This research is focused on identifying a single-step procedure that, upon adapting to the data through estimating the unknown parameters, would asymptotically control the False Discovery Rate when testing a large number of hypotheses simultaneously, and exploring some of the characteristics of this procedure. / Statistics

Orientador: Lucia Galvão de Albuquerque / Resumo: A habilidade de permanência no rebanho (HPR) é medida tardiamente na vida do animal. Com isso, quando esta característica é usada como critério de seleção, o intervalo de geração, definido como a média de idade dos pais ao nascimento da progênie, tende a aumentar, provocando a diminuição do ganho genético. A mensuração das fêmeas em uma idade mais precoce seria uma forma de contornar este problema. Neste sentido, um melhor entendimento das regiões genômicas envolvidas na expressão desta característica em diferentes idades/partos é necessário. O objetivo com o presente estudo foi, então, identificar regiões genômicas associadas à HPR medida em diferentes partos de fêmeas da raça Nelore. Considerando apenas fêmeas com idade ao primeiro parto de até 40 meses, os fenótipos para HPR foram gerados observando se cada fêmea teve oportunidade de permanecer no rebanho do segundo ao oitavo parto, de maneira que cada vaca poderia ter até sete observações para HPR. Ao final, o banco de dados possuía 195.452, 161.261, 130.236, 103.043, 79.844, 62.663 e 47.045 fêmeas com fenótipos para o segundo, terceiro, quarto, quinto, sexto, sétimo e oitavo parto, respectivamente. Do total de animais no banco de dados, 3.849 (2.720 fêmeas e 1.129 touros) apresentavam informações genotípicas de 472.640 marcadores do tipo SNPs (Illumina BovineHD BeadChip). Ao todo, foram realizadas sete análises uni-características, considerando modelos thresholds com função de ligação probit. A metodologia do single-step... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Stayability (STAY) is a trait measured late in the animal's life. Thus, when this trait is used as selection criteria, the generation interval, defined as the parents average age at the progeny birth, tends to increase, causing a decrease in the genetic gain. Measuring females at an earlier age could be a way to circumvent this problem. In this sense, a better understanding of genomic regions involved in the expression of this trait at different ages/calving is necessary. The objective of the present study was to identify genomic regions associated with STAY measured in different calving of Nelore females. Considering only females that had their first calving up to 40 months of age, the phenotypes for STAY were generated by observing whether each female had the opportunity to remain in the herd from the second to the eighth calving, in such a way that each cow could have up to seven records. The final dataset had 195,452, 161,261, 130,236, 103,043, 79,844, 62,663 and 47,045 females with phenotypes for the second, third, fourth, fifth, sixth, seventh and eighth calving, respectively. In total, 3,849 (2,720 females and 1,129 bulls) animals from the whole dataset used in the analyses had genotypic information of 472,640 SNPs (Illumina BovineHD BeadChip) markers. In total, seven single-trait analyzes were performed considering threshold animal models with probit link function. The single-step GBLUP methodology was used to estimate variance components for STAY at each calving as w... (Complete abstract click electronic access below) / Mestre

New strategies for integrating sample pretreatment with chemical analyses under a single format is required for rapid, sensitive and enantioselective analyses of low abundance metabolites in complex biological samples. Capillary electrophoresis (CE) offers a unique environment for controlling analyte/reagent band dispersion and electromigration properties using a discontinuous electrolyte system allowing for highly efficient separations to be achieved. A fundamental study of the thermodynamic and electrokinetic parameters influencing enantioselectivity in chiral CE separation is first examined. A new strategy for single-step analysis of low abundance metabolites via online sample preconcentration with chemical derivatization by CE (SPCD-CE) is then detailed within. In-capillary sample preconcentration serves to enhance concentration sensitivity via electrokinetic focusing of long sample injection volumes for lower detection limits, whereas chemical derivatization by zone passing of single or multiple reagents is used to expand detectability and selectivity, notably for enantiomeric resolution of metabolites lacking intrinsic chromophores. Together, on-line SPCD-CE can provide over a 100-fold improvement in concentration sensitivity, shorter total analysis times, reduced sample handling and improved reliability for a variety of biologically relevant amino acid and amino sugar metabolites, which is also amenable to automated high-throughput screening. The basic method development and optimization parameters relevant to SPCD-CE, including applications to bacterial metabolite flux and biomarker analyses are discussed. Insight into the mechanism of analyte focusing and labelling during electromigration by SPCD-CE is also presented, as well as future directions for continued research using this unique integrated analytical platform. / Thesis / Doctor of Philosophy (PhD)

