como para linhagens, a densidade de marcas pode ser reduzida significativamente por meio do LD existente entre os SNP\'s, sem gerar prejuízos quanto à acurácia da GS, mas reduzindo os custos com genotipagem e a demanda computacional. Para predição genômica das linhagens, a matriz de Vanraden (2008) apresenta o melhor custo benefício, pois tem menor demanda computacional e proporciona resultados satisfatórios quanto à acurácia e coincidência de seleção. Para a predição genômica de híbridos, as matrizes de Yang et al. (2010) são superiores em relação às demais testadas, quanto à acurácia preditiva e coincidência de seleção. / The efficiency of the Best Linear Unbiased Prediction (BLUP), along with the Restricted maximum likelihood (REML) methods, can be increased by incorporating genomic kinship matrices to Genomic Selection models (GS). Among the available algorithms to estimate these matrices from single-nucleotide polymorphism (SNP) data there are Vanraden (2008), Astle e Balding (2009) and Yang et al. (2010) (unified relationship matrix and adjusted unified relationship matrix). In addition to the estimation method of the relationship matrix, the accuracy of GS depends on the density of markers and the extent and pattern of linkage disequilibrium (LD) that there is in the panel. Thus, the aims were: i) assess the effect of marker density reduction, based on LD, on the estimative of the genetic relationship of individuals and, consequently, on the predictive accuracy of GS; ii) study the effects of types of genomic relationship matrices on the accuracy of genomic selection for tropical maize lines and hybrids. In order to achieve there, two distinct panel of tropical maize were used: the first consisting of 64 inbred lines and latter of 452 hybrids. These panels were evaluated in field trials for grain yield in eight and five environments, respectively. The lines and hybrids were genotyped by the Affymetrix® Axiom® Maize Genotyping Array platform with 612 thousand markers. Distinct scenarios of GS were comprised considering panel type (lines and hybrids), marker density (400k, 60k, 9586 and 1304 for lines and, 50k, 4458 and 495 for hybrids) and, types of kinship matrices cited aboved. In each of these scenarios heritability, accuracy, predictive capacity and the selection coincidence were estimated. From the results it was concluded that: for both, hybrids and lines, marker density can be significantly reduced based on LD between SNP\'s without affecting the accuracy. Furthermore, this reduction also decreases genotyping costs and computational requirements. For genomic prediction of lines, Vanraden (2008) matrix shows the best cost-benefit, because it demands less computer resources and provides satisfactory results in terms of accuracy and selection coincidence. On the other hand, for genomic prediction of hybrids, the matrices of Yang et al. (2010) yielded higher predictive accuracies and selection coincidences.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-04-29T17:56:26Z No. of bitstreams: 1 neyrismarfelipedossantos.pdf: 630131 bytes, checksum: de3b3423fef0e53aa949e010e4cb4c2c (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2016-05-02T01:25:15Z (GMT) No. of bitstreams: 1 neyrismarfelipedossantos.pdf: 630131 bytes, checksum: de3b3423fef0e53aa949e010e4cb4c2c (MD5) / Made available in DSpace on 2016-05-02T01:25:15Z (GMT). No. of bitstreams: 1 neyrismarfelipedossantos.pdf: 630131 bytes, checksum: de3b3423fef0e53aa949e010e4cb4c2c (MD5) Previous issue date: 2014-09-30 / Na atual conjuntura social, em que muitos dos valores perpetuados há gerações parecem ter se perdido ao longo do tempo, a escola, mais do que nunca tem sentido o reflexo deste fenômeno, pois cada vez mais vem tomando para si a tarefa de educar moral e tecnicamente, o que acaba por sobrecarregar ainda mais esta instituição. Neste contexto, surge como iniciativa adotada pela rede estadual de ensino no Estado do Ceará, o Projeto Diretor de Turma (PDT) que visa o estreitamento de laços entre os agentes educacionais, quais sejam: O aluno, a escola e a família. Advindo de Portugal e adotado na rede pública estadual cearense em meados de 2008, o PPDT tem como centro a proposta de desmassificar o ensino, tornando-o mais personalizado e tentando, ao máximo, suprir as necessidades educacionais dos agentes envolvidos no processo de educar. É a partir desse cenário que defino como objetivo principal para o meu trabalho avaliar a implementação e a execução deste projeto na escola que foi alvo desta pesquisa, bem como, fazendo um comparativo entre o desenho do projeto e a realidade encontrada na referida escola. A investigação tem como aporte teórico os estudos de Leite(2010), Mendonça(2009), Nogueira(2006), Peregrino(2010), Zenhas(2004), dentre outros. Com a intenção de construir um panorama sobre o funcionamento do projeto na escola estudada, utilizo a pesquisa documental e a pesquisa de campo. Neste trabalho de pesquisa, que tem como centralidade a análise do referido projeto que busca tornar-se uma política pública em educação, serão elencados pontos fortes, pontos que precisam ser melhorados, bem como, um plano de ação educacional, com base nos dados coletados na escola pesquisada. / In the current social climate that many values perpetuated for generations seem to have been lost over time, and the school, more than ever has felt the effect of this phenomenon, since increasingly been taking up the task of educating and moral technically, what ultimately overload this institution. In this context, emerges as an initiative adopted by state schools in the state of Ceará, the Project Director of Class (PPGP) aimed at strengthening ties between educational agents, which are: the student, the school and the family. Coming from Portugal and adopted in Ceará state public schools and in mid 2008, the center has as PPDT the proposed singularize the education, making it more personalized and trying as much as possible meet the educational needs of those involved in the education process. It is from this scenario which I define the main objective as my work to evaluate the implementation and execution of this project in school that was the target of this research, as well as making a comparison between the project design and the reality found in this school. Research has as the theoretical studies of Leite (2010), Mendonçaa (2009), Nogueira (2006), Peregrino (2010), Zenhas (2004), among others. With the intention to build a picture of the operation of the project at the school, I use the desk research and field research. In this research work, which has centered on the analysis of that project that seeks to become a public policy education, will be show strengths, areas that need improvement, as well as an educational action plan, based on the data collected will be listed at school studied.

