Cette thèse porte sur l’utilisation d’ontologies et de bases de connaissances pour guider différentes étapes du processus d’extraction de connaissances à partir de bases de données (ECBD) et une application dans le domaine de la pharmacogénomique. Les données relatives à ce domaine sont hétérogènes, complexes, et distribuées dans diverses bases de données, ce qui rend cruciale l’étape préliminaire de préparation et d’intégration des données à fouiller. Je propose pour guider cette étape une approche originale d’intégration de données qui s’appuie sur une représentation des connaissances du domaine sous forme de deux ontologies en logiques de description : SNP-Ontology et SO-Pharm. Cette approche a été implémentée grâce aux technologies du Web sémantique et conduit au peuplement d’une base de connaissances pharmacogénomique. Le fait que les données à fouiller soient alors disponibles dans une base de connaissances entraîne de nouvelles potentialités pour le processus d’extraction de connaissances. Je me suis d’abord intéressé au problème de la sélection des données les plus pertinentes à fouiller en montrant comment la base de connaissances peut être exploitée dans ce but. Ensuite j’ai décrit et appliqué à la pharmacogénomique, une méthode qui permet l’extraction de connaissances directement à partir d’une base de connaissances. Cette méthode appelée Analyse des Assertions de Rôles (ou AAR) permet d’utiliser des algorithmes de fouille de données sur un ensemble d’assertions de la base de connaissances pharmacogénomique et d’expliciter des connaissances nouvelles et pertinentes qui y étaient enfouies. / This thesis studies the use of ontology and knowledge base for guiding various steps of the Knowledge Discovery in Databases (KDD) process in the domain of pharmacogenomics. Data related to this domain are heterogeneous, complex, and disseminated through several data sources. Consequently, the preliminary step that consists in the preparation and the integration of data is crucial. For guiding this step, an original approach is proposed, based on a knowledge representation of the domain within two ontologies in description logics : SNP-Ontology and SO-Pharm. This approach has been implemented using semantic Web technologies and leads finally to populating a pharmacogenomic knowledge base. As a result, data to analyze are represented in the knowledge base, which is a benefit for guiding following steps of the knowledge discovery process. Firstly, I study this benefit for feature selection by illustrating how the knowledge base can be used for this purpose. Secondly, I describe and apply to pharmacogenomics a new method named Role Assertion Analysis (or RAA) that enables knowledge discovery directly from knowledge bases. This method uses data mining algorithms over assertions of our pharmacogenomic knowledge base and results in the discovery of new and relevant knowledge.

Potsdam, Universiẗat, Diss., 2005.

Citocinas são pequenas moléculas de sinalização celular que desempenham um papel muito importante no sistema imunológico e atuam na comunicação intracelular. Escolheu-se cinco genes pertencentes a essa família com o objetivo de se estudar SNPs que possam estar associados com a resistência à verminose gastrintestinal em caprinos. São eles: IL2, IL4, IL13, IFNg e TNFa. Para isso foi estudada uma população de 229 caprinos. Estes animais foram produzidos na Embrapa Caprinos e Ovinos (Sobral, CE) a partir de animais das Raças Saanen, raça considerada susceptível a endoparasitas gastrintestinais e Anglo-nubiana, raça considerada resistente aos mesmos endoparasitas. Após dois cruzamentos a terceira geração de animais, considerada F2, possuía 229 animais. Foram coletadas amostras de sangue para posteriores etapas de extração de DNA e quantificação; foram coletadas também amostras de fezes para contagem de ovos por grama de fezes (OPG). Os dados foram transformados em log10(n+1), onde n é número de ovos por grama de fezes, e analisados usando o procedimento dos modelos mistos do SAS (2002/2003). Os efeitos fixos incluídos no modelo foram sexo, coleta e idade a coleta e a variável animal foi utilizada como efeito aleatório. Com base no resultado dessa análise escolheu-se 44 animais com fenótipos extremos para resistência. Visando a prospecção de SNPs foram sequenciadas duas regiões do gene IL2, uma região do gene IL4, duas regiões do gene IL13, três regiões do gene IFNg e quatro regiões do gene TNFa. Foram encontrados dois SNPs no gene IL2 (intron 1 e intron 2), um SNP no gene IL4 (intron 3), um SNP no gene IL13 (intron 1), seis SNPs no gene IFNg (dois no exon 1, um no intron 1, um no intron 2, um no exon 3 e um no exon 4) e dez SNPs