Master of Science / Division of Biology / Michael A. Herman / Caenorhabditis elegans are free-living bacterivorous nematodes that naturally consume bacteria as food source. As an excellent genetic model, C. elegans has proven to be a successful system to study innate immune responses to human pathogens, which resulted in identification of many evolutionarily conserved defense pathways. Most of these studies examined innate immune pathway mutants in a single genetic background in response to monoculture of human pathogens that worms might not necessarily encounter in the wild. While this has led to the successful genetic dissection of these defense pathways, in order to fully understand their biological functions, the relevant ecological and evolutionary context needs to be taken into account. The bacterial environment C. elegans naturally encounter is likely to be highly heterogeneous. While many bacteria are mainly considered as dietary resource for worms, some could be potential pathogens. Worms thus constantly face the challenge to defend against the pathogens mixed in the food. Stenotrophomonas maltophilia is one such bacterium. S. maltophilia is a ubiquitous bacterium that has been found associated with native nematodes. But it can also cause nosocomial infections in human, especially in immune-compromised individuals. Due to its natural resistance to multiple antibiotics, it has been emerging as an opportunistic human pathogen. Our lab isolated a S. maltophilia strain, JCMS, which was found being pathogenic to C. elegans. Both C. elegans strains, N2 (Bristol, England) and CB4856 (Hawaii), showed decreased survivorship when fed on S. maltophilia JCMS compared to E. coli OP50. However, more interestingly, the specific responses towards bacteria are different between strains. This indicates that survivorship of C. elegans is determined by not only genetic and environmental factors, but also genotype by environment (G×E) interactions (GEI). In order to identify the underlying genetic basis, we mapped quantitative trait loci (QTL) in a N2×CB4856 recombinant inbred panel for the survivorship in response to E. coli OP50 and S. maltophilia JCMS.

Children who are more fearful and inhibited during early childhood are at greater risk for social problems (e.g., loneliness, social isolation) and clinically significant internalizing disorders during adolescence and adulthood (e.g., Rubin, Chen, McDougall, Bowker, & McKinnon, 1995; Williams et al., 2009). While the impact of fearful temperament on adjustment indices are regularly the focus of study, less well understood are biological and social processes that may affect the development of fearful temperament. The present study considered the role of the 5-HTTLPR polymorphism and parenting on change in fearful and inhibited temperamental characteristics during early childhood. The s/s genotype was expected to be associated with elevated and sustained levels of fearful temperament. Moreover, supportive parenting was expected to be associated with less fearful temperament while more harsh parenting would be associated with more fearful temperamental characteristics, especially for children with the s/s 5-HTTLPR genotype. Study hypotheses were tested using 165 families (i.e., biological mothers and fathers, 3-5 year old children) who participated in the Family Transitions Project (FTP: R. D. Conger & K. J. Conger, 2002). Children were genotyped using cheek swabs. Parents reported on children’s temperamental characteristics at ages 3, 4, and 5. Independent observations of mothers and fathers completing a puzzle with their 3 and 4 year old children were used to measure parenting. Results were partially supportive of predictions. Parenting interacted with the 5-HTTLPR genotype to predict trajectories of shyness and soothability dimensions of fearful temperament, but the pattern of findings varied for mothers and fathers. Results are discussed in terms of differential susceptibility and the conceptualization of risk and resilience.