Orientador: Ana Fabrícia Braga Magalhães / Resumo: ABSTRACT – Preweaning calf mortality is one of main causes of economic losses in beef cattle, since most of economic incomes are represented by the number of weaned calves available for sale. It is also detrimental for genetic progress due to the reduction of young candidates for selection. The inclusion of molecular markers in genetic analysis allows a better understanding of genetic mechanisms underlying calf mortality. The objectives of this study were: i) to estimate direct and maternal heritability of preweaning calf mortality in Nellore cattle and ii) to seek for genomic regions and candidate genes affecting direct and maternal effects of preweaning calf mortality in Nellore cattle. Variance components were estimated via Bayesian Inference using a threshold animal model, that included the systematic effects of contemporary group, birth weight as linear covariate, and age of dam at calving as linear and quadratic covariates. The direct and maternal genetics, and the residual were fitted as random effects. The final dataset used contained phenotypic records on 67,196 animals, offspring of 1,469 sires and 30,970 dams. The SNPs effects were estimated based on the weighted single-step GBLUP approach, using information of 8,443 genotyped animals with 410,936 SNPs. Direct and maternal heritability estimates were of 0.2143±0.0348 and 0.0137±0.0066, respectively. The top 10 genomic regions accounted for 13.61 and 14.23% of direct and maternal additive genetic variance and harbor... (Resumo completo, clicar acesso eletrônico abaixo) / Mestre

Genomische Selektion ist ein Routine-Verfahren bei verschiedenen Nutztierarten, aber noch nicht bei der Honigbiene wegen der Besonderheiten dieser Spezies. Für die Zuchtwertschätzung bei der Honigbiene ist eine spezielle genetische Verwandtschaftsmatrix erforderlich, da die Paarungsbiologie dieser Spezies ungesicherte Vaterschaft, diploide Königinnen und haploide Drohnen umfasst. Die Arbeit präsentiert einen neu-entwickelten Algorithmus zur effizienten Berechnung der Inversen der genetischen Verwandtschaftsmatrix und der Inzuchtkoeffizienten auf großen Datensätzen. Die Methode wurde zur Voraussage von genomischen und Stammbaum-basierten Zuchtwerten in einer Simulationsstudie genutzt. Die Genauigkeit und die Verzerrung der geschätzten Zuchtwerte wurden ausgewertet unter Berücksichtigung verschiedener Größen der Referenzpopulation. Außerdem wurde der Zuchtfortschritt im ersten Durchlauf von Zuchtprogrammen ausgewertet, die Zuchtschemata mit genomischer oder Stammbaum-basierter Selektion nutzten. Ein erheblich größerer Zuchtfortschritt als bei Stammbaum-basierter Selektion wurde mit genomischer Vorselektion erzielt, für die junge Königinnen genotypisiert wurden, und nur die Kandidaten mit den höchsten genomischen Zuchtwerten zur Anpaarung oder Leistungsprüfung zugelassen wurden. Für einen realen Datensatz von ungefähr 3000 genotypisierten Königinnen wurden Stammbaum-basierte und genomische Zuchtwerte für sechs wirtschaftlich bedeutende Merkmale vorhergesagt. Drei Merkmale zeigten eine signifikant höhere Vorhersagegenauigkeit bei genomischer Zuchtwertschätzung gegenüber Stammbaum-basierten Verfahren und die Unterschiede zwischen allen sechs Merkmalen konnten im Wesentlichen aus den genetischen Parametern der Merkmale und der begrenzten Größe der Referenzpopulation erklärt werden. Damit zeigt die Arbeit, dass die genomische Selektion bei der Honigbiene genutzt werden kann, den Zuchtfortschritt zu erhöhen. / Genomic selection is a routine practice for several important livestock species but not yet in honey bees, due to the peculiarities of this species. For honey bees, a specialized genetic relationship matrix is required for the prediction of breeding values, since their mating biology involves uncertain paternity, diploid queens, and haploid drones. The thesis presents a novel algorithm for the efficient computation of the inverse of the numerator relationship matrix and the coefficients of inbreeding on large data sets. The method was used to estimate genomic and pedigree-based breeding values in a simulation study. The accuracy and bias of the estimated breeding values were evaluated and various sizes of the reference population were considered. Subsequently, the genetic gain in the initial cycle of breeding programs was evaluated for several breeding schemes employing genomic or pedigree-based selection. A considerably higher genetic gain than with pedigree-based selection was achieved with genomic preselection, for which queens were genotyped early in life, and only the candidates of high genomic breeding value were admitted for mating or phenotyping. On a real data set of about 3000 genotyped queens, pedigree-based and genomic breeding values were predicted for six economically relevant traits. Three traits showed significantly higher prediction accuracy with genomic compared to pedigree-based methods, and the differences between all the six traits could be explained mainly from their genetic parameters and the limited size of the reference population. The results show that genomic selection can be applied in honey bees, and the thesis provides appropriate breeding schemes and mathematical methods for its implementation.