no gene TNFa (dois deles na região promotora do gene, dois no intron 2 e seis no exon 4). Verificou-se que há alteração de aminoácido na sequência de apenas um dos SNPs encontrados em regiões codificadoras de proteínas. A troca ocorre no segundo SNP localizado no exon 1 do gene IFNg (A/C), onde há alteração do aminoácido asparagina (considerando o alelo A) para treonina (alelo C). O estudo da associação entre as amostras extremos para resistência e os marcadores tipo SNP foi realizado com o teste de Fisher e observou-se que, dentre os vinte SNPs encontrados, oito deles apresentaram um valor de P ≤0,05, o que indica que os SNPs são potenciais marcadores moleculadores para resistência à verminose gastrintestinal, ou seja, provavelmente associados ao fenótipo estudado. Para essa associação ser validada é necessário estudar o efeito desses SNPs na população completa e em outras populações. / The cytokines are small cell-signaling proteins that play important role in immunologic system acting in intracellular communication. Five genes from cytokine family, i.e., IL2, IL4, IL13, IFNg, and TNFa were selected to search for SNPs, which may be associated with goat gastrointestinal endoparasites resistance. A population of 229 goats was produced in Embrapa Caprinos (Sobral, CE, Brazil). This population was an F2 offspring from a F1 intercross, which was in turn produced by crossing Saanen pure breed considered to be susceptible to gastrointestinal endoparasites with Anglo-nubiana pure breed considered to be resistant. Blood samples were collected for DNA extraction and fecal samples were collected for parasite egg counting. The data were transformed in log10(n+1), where n is the number of eggs per gram of feces, and analyzed by using the mixed model procedure of SAS (2002/2003). The fixed effects included were sex, sampling and age at sampling. The animal variable was used as random effect. After data analyses, forty four phenotypic extremes for endoparasite resistance were selected. Two regions of the gene IL2, one region of each gene IL4 and IL13, three regions of IFNg, and four regions of TNFa were sequenced in the search for SNPs. Two SNPs were found in the gene IL2 (intron 1 and intron 2), one SNP was found in IL4 (intron 3) one SNP in IL13 (intron 1) six SNPs in IFNg (two in the exon 1, one in the intron 1, one in the intron 2, one in the exon 3, and one in the exon 4) and ten SNPs were found in the gene TNFa (two in the promoter region, two in the intron 2 and six in the exon 4). Among all the SNPs found within exons only the second SNP of the IFNg exon 1 changes the amino acid. This SNP replaces an asparagine (allele A) by a threonin (allele C). The association study between the extremes and SNPs was performed using the Fisher exact test. A number of eight of the twenty described SNPs presented significant P value (P ≤0.05) indicating association with gastrointestinal endoparasite resistance and thus, the potential applicability as molecular markers for genetic improvement efforts involving this disease. To validate the associations, however, is necessary to study the effect of SNPs in a great number of animals and also in a variety of breeds.

Citocinas são pequenas moléculas de sinalização celular que desempenham um papel muito importante no sistema imunológico e atuam na comunicação intracelular. Escolheu-se cinco genes pertencentes a essa família com o objetivo de se estudar SNPs que possam estar associados com a resistência à verminose gastrintestinal em caprinos. São eles: IL2, IL4, IL13, IFNg e TNFa. Para isso foi estudada uma população de 229 caprinos. Estes animais foram produzidos na Embrapa Caprinos e Ovinos (Sobral, CE) a partir de animais das Raças Saanen, raça considerada susceptível a endoparasitas gastrintestinais e Anglo-nubiana, raça considerada resistente aos mesmos endoparasitas. Após dois cruzamentos a terceira geração de animais, considerada F2, possuía 229 animais. Foram coletadas amostras de sangue para posteriores etapas de extração de DNA e quantificação; foram coletadas também amostras de fezes para contagem de ovos por grama de fezes (OPG). Os dados foram transformados em log10(n+1), onde n é número de ovos por grama de fezes, e analisados usando o procedimento dos modelos mistos do SAS (2002/2003). Os efeitos fixos incluídos no modelo foram sexo, coleta e idade a coleta e a variável animal foi utilizada como efeito aleatório. Com base no resultado dessa análise escolheu-se 44 animais com fenótipos extremos para resistência. Visando a prospecção de SNPs foram sequenciadas duas regiões do gene IL2, uma região do gene IL4, duas regiões do gene IL13, três regiões do gene IFNg e quatro regiões do gene