Orientador: Lucia Galvão de Albuquerque / Banca: Mário Luiz Santana Júnior / Banca: Fernando Sebastian Baldi Rey / Banca: Ana Fabrícia Braga Magalhães / Banca: Roberto Carvalheiro / Abstract: Genotype-environment (GxE) interactions could be an important source of variation in reproductive traits with a striking effect on the onset of animal puberty. Thus, the objectives of the present study were: i) to assess the GxE interaction in Nellore sexual precocity indicator traits under different environmental conditions (EC) and ii) to identify, genomic regions and biological pathways associated to Nellore sexual precocity indicator traits and to investigate whether their effects changes according to EC levels. Phenotypic records for age at first calving (AFC), heifer early pregnancy (HP), heifer rebreeding (HR) and scrotal circumference (SC) were collected on 128,994; 85,339; 90,831 and 151,053 animals, respectively. From those, 1800 heifers, 3050 young bulls, and 800 sires were genotyped with BovineHD BeadChip. A reaction norm model was used to estimate the animal's response to environmental conditions changes. To assess the predictive ability the younger scheme and environment-specific scheme were used. For genome-wide scan, the SNP effects for reproductive traits were estimated in three EC levels: Low (EC = -3.0), Medium (EC = 0.0) and High (EC = 3.0) using a linear transformation of the genomic breeding values. The pleiotropic regions associated to reproductive traits (AFC, SC, HP and HR) in three EC levels, were identified using the statistical combination of the single-trait GWAS results and considered significant when -log10(p-valor)>6.0. The inclusion of genomic... (Complete abstract click electronic access below) / Resumo: A interação genótipo-ambiente (GxE) pode ser uma importante fonte de variação em características reprodutivas com um efeito notável no início da puberdade animal. Desta forma, os objetivos do presente estudo foram: i) Avaliar a interação GxE em características indicadores de precocidade sexual em animais da raça Nelore em diferentes condições ambientais (EC) e ii) identificar regiões genômicas e vias biológicas associadas a características indicadores de precocidade sexual e verificar se seus efeitos mudam de acordo com os níveis de EC. Informações fenotípicas para idade ao primeiro parto (AFC), ocorrência de prenhez precoce (HP), reconcepção de novilhas (HR) e perímetro escrotal (SC), foram coletados em 128.994, 85.339, 90.831 e 151.053 animais, respectivamente. Destes, 1800 novilhas, 3050 touros jovens e 800 touros foram genotipados com BovineHD BeadChip. Um modelo de norma de reação foi usado para estimar a resposta do animal às mudanças nas condições ambientais. Para avaliar a capacidade preditiva, foram utilizados os esquemas de validação em animais jovens e em ambiente específico. Para varredura genômica ampla os efeitos dos marcadores SNP para as características reprodutivas foram estimados em três níveis de EC Baixo (EC = -3.0), Médio (EC = 0.0) e Alto (EC = 3.0) usando uma transformação linear dos valores genômicos genéticos. As regiões pleiotrópicas associadas com características reprodutivas (AFC, SC, HP e HR) em três EC foram identificadas utilizando a combinação ... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

Orientador: Sandra Helena Unêda Trevisoli / Banca: Ivana Marino Bárbaro Torneli / Banca: Viviane Formice Vianna / Resumo: A soja constitui-se na principal oleaginosa cultivada no mundo. Neste contexto, o Brasil se destaca como o segundo maior produtor mundial do grão. Dentre os muitos desafios encontrados pelo melhoramento genético, um dos principais está relacionado com a variação ambiental, que muitas vezes dificulta a seleção e recomendação de genótipos superiores. Sendo assim, faz-se necessário que os ensaios experimentais sejam conduzidos em vários ambientes, por vários anos para que possa ser analisado o comportamento quanto a adaptabilidade e estabilidade, visando futuras recomendações. Neste contexto, o objetivo do presente estudo consistiu em avaliar a desempenho agronômico, a adaptabilidade e estabilidade de genótipos de soja precoces. Os experimentos foram instalados em dois locais, a saber: localidade de Jaboticabal nos anos agrícolas 2012/2013, 2013/2014, 2015/2016 e 2016/2017 e localidade Piracicaba nos anos agrícolas 2014/2015 e 2015/2016. O delineamento utilizado foi de blocos ao acaso com três repetições. Foram avaliados os caracteres agronômicos número de dias para a maturidade e produtividade de grãos. Para estimar a adaptabilidade e estabilidade dos genótipos avaliados, foi utilizada a metodologia de Eberhart e Russell (1966). Desta maneira, foi possível detectar os genótipos mais responsivos e adaptados às regiões de cultivo. Para o caráter produtividade de grãos, merecem destaque os genótipos 4, 6,11, 26, 27, 29 e 34, sendo linhagens pertencentes ao programa de melhoramento... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Soy is the main oilseed crop in the world. In this context, Brazil stands out as the world's second largest producer of grain. Among the many challenges encountered by genetic improvement, one of the main challenges is related to environmental variation, which often hinders the selection and recommendation of higher genotypes. Thus, it is necessary that the experimental tests be conducted in several environments, for several years so that behavior can be analyzed for adaptability and stability, aiming at future recommendations. In this context, the objective of the present study was to evaluate the agronomic performance, adaptability and stability of early soybean genotypes. The experiments were installed in two locations, namely: Jaboticabal locality in the agricultural years 2012/2013, 2013/2014, 2015/2016 and 2016/2017 and locality Piracicaba in the agricultural years 2014/2015 and 2015/2016. The experimental design was a randomized block design with three replications. The agronomic characters were evaluated for the number of days for grain maturity and yield. To estimate the adaptability and stability of the evaluated genotypes, the methodology of Eberhart and Russell (1966) was used. In this way, it was possible to detect the genotypes more responsive and adapted to the growing regions. For grain yield, genotypes 4, 6, 11, 26, 27, 29 and 34 deserve special mention, being strains belonging to the soybean breeding program of UNESP Jaboticabal, all with averages above the ... (Complete abstract click electronic access below) / Mestre

