Since the late 1990s, common carp and koi production enterprises around the world have suffered enormous losses due to a viral disease caused by cyprinid herpesvirus-3 (CyHV-3). Genetic variation in resistance to CyHV-3 infection was observed in different common carp strains, indicating that disease resistance can be improved by selective breeding. Marker-assisted selection is a breeding strategy that can accelerate genetic gain; however, this approach requires genetic markers and a genetic linkage map. To develop molecular tools for breeding CyHV-3-resistant aquaculture stock, several candidate genes for antiviral innate immune response from common carp were isolated, and single nucleotide polymorphisms (SNPs) were identified. SNP markers for common carp immune response genes were developed for testing their linkage to disease resistance and for generating a genetic linkage map. Common carp immune response genes were isolated using degenerate primers developed from conserved peptide regions among other fish species for polymerase chain reaction (PCR) amplification. The amplified products were cloned and sequenced. Gene-specific primers were designed based on the isolated carp gene sequences to amplify gene fragments from genomic DNA of three carp strains and koi. The amplified products were cloned and sequenced to identify SNPs. For the genes that are duplicated, locus-specific primers were used for PCR amplification. SNPs were identified in several genes, including TLR2, TLR3a, TLR3b, TLR4a, TLR4b, TLR7a, TLR7b, TLR9, TLR21, TLR22, MyD88a, MyD88b, TRAF6a, TRAF6b, type I IFN, IL-1β, IL10a and IL10b. Putative SNPs were genotyped in a SNP discovery panel consisting of different common carp strains and koi to evaluate their allele frequencies and in a full-sib family to validate their segregation patterns using the SNaPshot method. Validated SNPs were used to genotype a mapping family. Twenty-three SNPs (19 exonic and 4 intronic SNPs) were informative in a mapping family. Among these genes, polymorphisms in IL10a suggested a possible association with resistant and susceptible phenotypes of CyHV-3-challenged fish. These SNPs will be analyzed with a set of approximately 300 microsatellites to generate a second-generation genetic map and to identify quantitative trait loci (QTLs) affecting resistance to CyHV-3. Among the common carp genes that were isolated and sequenced, TLR9 is known for its ability to detect viral DNA and requires adaptor molecules MyD88 and TRAF6 for signal transduction. Therefore TLR9, MyD88 and TRAF6 may be important candidate genes for mediating host antiviral response to CyHV-3. To elucidate possible functions of these genes, full-length cDNAs of common carp TLR9, MyD88 and TRAF6 were isolated and tissue-specific mRNA expression was determined. cDNA sequences of MyD88 and TRAF6 revealed that these genes are duplicated. These findings were the first report of MyD88 and TRAF6 duplications in a vertebrate. Protein domain characterization demonstrated that structural characteristics of these genes are conserved and resemble those of other vertebrates, indicating that common carp TLR9, MyD88 and TRAF6 genes may have identical functions with their mammalian orthologs. The mRNA expression of TLR9, MyD88a and b, and TRAF6a and b varied among tissues. Differential expression of the MyD88 and TRAF6 paralogous transcripts were observed in muscle tissues, suggesting that one paralog has evolved and attained a non-immune function. This genomic information will facilitate further research to better understand the ligand specificity of TLR9 and the role of TLR9, MyD88 and TRAF6 in the common carp immune response. / Ph. D.

S'ha estudiat la variabilitat genètica de les poblacions del nord d'Àfrica a partir de l'anàlisi de diverses regions genòmiques per tal d'entendre les poblacions analitzades d'una banda, i comprendre la dinàmica del genoma per l'altra. Els resultats obtinguts ens han permès verificar diferents hipòtesis sobre la història de les poblacions d'aquesta regió com són l'efecte paral·lel i independent de l'onada de difusió del neolític des de l'Orient Mitjà al llarg d'ambdues ribes de la Mediterrànea; i l'efecte de l'arabització. S'ha pogut estimar també la contribució genètica masculina nord africana a la península ibèrica i detectat certa contribució genètica del pobles sub-saharians a les poblacions nordafricanes. Per altra banda, el tipatge de marcadors genètics que evolucionen a velocitats diferents al cromosoma Y ha permès mostrar que el background genètic predomina sobre el background poblacional en l'estructura de la variació genètica dels microsatèl·lits en la regió no recombinant del cromosoma Y humà. / The genetic variability of the North African populations has been studied through the analysis of different genomic regions in order to understand both the analysed populations and the dynamics of the genome. The obtained results allow us to verify different hypotheses about the population history of this region including the parallel and independent effect of the Neolithic wave of advance from the Middle East and along both Mediterranean coasts; and the effect of Arabization phenomena. We also tried to estimate the North African male genetic contribution to the Iberian peninsula and detected Sub-Saharian genetic influences to the North African peoples. Moreover, the typing of genetic markers with different evolutionary rates on the Y chromosome allowed us to demonstrate that variation in microsatellites is deeply structured by genetic background on the non-recombining region of the human Y chromosome.