TNFa. Foram encontrados dois SNPs no gene IL2 (intron 1 e intron 2), um SNP no gene IL4 (intron 3), um SNP no gene IL13 (intron 1), seis SNPs no gene IFNg (dois no exon 1, um no intron 1, um no intron 2, um no exon 3 e um no exon 4) e dez SNPs no gene TNFa (dois deles na região promotora do gene, dois no intron 2 e seis no exon 4). Verificou-se que há alteração de aminoácido na sequência de apenas um dos SNPs encontrados em regiões codificadoras de proteínas. A troca ocorre no segundo SNP localizado no exon 1 do gene IFNg (A/C), onde há alteração do aminoácido asparagina (considerando o alelo A) para treonina (alelo C). O estudo da associação entre as amostras extremos para resistência e os marcadores tipo SNP foi realizado com o teste de Fisher e observou-se que, dentre os vinte SNPs encontrados, oito deles apresentaram um valor de P ≤0,05, o que indica que os SNPs são potenciais marcadores moleculadores para resistência à verminose gastrintestinal, ou seja, provavelmente associados ao fenótipo estudado. Para essa associação ser validada é necessário estudar o efeito desses SNPs na população completa e em outras populações. / The cytokines are small cell-signaling proteins that play important role in immunologic system acting in intracellular communication. Five genes from cytokine family, i.e., IL2, IL4, IL13, IFNg, and TNFa were selected to search for SNPs, which may be associated with goat gastrointestinal endoparasites resistance. A population of 229 goats was produced in Embrapa Caprinos (Sobral, CE, Brazil). This population was an F2 offspring from a F1 intercross, which was in turn produced by crossing Saanen pure breed considered to be susceptible to gastrointestinal endoparasites with Anglo-nubiana pure breed considered to be resistant. Blood samples were collected for DNA extraction and fecal samples were collected for parasite egg counting. The data were transformed in log10(n+1), where n is the number of eggs per gram of feces, and analyzed by using the mixed model procedure of SAS (2002/2003). The fixed effects included were sex, sampling and age at sampling. The animal variable was used as random effect. After data analyses, forty four phenotypic extremes for endoparasite resistance were selected. Two regions of the gene IL2, one region of each gene IL4 and IL13, three regions of IFNg, and four regions of TNFa were sequenced in the search for SNPs. Two SNPs were found in the gene IL2 (intron 1 and intron 2), one SNP was found in IL4 (intron 3) one SNP in IL13 (intron 1) six SNPs in IFNg (two in the exon 1, one in the intron 1, one in the intron 2, one in the exon 3, and one in the exon 4) and ten SNPs were found in the gene TNFa (two in the promoter region, two in the intron 2 and six in the exon 4). Among all the SNPs found within exons only the second SNP of the IFNg exon 1 changes the amino acid. This SNP replaces an asparagine (allele A) by a threonin (allele C). The association study between the extremes and SNPs was performed using the Fisher exact test. A number of eight of the twenty described SNPs presented significant P value (P ≤0.05) indicating association with gastrointestinal endoparasite resistance and thus, the potential applicability as molecular markers for genetic improvement efforts involving this disease. To validate the associations, however, is necessary to study the effect of SNPs in a great number of animals and also in a variety of breeds.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / Atualmente, existe uma grande possibilidade de associaÃÃo entre as Ãreas de genÃtica quantitativa e de genÃtica molecular. Isto pode causar importante impacto na seleÃÃo de ovinos, com o estabelecimento de eficientes critÃrios de seleÃÃo para produÃÃo de carne. Com isso, os objetivos deste trabalho foram: verificar polimorfismos nos genes GDF9, Calpastatina e Aromatase (CYP19); verificar a freqÃÃncia de variantes alÃlicas do tipo SNP nestes genes; verificar os efeitos destas variantes sobre caracterÃsticas produtivas e reprodutivas de ovinos de uma populaÃÃo multirracial; estimar os parÃmetros genÃticos e os valores genÃticos destas caracterÃsticas, nesta populaÃÃo; verificar o efeito da inclusÃo do genÃtipo para estes genes nos modelos para estimativas de parÃmetros genÃticos e verificar o efeito do genÃtipo para estes genes sobre os valores genÃticos estimados. O gene GDF9 à um gene candidato relacionado com o fenÃtipo de alta prolificidade. O gene da Calpastatina possui importÃncia na produÃÃo de animais de corte, por està relacionado ao crescimento e a qualidade da carne. O gene da aromatase à um candidato afetando o desempenho produtivo e reprodutivo, pelo seu importante papel no metabolismo