Em estudos de divergência genética por métodos multivariados, a distância euclidiana é a medida de distância mais amplamente utilizada e essa distância é a mais recomendada quando as unidades de cálculos são escores de componentes principais, como é o caso da análise AMMI (additive main effects and multiplicative interaction analysis). Tal análise permite a obtenção de estimativas mais precisas das respostas genotípicas e possibilita a análise da divergência genética por métodos aglomerativos. A análise dos modelos AMMI combina, num único modelo, componentes aditivos para os efeitos principais (genótipos e ambientes) e componentes multiplicativos para os efeitos da interação genótipos × ambientes. Os melhoristas de plantas compreendem que a interação genótipos × ambientes é de suma importância para a obtenção de variedades superiores e as estimativas de dissimilaridade atendem aos objetivos do melhorista, por quantificarem e informarem sobre o grau de semelhança ou de diferença entre pares de indivíduos. Entretanto, quando o número de indivíduos é grande, torna-se inviável o reconhecimento de grupos homogêneos pelo exame visual das estimativas de distância. Portanto, é importante proceder à análise de agrupamentos, obter dendrogramas por meio de métodos hierárquicos e posteriormente, analisar os grupos formados. A fim de determinar e classificar os grupos formados na clusterização hierárquica foram utilizados comandos específicos do programa computacional R que desenha no dendrograma os retângulos de cada grupo e os numera. Desta forma, o objetivo deste trabalho foi analisar a divergência genética via modelo AMMI, utilizando-se de técnicas multivariadas e reamostragem \"bootstrap\". / In studies of genetic diversity using multivariate approaches, the Euclidean distance is the most common measure used. This method is recommended when data are scores of principal components, such as in AMMI analysis (additive main effects and multiplicative interaction analysis). The AMMI method allows obtaining more precise estimates for genotypic results and also permits the use of genetic diversity analysis by using agglomerative approaches. Furthermore, this method combines additive components for the main effects (genotypes and environments) and multiplicative components for genotypes x environment interaction effects in a unique model. Plant breeders understand the importance of genotype and environment interaction to obtain superior varieties and the dissimilarity estimation meets breeders\" objectives since it quantifies and determines the similarity or the divergence between pairs of individuals. However, when the number of individuals is large it is unfeasible to recognize the group homogeneity by using a visual analysis of the distances estimation. Therefore, is important to use cluster analysis to obtain dendograms based on hierarchical methods and then analyze the groups obtained. In order to determine and classify the obtained groups from hierarchical cluster analysis specifics commands in the R software were used which shows in the dendrogram rectangles and numbers for each group. In this way, the objective of this work was to analyze the genetic divergence through AMMI model, by using multivariate approaches and \"bootstrap\" resampling.