No description available.

Η πιο απλή μορφή γενετικής διαφοροποίησης στον άνθρωπο είναι οι μονονουκλεοτιδικοί πολυμορφισμοί (Single Nucleotide Polymorphisms - SNPs). Ο αριθμός αυτού του είδους πολυμορφισμών που έχουν βρεθεί στο ανθρώπινο γονιδίωμα και επηρεάζουν την παραγόμενη πρωτεΐνη αυξάνεται συνεχώς, αλλά η αντιστοίχηση τους σε πιθανές ασθένειες με πειραματικές μεθόδους είναι ασύμφορη από θέμα χρόνου και κόστους. Για αυτό τον λόγο έχουν αναπτυχθεί διάφορες υπολογιστικές μέθοδοι με σκοπό να ταξινομήσουν τους μονονουκλεοτιδικούς πολυμορφισμούς σε παθογόνους και μη. Οι περισσότερες από αυτές τις μεθόδους χρησιμοποιούν ταξινομητές, οι οποίοι παίρνοντας σαν είσοδο ένα σύνολο δομικών, λειτουργικών, ακολουθιακών και εξελικτικών χαρακτηριστικών, επιχειρούν να προβλέψουν αν ένας μονονουκλεοτιδικός πολυμορφισμός είναι παθογόνος ή μη. Για την εκπαίδευση αυτών των ταξινομητών, χρησιμοποιούνται δύο σύνολα μονονουκλεοτιδικών πολυμορφισμών. Το πρώτο αποτελείται από μονονουκλεοτιδικούς πολυμορφισμούς που έχει βρεθεί πειραματικά ότι οδηγούν σε παθογένεια και το δεύτερο από μονονουκλεοτιδικούς πολυμορφισμούς που έχει αποδειχθεί πειραματικά ότι είναι αδρανείς. Οι μέθοδοι αυτές διαφέρουν στα χαρακτηριστικά των μεταλλάξεων που λαμβάνουν υπόψη στην πρόβλεψη τους, καθώς επίσης και στην εκπαίδευση και τη φύση των τεχνικών ταξινόμησης, που χρησιμοποιούν για τη λήψη των αποφάσεων. Το βασικότερο προβλήματα τους ωστόσο έγκειται στο γεγονός ότι καθορίζουν τα χαρακτηριστικά, που θα χρησιμοποιήσουν σαν είσοδο στους ταξινομητές τους με τρόπο εμπειρικό και μάλιστα διαφορετικές μέθοδοι προτείνουν και χρησιμοποιούν διαφορετικά χαρακτηριστικά, χωρίς να τεκμηριώνουν επαρκώς τις αιτίες αυτής της διαφοροποίησης. Δύο ακόμα προβλήματα που δεν έχουν καταφέρει να αντιμετωπίσουν οι υπάρχουσες μεθοδολογίες είναι το πρόβλημα της ανισορροπίας των δύο κλάσεων ταξινόμησης και των ελλιπών τιμών σε πολλά από τα χαρακτηριστικά εισόδου των ταξινομητών, ώστε να επιτυγχάνουν πιο ακριβή και αξιόπιστα αποτελέσματα. Από τα παραπάνω είναι ξεκάθαρο πως υπάρχει μεγάλο περιθώριο βελτίωσης των υπάρχουσων μεθοδολογιών για το συγκεκριμένο πρόβλημα ταξινόμησης. Στην παρούσα διπλωματική εργασία προτείνουμε μια νέα υβριδική μεθοδολογία υπολογιστικής νοημοσύνης, που ξεπερνά πολλά από τα προβλήματα των υπάρχοντων μεθοδολογιών και βελτιώνει με τον τρόπο αυτό την απόδοσή τους. Δύο είναι τα βασικά βήματα που ακολουθήσαμε για την επίτευξη του στόχου αυτού. Πρώτον, συγκεντρώσαμε από τις διαθέσιμες δημόσιες βάσεις δεδομένων, τους μονονουκλεοτιδικούς πολυμορφισμούς που χρησιμοποιήθηκαν για την εκπαίδευση και τον έλεγχο των μοντέλων μηχανικής μάθησης. Συγκεκριμένα, συλλέχθησαν και φιλτραρίστηκαν τα θετικά και αρνητικά σύνολα εκπαίδευσης και ελέγχου, που αποτελούνται από μονονουκλεοτιδικούς πολυμορφισμούς που είτε οδηγούν σε παθογένεια, είτε είναι ουδέτεροι. Για κάθε πολυμορφισμό των δύο συνόλων υπολογίσαμε χρησιμοποιώντας υπάρχοντα διαθέσιμα εργαλεία όσο το δυνατό περισσότερα δομικά, λειτουργικά, ακολουθιακά και εξελικτικά χαρακτηριστικά. Για εκείνα τα χαρακτηριστικά, για τα οποία δεν υπήρχε κάποιο διαθέσιμο εργαλείο υπολογισμού τους, υλοποιήσαμε τον κατάλληλο κώδικα για τον υπολογισμό τους. Το δεύτερο βήμα της διπλωματικής αφορούσε το σχεδιασμό και την υλοποίηση της κατάλληλης υβριδικής μεθόδου για την επίλυση του προβλήματος που μελετάμε. Χρησιμοποιήσαμε μια νέα μέθοδο ταξινόμησης την EnsembleGASVR. Πρόκειται για μια ensemble μεθοδολογία, που συνδυάζει σε ένα ενιαίο πλαίσιο ταξινόμησης οκτώ διαφορετικούς ταξινομητές. Κάθε ένας από αυτούς τους ταξινομητές βασίζεται στον υβριδικό συνδυασμό των Γενετικών Αλγορίθμων και των μοντέλων Παλινδρόμησης Διανυσμάτων Υποστήριξης (nu-Support Vector Regression). Συγκεκριμένα ένας Προσαρμοζόμενος Γενετικός Αλγόριθμος χρησιμοποιείται για να καθοριστεί το βέλτιστο υποσύνολο χαρακτηριστικών, καθώς και οι βέλτιστες τιμές των παραμέτρων των ταξινομητών. Σαν