The aim and objective of this study was to determine the bond strength of a twostep and a single-step dentin bonding agent and to determine the effect of repeated thermal-cycling from 50C and 550C on the bond strength values of these dentin bonding agents.

The aim and objective of this study was to determine the bond strength of a twostep and a single-step dentin bonding agent and to determine the effect of repeated thermal-cycling from 50C and 550C on the bond strength values of these dentin bonding agents.

Knorpeldefekte des Kniegelenks zeichnen sich durch eine sehr begrenzte spontane Heilungstendenz aus und führen im Verlauf häufig zur Arthrose. Trotz intensiver Forschungsbemühungen konnte bisher keine neue Therapieoption eine zufrieden-stellende Alternative zu den bisherigen Therapien hervorbringen. Eine ACI in Kombination mit einem künstlich hergestellten Knorpel-Knochen-Ersatzmaterial scheint jedoch großes Potential für die Therapie von Knorpel-Knochen-Schäden zu besitzen. Im vorliegenden Langzeittierversuch mit Kaninchen wurde eine einzeitige ACI mit einem biphasischen Ersatzmaterial (TruFit®) und platelet-rich-plasma (PRP) kombiniert. Zu diesem Zweck wurde in der medialen Femurkondyle ein critical-size-Defekt mit einem Durchmesser von 4,5 mm gesetzt. In der ersten Versuchsgruppe blieb der Defekt unbehandelt (Leer). Bei der zweiten Gruppe wurde die Defekthöhle mit einem TruFit®-Zylinder aufgefüllt (TFP). Gruppe drei erhielt zusätzlich PRP (TFP+PRP) und Gruppe vier wurde darüber hinaus mit einer einzeitigen ACI kombiniert (TFP+PRP+C), bei der Chondrozyten mit Hilfe eines speziellen Kollagenase-Schnellverdaus isoliert werden konnten. Die Auswertung der Knorpel-Knochen-Regeneration erfolgte nach 12 Monaten durch eine Mikroradiographie, eine intravitale Fluoreszenzmarkierung des Knochens und durch Toluidinblau-O- und Safranin-O-Färbungen. Verwendet wurden die Scores nach Wakitani und O’Driscoll. Dabei konnte gezeigt werden, dass eine TruFit®-Therapie die Knochenregeneration positiv beeinflussen kann. Die Zugabe von PRP bewirkte die Bildung von zahlreichen dünnen Trabekeln mit einer erhöhten Anzahl trabekulärer Verbindungen, allerdings auch eine schlechtere Rekonvaleszenz der subchondralen Knochenschicht. Bezüglich der Knorpelheilung schnitt die Gruppe TFP+PRP+C am besten ab, wobei die Unterschiede nicht signifikant waren. Insgesamt zeigten alle Versuchsgruppen eine unzureichende osteochondrale Regeneration, so dass für die Therapie am Menschen zunächst weitere Studien nötig sind, die sowohl ossär als auch chondral eine verbesserte Heilungspotenz demonstrieren können. Bisher fehlen groß angelegte Studien um Therapieempfehlungen bezüglich des Ersatzmaterials, der genauen Durchführung der einzeitigen ACI und Zusätzen wie Wachstumsfaktoren zu machen.