A raça Holandesa apresenta alto rendimento na produção de leite, por isto, diversos países têm optado pela importação de sêmen para substituir as raças leiteiras locais. Esta estratégia seria eficaz se o sêmen importado fosse utilizado nas mesmas circunstâncias em que foram selecionados. Caso exista interação genótipo ambiente significativa, é esperada uma nova classificação dos touros, porém se o efeito da interação genótipo ambiente não é levada em consideração, os valores genéticos preditos (EBVs) podem ser tendenciosos, reduzindo a resposta de seleção. Diante disso, os objetivos deste trabalho foram comparar modelos de diferentes ordens de ajuste por meio de funções polinomiais de Legendre, utilizando modelos de regressão aleatória e estimar os coeficientes de herdabilidade para os teores de gordura, proteína, ácido graxo saturado, ácido graxo insaturado, e produção de leite. Além de estimar o valor genético dos animais, sob a interferência do estresse térmico. Foram utilizadas informações fenotípicas coletadas mensalmente ao longo da lactação e modelos com polinômios ortogonais de Legendre de primeira a sexta ordem, para verificar a interferência de estresse térmico, foram utilizadas informações de temperatura e umidade do dia de coleta. Os modelos que melhor se ajustaram foram os de primeira e segunda ordem. As estimativas de herdabilidade variaram de 0,02 a 0,52 para teor de gordura; de 0,03 a 0,63 para teor de proteína; de 0,05 a 0,63 para ácido graxo saturado; de 0,019 a 0,364 para ácido graxo insaturado e de 0,133 a 0,390 para produção de leite nos diferentes modelos estudados. As estimativas de valores genéticos variaram de -0,5 a 0,5 em ambiente sem estresse térmico e de -0,2 a 0,2 em ambiente com estresse térmico para o teor de gordura; de -0,4 a 0,4 para ambiente sem estresse térmico e de -0,2 a 0,2 em ambiente com estresse térmico para o teor de proteína; de -0,3 a 0,3 em ambiente sem estresse térmico e de -0,2 a 0,2 em ambiente com estresse térmico para ácido graxo saturado; de -0,1 a 0,1 em ambiente sem estresse térmico e de -0,1 a 0,1 em ambiente com estresse térmico para ácido graxo insaturado e de - 6 a 6 em ambiente sem estresse térmico e de -2 e 2 em ambiente com estresse térmico para produção de leite. De acordo com os resultados, as herdabilidades indicam que o teor de gordura, proteína, ácido graxo saturado produção de leite podem ser utilizados como critério de seleção. Com o uso de informações de temperatura e umidade do ar, foi possível verificar a presença de interação genótipo ambiente para teor de gordura, proteína, ácido graxo saturado e produção de leite aos 205 dias em lactação. / Due to the high milk production of Holstein cattle, many countries have chosen to import semen to replace local dairy breeds. This strategy would be effective if these semen was used in the same circumstances in which they were selected. However, if there is significant genotype environment interaction, it is expected a new bulls ranking, but if the effect of genotype environment interaction is not considered, the estimated breeding values (EBVs) may be tendentious, reducing the selection response. The objectives of this study were estimate breeding value under heat stress and heritability coefficients, and also to compare models of different adjustment orders through Legendre polynomials, using random regression models for fat, protein, saturated fatty acid, unsaturated fatty acid and milk production. There were used phenotypic information collected monthly through the lactation period and Legendre orthogonal polynomials models from the first to sixth order. To verify the interference of heat stress, there was used temperature and humidity information on the day of the evaluation was performed. The first and second order models were the ones that better fitted. Heritability estimates were from 0.02 to 0.52 for fat; 0.03 to 0.63 for protein; 0.05 to 0.63 for saturated fatty acid; 0.019 to 0.364 for unsaturated fatty acid and 0.133 to 0.390 for milk production on the different models tested. Estimates of the genetic value were from -0.5 to 0.5 on environment without heat stress and -0.2 to 0.2 on environment with heat stress for fat; -0.4 to 0.4 on environment without heat stress and -0.2 to 0.2 on environment with heat stress for protein; -0.3 to 0.3 on environment without heat stress and -0.2 to 0.2 on environment with heat stress for saturated fatty acid; -0.1 to 0.1 on environment without heat stress and of -0.8 to 0.8 on environment with heat stress for unsaturated fatty acid; -6 to 6 on environment without heat stress and -2 to 2 on environment with heat stress for milk production. The heritability indicates that the fat, protein, saturated fatty acid and milk production can be used as selection criteria. With the use of temperature and humidity information, it was possible to verify the presence of genotype environment interaction for fat, protein, saturated fatty acid and milk production at 205 days in milk.