Influenza A viruses are important pathogens of humans, other mammals and birds. Swine are considered to be the ‘mixing vessel’ for influenza viruses because of their susceptibility to infection with not only swine influenza viruses but also human and avian influenza viruses. After infection of pigs with different influenza viruses, reassortment events between genomic RNA segments and point mutations can take place which can result in novel influenza virus strains capable of causing human pandemics. To combat infections, vaccination is available in many countries for humans, but not typically used in pigs. However, anti-influenza drugs have been used to treat livestock, and mutations conferring drug resistance occur in circulating strains. The mechanisms responsible for the emergence and spread of drug resistant mutations against amantadine and oseltamivir have been studied previously but often gave conflicting results. Therefore, this PhD thesis focused on resolving the mechanisms responsible for this rapid drug resistance spread. In chapter one I examine the extent of reassortment events in swine influenza A viruses by analysing within subtype reassortment and extrapolating the results for the between subtype reassortment. Reassortment is one of the mechanisms that can be responsible for mutations, conferring resistance to drugs, to spread between strains, and thus spread in the host population. The findings of this chapter show that the genomic segments most prone to reassortment code for a polymerase (PB1) and both glycoproteins, within all three subtypes studied. Since particular mutations in the matrix protein (MP) segment cause resistance to amantadine, my study focused on MP compared to other segments and revealed moderate level of reassortment. MP reassorts well with polymerases, both within and between subtype, while nonstructural (NS) is least likely to reassort. Chapter two of this thesis aimed at resolving the origin and spread of the most common drug resistance conferring mutation in swine influenza viruses which causes amantadine resistance. I show first that this mutation occurred in swine influenza viruses and was therefore not transmitted from the recently ancestral avian influenza strains, and second that the prevalence of resistance in swine influenza viruses is due to functional linkage of mutations at other sites and not by direct drug pressure. In chapter three I examine the mechanisms responsible for the rapid rise and spread of oseltamivir resistance in human influenza H1N1 viruses which arose in the absence of drug use. The primary mutation lies in the neuraminidase glycoprotein but because of the close functional interaction I focus on changes in haemagglutinin that occurred in association with resistance. The results showed several mutations in haemagglutinin were associated with resistance suggesting selection acting on haemagglutinin in order to balance the activity of both glycoproteins. Overall these results show the importance of functional linkage between segments as a mechanism for the occurrence of drug resistance conferring mutations, and reassortment as a means of spreading these mutations into newly emerging strains.