dos hormÃnios esterÃides. O polimorfismo do tipo (SNP) do gene CYP19 foi investigado pela tÃcnica PCR-RFLP em uma amostra de 133 animais de diversos grupos genÃticos de ovinos de corte. Foram estimadas as freqÃÃncias alÃlicas e genotÃpicas de polimorfismos deste gene e investigado o efeito destas variantes sobre caracterÃsticas de crescimento, reprodutivas e de habilidade materna, utilizando o procedimento GLM do software SAS. As caracterÃsticas estudadas foram peso ao nascer (PN), peso ao desmame (PD), peso ao abate (PA), peso a um ano de idade (P1), ganho de peso mÃdio diÃrio do nascimento ao desmame (Gn_d), ganho de peso mÃdio diÃrio do desmame ao abate (Gdes_abat), ganho de peso mÃdio diÃrio do desmame a um ano de idade (Gdes_ano), idade ao primeiro parto (IPP), intervalo de partos (IP), perÃodo de gestaÃÃo (PG), dias para o parto (DP), peso total de crias nascidas por matriz por parto (PTCN) e peso total de crias desmamadas por matriz por parto (PTCD). ParÃmetros genÃticos e valores genÃticos foram estimados utilizando o mÃtodo da MÃxima VerossimilhanÃa Restrita Livre de Derivadas (DFREML). Foi avaliado o efeito da inclusÃo do genÃtipo para o gene da aromatase nos modelos para estimativas de parÃmetros genÃticos. Foi verificado o efeito do genÃtipo sobre os valores genÃticos estimados. NÃo foi possÃvel genotipar os animais para os genes GDF9 e Calpastatina, devido a dificuldades de padronizar as reaÃÃes. Assim, os animais foram genotipados apenas para o gene da aromatase. Na amostra estudada para o gene da aromatase, nÃo foram observados indivÃduos com genÃtipo AA. As freqÃÃncias para os genÃtipos AB e BB foram 0,65 e 0,35, respectivamente. A freqÃÃncia alÃlica diferiu entre os grupos genÃticos estudados. O gene da aromatase apresentou influÃncia sobre a maioria das caracterÃsticas estudadas, havendo diferenÃas no padrÃo desta influÃncia, de acordo com o grupo genÃtico considerado. As herdabilidades diretas estimadas foram 0,21, 0,25, 0,52, 0,39, 0,24, 0,20, 0,21, respectivamente, para PN, PD, PA, P1, Gn_d, Gdes_abat e Gdes_ano, e 0,01, 0,06, 0,14, 0,06, 0,20 e 0,11, respectivamente, para IPP, IP, PG, DP, PTCN e PTCD. CorrelaÃÃes genÃticas positivas foram estimadas entre os pesos corporais. A correlaÃÃo genÃtica entre Gn_d e Gdes_abat foi de 0,37 e entre Gn_d e Gdes_ano foi de 0,55. CorrelaÃÃes genÃticas negativas foram estimadas entre IPP com IP e PG. PTCN apresentou correlaÃÃo genÃtica de 0,52 com PTCD. O uso da informaÃÃo do genÃtipo dos animais para o gene da aromatase melhorou o ajuste dos modelos de anÃlises genÃtica sob metodologia BLUP. Os indivÃduos com genÃtipo AB apresentaram superioridade genÃtica em relaÃÃo Ãqueles de genÃtipo BB para a maioria das caracterÃsticas estudadas. Pode se concluir que o uso da seleÃÃo assistida por marcadores permitirà o aumento da eficiÃncia da seleÃÃo atualmente em prÃtica com o uso das metodologias tradicionais de genÃtica quantitativa / Nowadays, there is great possibility of association between quantitative and molecular genetics. An important impact would be expected in the sheep selection, with the establishment of efficient criteria for meat production selection. The aims of this work were to verify polymorphisms in GDF9, Calpastatine and Aromatase (CYP19) genes; to verify the frequencies of SNP allelic variants in these genes; to verify the effects of these variants on productive and reproductive traits in a multiracial sheep population; to estimate genetic parameters and breeding values of these traits in this population; to verify the effect of genotype of these genes on models to estimate the genetic parameters and to verify the effect of genotype for these genes on estimated breeding values. GDF9 gene is a candidate related to phenotype of high prolificacy. The calpastatine gene has importance on production of meat animals, as it is related to growth and meat quality. Aromatase gene is a candidate affecting the productive and reproductive performance, by its important role in the steroid hormone metabolism. SNP polymorphism of CYP19 gene was investigated by PCR-RFLP technique in a sample of 133 animals from several breed groups of meat sheep. Allelic and genotypic frequencies were estimated for this polymorphism and the effect of these variants on growth,reproductive and maternal traits were investigated, using GLM procedure of SAS software. The studied traits were birth weight (PN), weaning weight (PD), slaughter weight (PA), yearling weight (P1), weight gain from birth to weaning (Gn_d), weight gain from weaning to slaughter (Gdes_abat), weight gain from weaning to yearling (Gdes_ano), age at first lambing (IPP), lambing interval (IP), gestation length (PG), lambing