O presente estudo teve por objetivo estudar os efeitos da interação genótipos x ambientes sobre as características peso à desmama, peso ao sobreano e ganho de peso da desmama ao sobreano em bovinos de corte da raça Nelore. Foram analisados 45.697 registros de peso à desmama ajustados para 205 dias (PD), 34.773 registros de peso ao sobreano ajustados para 550 dias (PS) e 34.753 registros de ganho de peso da desmama ao sobreano (GP), originários de três fazendas localizadas nas regiões sudeste e centro-oeste do Brasil. Os componentes de variância foram estimados utilizando-se o programa MTDFREML. Os dados foram submetidos a análises de duas formas distintas: primeiramente processaram-se análises de características únicas para os dados de cada fazenda e para conjuntos de dados formados por pares de fazendas. Em seguida, processaram-se análises de características múltiplas, em que a mesma característica foi considerada como variáveis distintas em cada par de fazendas. A partir da obtenção dos valores genéticos dos animais, foram calculadas as diferenças esperadas na progênie (DEPs) dos mesmos, bem como as correlações de Pearson entre os valores das DEPs dos touros para as três características estudadas. As estimativas dos coeficientes de herdabilidade variaram de 0,17 a 0,33 para a característica PD, 0,31 a 0,48 para a característica PS e 0,11 a 0,32 para a característica GP. Os coeficientes de correlação genética encontrados variaram de 0,82 a 1,00, enquanto as correlações de Pearson entre as DEPs dos touros variaram de 0,89 a 0,99. Os resultados levam a sugerir pequeno ou nenhum efeito da interação genótipo x ambiente nos rebanhos incluídos neste estudo. / The objective of the present study was to evaluate the genotype x environment interaction effect on weaning weight, post-weaning weight and weight gain post-weaning in Nellore beef cattle herds. There were analyzed 45,697 data of weaning weight adjusted to 205 days (PD), 34,773 data of post-weaning weight adjusted to 550 days (PS) and 34,753 data of weight gain post-weaning (GP), which were collected from three farms localized in southwest and middle-east of Brazil. The variance components were estimated by MTDFREML. Those data were analyzed applying two different methods: the first proceeding was of considering single traits to the data of each farm and also to the data-set originated by pair of farms. The second method was performing the analysis of multiple traits once the same trait was considered as a distinct variable in each pair of farms. Since genetic values were obtained there were calculated the expected breeding values (EPD) of the sires as the Pearson correlations between the EPD values and the traits analyzed. The estimative of heritability coefficients ranged from 0.17 to 0.33, 0.31 to 0.48 and 11 to 0.32 to PD, PS and GP respectively. The genetic correlations varied from 0.82 to 1.00, while the Pearson correlation between the EPDs ranged from 0.96 to 0.99. The results suggest a modest or inexistent genotype x environment interaction effect in the herds evaluated.

Thesis (M.Sc. Agriculture (Crop Science)) -- University of Limpopo, 2011 / The nature and magnitude of the genotype by environment interactions is important to identify superior and stable genotypes under the target environments. This will assist to maximize specific adaptation and to speed up the transfer of new cultivars to growers. The objective of this study was to determine the stability of selected soybean genotypes with regards to the agronomic traits, high yield and nodule formation. Field experiments were conducted under dryland conditions during the 2007/2008 and 2008/2009 growing seasons at the University of Limpopo’s experimental farm (Syferkuil) and at a farmer’s field at Gabaza community, Mopani District near Tzaneen. Ten selected soybean cultivars were evaluated under a randomised complete block design with three replications. Stability was assessed via joint regression and superiority analyses. Significant differences were found for genotypes, environments and genotype by environment interactions. Stability analysis after Eberhart and Russell’s model suggested that the genotypes showed marked differences to environmental changes. The cultivar superiority measure for seed yield indicated that variety Clark was the most stable genotype with an average yield of 5235 kg/ha, followed by L81-4858 and Barc-2 that provided average yield of 4839 kg/ha and 4582 kg/ha, respectively. In terms of number of nodules Magoye was observed to be stable with average of five nodules per plant. Cultivar Barc-2 was found stable for number of active nodules with an average of 3.17 active nodules per plant. Most of the genotypes performed better at Syferkuil than at Gabaza. In general Barc-2 was found stable for yield and other agronomic traits considered in this study. This variety could be suitable for large scale production in these or other similar environments in Limpopo Province.

Karst topography is the result of a specific combination of geological conditions, precipitation, biota, and temperature, and is characterized by the gradual solution of the underlying bedrock and the development of underground drainage routes for surficial runoff. Many of these karst landscapes are found in urbanized areas, where the potential for anthropogenic impact is quite high. In many instances, municipalities on karst terrains choose to mitigate these impacts by implementing ordinances that place restrictions on permissible land uses near karst landforms. This dissertation asks the question: are the impacts of karst-related land use regulation on human / social systems significant enough to merit consideration during the regulation writing and implementation process? In the process of answering this question, it is hoped that a broader understanding will be developed of how land use regulations are used to control and regulate human activity on karst lands, particularly (but not exclusively) in the United States; and that the conclusions drawn from that overview might serve as the beginnings of a generally applicable framework for the development of karst regulation.

acase@tulane.edu