Objetivou-se com este trabalho: (1) avaliar parâmetros de diversidade genética e de estrutura populacional com base nas raças Angus, Devon, Hereford e Shorthorn. Taxa de endogamia (ΔF), tamanho efetivo (Ne), grau de parentesco, entre outros parâmetros, foram estimados para fornecer subsídios aos programas de melhoramento. Os parâmetros indicaram adequada diversidade genética, com Ne variando entre 128 no Devon e 303 no Shorthorn e ΔF variando entre 1,50 no Angus e 3,92 no Devon; (2) avaliar estratégias de imputação de genótipos utilizando dados de Braford e Hereford através de painéis de baixa densidade (3K, 6K, 8K, 15K e 20K) para os painéis de 50K e 777K. Para o painel de 777K, também foram utilizados na imputação os painéis de 50K, 90iK e 90tK. Os resultados indicaram que, com exceção do painel de 3K, todos os demais painéis de baixa densidade poderiam ser utilizados como base visando à imputação para o painel de 50K e também que os painéis de média densidade (50K, 90iK e 90tK), poderiam ser utilizados como base na imputação para o painel de 777K. Esses painéis mostraram-se eficientes e possuem, em geral, custos compatíveis com a atividade pecuária; (3) avaliar a acurácia de predição dos valores genômicos utilizando alguns painéis de baixa densidade (8K e 15K) imputados para o painel de 50K, relacionando os resultados com o uso do painel original de 50K. A acurácia do valor genômico direto (DGV) e do valor genético genômico (GEBV) com o valor genético (EBV) utilizando painéis imputados ou não, indicaram que não houveram diferenças em acurácia e as perdas em acurácia por utilizar os painéis imputados ficaram entre -0,0002 e -0,0021 dependendo do painel, do cenário e da característica analisada; (4) usar marcadores moleculares na seleção genômica testando dois métodos BLUP (procedimento de passo único ou de multi passo) com dados simulados de bovinos de corte. Os resultados demonstraram, com base nos parâmetros estudados, igualdade de resultados entre os dois procedimentos; (5) avaliar a viabilidade do uso da seleção genômica usando dados de campo de animais Braford e Hereford, testando os dois métodos BLUP (passo único e multi passo). Os resultados com base nos parâmetros estudados, mostraram que as acurácias de predição do DGV e do GEBV foram iguais nos dois procedimentos, porém no método multi passo as predições genômicas foram menos viesadas. / The aim of this work were: (1) to evaluate parameters of genetic diversity and population structure based on Angus, Devon, Hereford and Shorthorn breeds. Inbreeding rate (ΔF), effective size (Ne), relatedness, among other parameters, were estimated to provide subsidies for breeding programs. The parameters indicated a good genetic diversity, with Ne ranging from 128 in Devon to 303 in Shorthorn and ΔF ranging from 1.50 in Angus to 3.92 in Devon; (2) to evaluate strategies of genotype imputation with Braford and Hereford beef data using low density panels (3K, 6K, 8K, 15K and 20K) for 50K and 777K panels. For imputation to the 777K panel were also used the 50K, 90iK and 90tK panels. The results indicated that, except for the 3K panel, all other low density panels could be used of imputation the 50K panel and also the medium density panels (50K, 90iK and 90tK), could be used of imputation the 777K panel. These panels have been efficient and have, in general, compatible costs of the beef cattle operation; (3) to evaluate the accuracy of genomic prediction using some low density panels (8K and 15K) imputed to the 50K panel, relating the results with 50K original panel. The accuracy of direct genomic value (DGV) and genomic estimated breeding value (GEBV) with estimated breeding value (EBV) using imputed or not panels, indicated that there were no differences in accuracy and the losses in accuracy by using the imputed panels ranged from -0.0002 to -0.0021 depending on the panel, the scenario and the trait; (4) to use molecular markers in genomic selection testing two BLUP methods (single and two steps) with simulated beef cattle data. The results showed, based on the parameters studied, equality of results between the two methods; (5) to evaluate the viability of using the genomic selection using Braford and Hereford beef cattle and testing the two BLUP methods (single and two steps). The results, based on the parameters studied, showed that DGV and GEBV accuracies were similar in both methods, but the genomic predictions were less biased with then two-step method.