date (DP), total weight of lambs born for female for lambing (PTCN) and total weight of weaned lambs for female for lambing (PTCD). Genetic parameters and breeding values were estimated by Derivative Free Restricted Maximum Likelihood (DFREML) method. The effect of genotype inclusion in analysis models for estimation of genetic parameters was evaluated. The effect of genotype on estimated breeding value was verified. It was not possible to verify the genotype of the animals for GDF9 and Calpastatine genes due the difficulties on the reactions standardizations. So the animals were genotyped only for aromatase gene. In studied sample, it is not observed animals with AA genotype. The frequencies for AB and BB were 0.65 and 0.35,respectively. The allelic frequency did differ among studied breed groups. The aromatase gene presented influence on most studied traits, with difference in this influence according to breed group. The direct heritabilities were 0.21, 0.25, 0.52, 0.39, 0.24, 0.20, 0.21, respectively, for PN, PD, PA, P1, Gn_d, Gdes_abat and Gdes_ano, and 0.01, 0.06, 0.14, 0.06, 0.20 and 0.11, respectively, for IPP, IP, PG, DP, PTCN and PTCD. Positive genetic correlations were estimated among corporal weights. Genetic correlation between Gn_d and Gdes_abat was 0.37 and between Gn_d and Gdes_ano was 0.55. Negative genetic correlations were estimated between IPP with IP and PG. PTCN presented genetic correlation of 0.52 with PTCD. The use of information of genotype of aromatase gene increased the efficiency of models for genetic analyses by BLUP methodology. The animals with AB genotype presented genetic superiority for most studied traits in relation to those with BB genotype. It is possible conclude that the use of marked assisted selection will permit increase the efficiency of selection today in practice with the use of traditional quantitative genetic methodologies

Lentils are an inexpensive source of protein, vitamins and minerals. Lentil seeds contain carotenoids that have antioxidant properties and play an important nutritional role as precursors of vitamin A. Improving concentration of carotenoids in lentils has potential as component of a bio-fortification program. The understanding of the genetic control of carotenoids in lentil will help breeders develop strategies for developing varieties with higher carotenoid concentration. The objectives of this research program were to evaluate the concentration of carotenoids in mature lentil seeds and to identify genomic regions that possibly influence carotenoid concentration. The experimental program involved: i) analyzing the carotenoid concentration in seeds produced from the specific crosses among lentil genotypes with three cotyledon colours using high pressure liquid chromatography (HPLC) ii) analyzing an association mapping panel to develop potential single nucleotide polymorphism (SNP) markers for genes associated with carotenoid concentration For the first objective, dihybrid crosses were made between lentil cultivars with red, yellow and green cotyledons. Hybridized lentil populations were grown in the greenhouse and phytotron chamber up to the F3 generation and then seeds were analyzed for carotenoid concentration. As expected, the expression of red cotyledon colour was dominant over yellow, and these two cotyledon colours were inhibited by an epistatic interaction with green cotyledon colour. Lentil seeds with green cotyledon colour had higher carotenoid concentration than red cotyledon types which in turn had higher carotenoid concentration compared to yellow cotyledon lentils. Identifying molecular markers associated with carotenoids can be part of a crop improvement strategy for both marker-assisted selection and marker-assisted breeding (MAS; MAB). Association mapping using broad genetic materials might result in high resolution. For this purpose an association mapping panel of 143 lentil genotypes was grown at two different locations near Saskatoon, Canada, in 2011 and 2012. Concentration of three carotenoids in lentil seed samples was measured using reverse phase HPLC. Of the 143 genotypes, 60 accessions were common for both years and locations. Concentrations of lutein, zeaxanthin and violaxanthin in seed samples were determined. Genotyping was accomplished using 1536 SNP (single nucleotide polymorphism) markers of an Illumina Golden-Gate assay. It was determined that 168 of the SNP markers were significantly associated with carotenoid concentration components using the GLM (generalized linear model) model. These putative SNPs could be used for MAS and MAB to improve selection for carotenoids in lentil to increase the nutritional value of lentil.