Dans cette thèse, nous étudions les opéras de Pierre Bartholomée composés d'après les romans d'Henry Bauchau à partir de la thématisation de la voix qu'ils proposent. Ce schème narratif, décliné tantôt sous la forme d'un chant épique, tantôt comme musique pure, est isolé pour devenir le sujet des livrets. C'est un sujet problématique car la voix révèle le ratage irréductible de la rencontre d'un texte et d'une musique. Or, depuis la fondation du genre, l'opéra a pensé leurs rapports en termes de fusion du sens et du son. Au contraire, l'étude comparative des opéras de Bartholomée, du livret à la scénographie en passant par la partition, met en évidence ce nouage en forme de déliaison. En effet, les différences repérées entre ces deux opus permettent de dégager les modes de représentation de cette rencontre toujours manquée. La musique et le texte ne s'additionnent pas pour former un objet homogène mais s'accolent le long de leur commun littoral, la voix, ce reste de la langue à laquelle on a retranché le signifié des mots. Sur le mode narratif, poétique et musical, le diptyque bauchalien de Bartholomée raconte le renoncement au leurre d'une conception de l'opéra comme lieu de la coïncidence entre un texte et une musique au profit de la reconnaissance de leur hétérogénéité. La description comparée des scénographies corrobore cette affirmation dans la mesure où l'estompe grandissante du réalisme neutralise progressivement l'illusion théâtrale. Le choix de faire des visages la pierre de touche des mises en scène successives offre ainsi un prolongement visuel à la voix. Visage et voix deviennent le paradigme d'une altérité valorisée dont Antigone est le héraut. Réclamant pour son frère et la femme qu'elle est le droit de cité, elle s'oppose à la réduction de l'autre au même / In this dissertation, Pierre Bartholomée's operas composed after Henry Bauchau's novels are studied through the theme of voice. This narrative pattern, sometimes as epic singing, sometimes as pure music, becomes the subject of the librettos. It is a problematic issue because the voice reveals the missed encounter between text and music. &et, since the foundation of the genre, opera has described their relations as a melting of meaning and sound. But a comparative study of Bartholomée's operas, from the libretto to the stage design including the score, underlines a de-linkage. Indeed, the differences between the two opuses allow to highlight how this disconnection is represented. The reunion of music and text don't mount up to a homogeneous object. Theyjoin and share a border, the voice, which remains after the removal of the meaning from the language. The diptych tells the forsaking of the irrelevant conception of the opera as a coïncidence between text and music in favour of its heterogeneous nature. Comparative descriptions of the stagings reinforce this idea. In fact, realism fades gradually out and neutralises the theatrical illusion. Faces are the core of the stagecrafts and provide a visible extension of the voice. Thus, face and voice are the epitom of a positive alterity which is embodied by Antigone. She begs for her brother and herself as a woman the right to be part of the city-state. In other words, she sets against the incorporation of the otherinto the same.

As the problem of urban-rural inequality in China becomes increasingly severe, urban-rural integration has become a hot topic among both researchers and policymakers. However, to achieve urban-rural integration faces the challenges from dualism in institutional arrangements, diversity in territorial contexts, and uncertainty in development environments. In response to these challenges, this research employs the idea of ‘economic linkages of small towns’ to develop a rural-centred, place-based, and process-oriented approach towards urban-rural integration. This research examines the functions, patterns, and dynamics of economic linkages of small towns under the wider economic-spatial restructuring process brought by rapid economic growth and urbanisation in China. More specifically, this research explores the implications of small towns’ economic linkages for integrated development of urban and rural areas. Based on the idea of ‘problem-solving’, this research develops the conceptual framework of ‘Learning-based Territorial Economic System (TES)’ which includes ‘knowledge system’, ‘organisational system’, and ‘territorial system’. This conceptual framework conceptualises ‘economic linkages’ as interactions between economic actors who participated in various ‘interactive situations’ in solving local development problems. This research carried out two case studies of successful small town and rural development in Kunshan, Jiangsu and Shunde, Guangdong. The empirical findings demonstrate that economic linkages are crucial in identifying local development problems, getting access to key economic resources, and coordinating economic activities in uncertain circumstances. Based on the empirical findings, this research develops two development models of Learning-based TES – the Kunshan Model and the Shunde Model – as coherent systems of economic linkages in problem-solving processes. Explicitly, the Kunshan Model features interactive situations of competitive positioning, elite coalition-building, and synchronised operation and the Shunde Model features interactive situations of reflective monitoring, skill matching, and communicative mediation. In application of these two development models, this research formulates a ‘3-step formula’ as key policy implication, including assessment, experiment, and institutionalisation. Such ‘3-step formula’ can contribute to build up local problem-solving capacities that lead to more substantial urban-rural integration.

The ability of Next-Generation Sequencing (NGS) to produce massive quantities of genomic data inexpensively has allowed to study the structure of viral populations from an infected host at an unprecedented resolution. As a result of a high rate of mutation and recombination events, an RNA virus exists as a heterogeneous "swarm". Virologists and computational epidemiologists are widely using NGS data to study viral populations. However, discerning rare variants is muddled by the presence of errors introduced by the sequencing technology. We develop and implement time- and cost-efficient strategy for NGS of multiple viral samples, and computational methods to analyze large quantities of NGS data and to handle sequencing errors. In particular, we present: (i) combinatorial pooling strategy for massive NGS of viral samples; (ii) kGEM and 2SNV — methods for viral population haplotyping; (iii) ShotMCF — a Multicommodity Flow (MCF) based method for frequency estimation of viral haplotypes; (iv) QUASIM — an agent-based simulator of viral evolution taking in account viral variants and immune response.