Objetivou-se com este trabalho: (1) avaliar parâmetros de diversidade genética e de estrutura populacional com base nas raças Angus, Devon, Hereford e Shorthorn. Taxa de endogamia (ΔF), tamanho efetivo (Ne), grau de parentesco, entre outros parâmetros, foram estimados para fornecer subsídios aos programas de melhoramento. Os parâmetros indicaram adequada diversidade genética, com Ne variando entre 128 no Devon e 303 no Shorthorn e ΔF variando entre 1,50 no Angus e 3,92 no Devon; (2) avaliar estratégias de imputação de genótipos utilizando dados de Braford e Hereford através de painéis de baixa densidade (3K, 6K, 8K, 15K e 20K) para os painéis de 50K e 777K. Para o painel de 777K, também foram utilizados na imputação os painéis de 50K, 90iK e 90tK. Os resultados indicaram que, com exceção do painel de 3K, todos os demais painéis de baixa densidade poderiam ser utilizados como base visando à imputação para o painel de 50K e também que os painéis de média densidade (50K, 90iK e 90tK), poderiam ser utilizados como base na imputação para o painel de 777K. Esses painéis mostraram-se eficientes e possuem, em geral, custos compatíveis com a atividade pecuária; (3) avaliar a acurácia de predição dos valores genômicos utilizando alguns painéis de baixa densidade (8K e 15K) imputados para o painel de 50K, relacionando os resultados com o uso do painel original de 50K. A acurácia do valor genômico direto (DGV) e do valor genético genômico (GEBV) com o valor genético (EBV) utilizando painéis imputados ou não, indicaram que não houveram diferenças em acurácia e as perdas em acurácia por utilizar os painéis imputados ficaram entre -0,0002 e -0,0021 dependendo do painel, do cenário e da característica analisada; (4) usar marcadores moleculares na seleção genômica testando dois métodos BLUP (procedimento de passo único ou de multi passo) com dados simulados de bovinos de corte. Os resultados demonstraram, com base nos parâmetros estudados, igualdade de resultados entre os dois procedimentos; (5) avaliar a viabilidade do uso da seleção genômica usando dados de campo de animais Braford e Hereford, testando os dois métodos BLUP (passo único e multi passo). Os resultados com base nos parâmetros estudados, mostraram que as acurácias de predição do DGV e do GEBV foram iguais nos dois procedimentos, porém no método multi passo as predições genômicas foram menos viesadas. / The aim of this work were: (1) to evaluate parameters of genetic diversity and population structure based on Angus, Devon, Hereford and Shorthorn breeds. Inbreeding rate (ΔF), effective size (Ne), relatedness, among other parameters, were estimated to provide subsidies for breeding programs. The parameters indicated a good genetic diversity, with Ne ranging from 128 in Devon to 303 in Shorthorn and ΔF ranging from 1.50 in Angus to 3.92 in Devon; (2) to evaluate strategies of genotype imputation with Braford and Hereford beef data using low density panels (3K, 6K, 8K, 15K and 20K) for 50K and 777K panels. For imputation to the 777K panel were also used the 50K, 90iK and 90tK panels. The results indicated that, except for the 3K panel, all other low density panels could be used of imputation the 50K panel and also the medium density panels (50K, 90iK and 90tK), could be used of imputation the 777K panel. These panels have been efficient and have, in general, compatible costs of the beef cattle operation; (3) to evaluate the accuracy of genomic prediction using some low density panels (8K and 15K) imputed to the 50K panel, relating the results with 50K original panel. The accuracy of direct genomic value (DGV) and genomic estimated breeding value (GEBV) with estimated breeding value (EBV) using imputed or not panels, indicated that there were no differences in accuracy and the losses in accuracy by using the imputed panels ranged from -0.0002 to -0.0021 depending on the panel, the scenario and the trait; (4) to use molecular markers in genomic selection testing two BLUP methods (single and two steps) with simulated beef cattle data. The results showed, based on the parameters studied, equality of results between the two methods; (5) to evaluate the viability of using the genomic selection using Braford and Hereford beef cattle and testing the two BLUP methods (single and two steps). The results, based on the parameters studied, showed that DGV and GEBV accuracies were similar in both methods, but the genomic predictions were less biased with then two-step method.