Schizophrenie und die bipolar-affektive Erkrankung sind mit einer Lebenszeitprävalenz von ca. 1% häufige psychiatrische Krankheitsbilder. Die genaue Ätiologie beider Krankheiten ist bisher noch nicht eindeutig geklärt, allerdings nimmt man jeweils eine multifaktorielle Genese an, bei der eine genetische Anfälligkeit im Zusammenspiel mit Umweltfaktoren zur Krankheitsentstehung führt. Es bestehen für beide Krankheiten diverse pathophysiologische Modelle, besonders interessant ist dabei eine Dysregulation der Neurotransmitter. Neben Dopamin und GABA steht auch Glutamat, ein häufiger exzitatorischer Neurotransmitter im ZNS, im Verdacht, eine entscheidende Rolle bei der Entstehung der Schizophrenie zu spielen. Bei der bipolar-affektiven Erkrankung stehen besonders Veränderungen der monoaminergen Neurotransmission im Vordergrund. Eine Beteiligung des Glutamatsystems wird ebenfalls diskutiert. NOS1AP liegt auf Chromosom 1q22, einem aus Kopplungsstudien bekannten Suszeptibilitätslokus für Schizophrenie. Bereits in diversen anderen Studien wurde Assoziation auf Einzelmarker- und Haplotypebene festgestellt. NOS1AP interagiert mit der NOS-I und führt zu einer Translokation dieses Enzyms ins Zytosol, wodurch es dem Calciumeinstrom durch den glutamatergen NMDA-Rezeptor entzogen wird. Auf diese Weise ist es zu einem geringeren Grad aktiv und produziert weniger NO. Aufgrund der funktionellen Verbindung mit dem NMDA-Rezeptor und der NOS-I, die beide im Verdacht stehen, an der Pathogenese der Schizophrenie beteiligt zu sein, ist NOS1AP ein interessantes Kandidatengen. 14 SNPs im Bereich des NOS1AP-Gens und daraus resultierende Haplotypen wurden mittels Primerextension und MALDI-ToF Massenspektrometrie bei 245 Patienten mit Schizophrenie, 90 Patienten mit bipolar-affektiver Erkrankung und 360 Kontrollpersonen analysiert. Dabei konnte für drei SNPs (rs1538018, rs945713 und rs4306106) jeweils eine nominelle Assoziation mit Schizophrenie festgestellt werden. Auch nach Durchführung eines Permutationstests blieb für rs1538018 und rs945713 ein statistischer Trend bestehen. Bei Betrachtung der Haplotypen ließ sich lediglich nominelle Assoziation eines Haplotyps mit Schizophrenie nachweisen. Die geschlechtsspezifische Analyse ergab für die männlichen Patienten im Permutationstest eine grenzwertig signifikante Assoziation von rs1538018 und rs945713, während zwei Haplotypen nur eine nominelle Assoziation zeigten. Bei den weiblichen Patienten ließ sich weder eine allelische noch eine haplotypische Assoziation nachweisen. Für die bipolar-affektive Erkrankung wurden keine Assoziationen, weder auf Einzelmarker- noch auf Haplotyp-Ebene festgestellt. Die grenzwertige Assoziation der SNPs mit Schizophrenie macht eine pathogenetische Beteiligung von NOS1AP an Schizophrenie denkbar. Es sind jedoch noch weitere Replikationsstudien, auch in anderen Kollektiven, notwendig, um besser einschätzen zu können, welchen Einfluss NOS1AP tatsächlich für die Krankheitsentstehung hat. / With a lifetime prevalence of 1%, schizophrenia and bipolar affective disorder are common psychiatric diseases. The etiology of both disorders is still not completely understood, but a multifactorial genesis where genetic susceptibility and environmental factors interact and lead to the development of the disease is assumed. For both disorders there exist diverse pathophysiological models, of which a dysregulation of neurotransmission is especially interesting. Glutamate, a common excitatory neurotransmitter in CNS, is supposed to play an important role in the formation of schizophrenia and bipolar disorder. NOS1AP is located on chromosome 1q22, a susceptibility locus for schizophrenia. Several studies have already shown association of SNPs and haplotypes with schizophrenia. NOS1AP interacts with NOS-I and leads to a dislocation of this enzyme into the cytosol, where it is activated to a lesser degree by calcium influx through the glutamatergic NMDA receptor and consequently produces less NO. Because of this interaction with NOS-I and the NMDA receptor which have been shown to be involved in schizophrenia, NOS1AP is an interesting functional candidate gene. In this thesis 14 SNPs within the genomic extent of NOS1AP and resulting haplotypes were genotyped by primer extension and MALDI-ToF analysis in 245 patients suffering from schizophrenia, 90 patients with bipolar disorder and 360 controls. Three SNPs (rs1538018, rs945713 and rs4306106) showed nominal association with schizophrenia. After a permutation test rs1538018 and rs945713 still showed a statistical trend. Only one haplotype was found to be nominally associated with schizophrenia. When including only the male patients rs1538018 and rs945713 showed an association of borderline significance and two haplotypes were nominally associated. Among the female patients there were neither allelic nor haplotypic associations. NOS1AP showed no association with bipolar affective disorder in this study. The borderline association of two SNPs with schizophrenia suggests a possible role of NOS1AP in the pathogenesis of schizophrenia. However, further studies are necessary to clarify the influence of NOS1AP on the development of schizophrenia.

Orientador: Flávia Lombardi Lopes / Resumo: Os microRNAs (miRNAs) são pequenos RNAs não-codificadores (20-22 nucleotídeos) que exercem uma função de controle pós-transcricional em RNA mensageiro (RNAm), regulando a produção de proteínas. Variações genéticas, como os polimorfismos de nucleotídeo único (SNPs), quando estão presentes em sequências de miRNA, podem alterar o controle pós-transcricional, baseado em similaridade aos seus respectivos alvos. Na produção de suínos, a identificação de fenótipos, como crescimento e características da carne, é vital. Nosso objetivo foi identificar SNPs em sequências genômicas que dão origem a miRNAs, bem como investigar, in silico, possíveis alterações na regulação de alvos que poderiam estar relacionados a fenótipos de produção em suínos. A montagem do assembly Sscrofa10.2 foi utilizada como genoma de referência para a localização dos SNPs e dos miRNAs descritos em suínos. Utilizando um script desenvolvido em Python, foi possível localizar 86 SNPs em sequencias miRNAs maduros. Para a predição dos genes alvos, foram utilizados sequência do 3´UTR de suínos com a adaptação do pacote Mirmap. Descobrimos que 55 das sequências de miRNA geraram mais de 28.570 genes alvos, indicando a criação de novos miRNAs Interagindo com RNAm alvos. Nossos resultados indicam que SNPs afetam a predição de alvos para miRNAs em suínos. / Abstract: The microRNAs (miRNAs) are small non-coding RNAs (20-22 nucleotides) that exert a post-transcriptional control function in messenger RNA (mRNA), regulating the production of proteins. Genetic variations, such as single nucleotide polymorphisms (SNPs), when present in miRNA sequences, may change post-transcriptional control, based on similarity to their target genes. Pig production, identification of phenotypes, growth and meat characteristics is vital. Other in which SNPs in genetic sequences that give from miNNAs, as well as investigate, in silicon, changes in the data of alves, which are behaviert on a phenotypes of production in swines. The assembly of the Sscrofa10.2 assembly was used as a reference reference for the location of SNPs and panel miRNAs in swine. Using a script deployed in Python, it was possible to locate 86 SNPs in mature miRNAs sequences. For a prediction of the target genes, the 3'UTR of pigs were completed with an adaptation of the Mirmap package. Discoveries that 55 of the miRNA sequences generated more than 28,570 target genes, pointing to a new creation of miRNAs interacting with mRNA targets. Cloister all SNPs for a target prediction for miRNAs in pigs. / Mestre

Gastric cancer is the second leading cause of cancer death worldwide, killing upwards of one million people each year. Apoptosis, a genetically controlled cell death in multicellular eukaryotic organisms, is an important mechanism for embryonic development, immune-system function and maintenance of tissue homeostasis through activation of an intrinsic suicide program to eliminate superfluous, infected, transformed or damaged cells. Single nucleotide polymorphism (SNP) is the most abundant type of genetic variations and is considered to be an important endogenous cause and fundamental factor influencing cancer risk. We conducted a hospital-based case-control study to investigate the association between apoptosis related genes and the risk for gastric cancer. We continuously enrolled 205 patients with pathologically proved gastric cancer and 397 frequency-matched healthy controls at Kaohsiung Veterans General Hospital from 2003 to 2006. Blood derived DNA samples from all participants were genotyped by PCR-RFLP to identify eight SNPs on seven key genes (FAS, FASL, SURVIVIN, XIAP, CASP3, CASP8, CASP9) in apoptotic pathway, but only five SNPs on four genes (FAS, FASL, CASP3, CASP9) were eventually valid for subsequent analyses. Our results showed that significant effects of H. pylori infection, cigarette smoking, alcohol drinking, and consumption of salted food and fermented food on gastric cancer risk while coffee drinking and consumption of vegetables and fruits had significant protective effects against gastric cancer in our study cohort. None of the individual gene polymorphism was associated with the risk of gastric cancer. However, the gene-gene interaction between CASP3 A21926C and CASP9 codon Arg221Gln polymorphisms was significantly associated with gastric cancer risk. In the combined analysis of four apoptosis related genes, our data showed that individuals carrying three or more putative high-risk genotypes were significantly associated with the development of gastric cancer than those who carrying two or less putative high-risk genotypes. Besides, the CASP9 codon Arg221Gln polymorphism was a risk factor for gastric cancer in people equal to or elder than fifty, though not in people younger than fifty. Taken together, our results indicated that SNPs on apoptosis related genes were associated to the development of gastric cancer.

Infertility in dairy cattle remains a major economic loss to dairy producers. Identifying dairy cattle with superior genetic potential for improved fertility would increase dairy farm profitability. Dairy heifers were classified into two groups based upon services per conception (SPC); those animals with a single SPC were determined to be highly fertile and animals with greater than or equal to 4 SPC were classified as sub-fertile. Whole genome association analysis was performed on 20 individual heifers from each group utilizing a 777K highly density (HD) single nucleotide polymorphism (SNP) chip. Genomic data were evaluated utilizing PLINK, a whole genome association analysis toolset, and 570,620 SNP were available for analysis with a total of 39 samples being analyzed. Forty-four SNP were determined to be associated with fertility classification (P <= 0.00001) and were located on Bos taurus chromosome (BTA) 2, 4, 9, 19, and 26. The SNP and ranges between SNP were analyzed using BLAST-Like Alignment Tool (BLAT); SNP were associated with 5 candidate genes for reproduction. The SNP on BTA 2 were located within the region coding for the non-imprinted Prader-Willi/Angelman syndrome 2 (NIPA2) gene, which is involved in gestational magnesium transport. Also on BTA 2, SNP were identified within the region encoding for cytoplasmic fragile X mental retardation 1 (FMR1) interaction protein 1 (CYFIP1). The CYFIP1 gene is involved with the functionality of FMR1 and has been linked to premature ovarian failure in humans. Additionally, 3 SNP on BTA 9 were located near monofunctional C1-tetrahydrofolate synthase (MTHFD1L), which has been linked to neural tube defects during gestation in humans A difference in allele frequency was observed between the two groups for SNP located on BTA19 in proximity to two genes, zinc finger 18 (ZNF18) and mitogen activated protein kinase 4 (MAP2K4). The ZNF18 motif and MAP2K4 were found to be involved in heart development of the early embryo and associated with toll-like receptors (TLR) involved in gonadotropin releasing hormone (GnRH) signaling, respectively. The involvement of one or all of these genes may further explain reduced fertility in dairy cattle.