μέθοδο ταξινόμησης των μεταλλάξεων σε ουδέτερες και παθογενείς, προτείνουμε τον nu-SVR ταξινομητή, καθώς παρουσιάζει υψηλή απόδοση, καλή γενίκευση, δεν παγιδεύεται σε τοπικά βέλτιστα, ενώ ταυτόχρονα επιτυγχάνει την ισορροπία μεταξύ της ακρίβειας και της πολυπλοκότητας του μοντέλου. Μάλιστα για να ξεπεράσουμε τα πρόβληματα των ελλιπών τιμών και της ανισορροπίας των δύο κλάσεων ταξινόμησης, αλλά και για να βελτιώσουμε τη συνολική απόδοση της μεθοδολογίας μας, επεκτείναμε τον υβριδικό αλγόριθμο, ώστε να λειτουργεί σαν μία ensemble-συλλογική τεχνική, συνδυάζοντας οκτώ επί μέρους μοντέλα ταξινόμησης. Τα πειραματικά αποτελέσματα της προτεινόμενης μεθοδολογίας ήταν εξαιρετικά ελπιδοφόρα, καθώς η EnsembleGASVR μεθοδολογία υπερτερεί σημαντικά έναντι άλλων ευρέως γνωστών μεθόδων ταξινόμησης παθογενών μεταλλάξεων. / Single Nucleotide Polymorphisms (SNPs) are the most common form of genetic variations in humans. The number of SNPs that have been found in human genome and affect protein functionality is constantly increasing. Finding matches between SNPs and diseases using experimental techniques, is excessive disadvantageous in terms of time and cost. For this reason, several computational methods have been developed. These methods classify polymorphisms as pathogenic and non-pathogenic. Most of them use classifiers, which take as input a set of structural, functional, sequential and evolutionary features and predict whether a single nucleotide polymorphism is pathogenic or neutral. For training these classifiers use two sets of SNPs. The first one consists of SNPs that have been experimentally proven as pathogenic, whereas the second set consists of SNPs that have been experimentally characterized as benign. These methods differ in the classification methods they deploy and in the features they use as inputs. However, the main problem is the determination of an empirically verified set of features for training. Specifically, different methods suggest different feature sets, without adequately documenting the causes of this differentiation. In addition, the existing methodologies do not tackle efficiently the class imbalance problem between positive and negative training sets and the problem of missing values in the datasets. In this thesis a new hybrid computational intelligence methodology is proposed, that overcomes many of the problems of existing methodologies. The proposed method achieves high classification performance and systematizes the selection of relevant features. In the first phase of this study the polymorphisms were gathered from the available public databases and they were used for training and testing of the machine learning models. Specifically, the positive and negative training and test sets were collected and filtered. They consist of single nucleotide polymorphisms that lead to either pathogenesis or are neutral. For each polymorphism of the two sets, using existing available tools, a wide range of structural, functional, sequential and evolutionary features were calculated. For those features for which there was no available tool, the suitable program (code) was developed in order to compute them. In the second step a new embedded hybrid classification method called EnsembleGASVR is designed and implemented. The method uses an ensemble methodology, based on hybrid combination of Genetic Algorithms and nu-Support Vector Regression (nu-SVR) models. An Adaptive Genetic Algorithm is used to determine the optimal subset of features and the optimal values of the parameters of classifiers. We propose the nu-SVR classifier, since it exhibits high performance, good generalization ability, it is not trapped in local optima and achieves a balance between accuracy and complexity of the model. In order to overcome the problem of missing values and class imbalance, we extended the above algorithm to function as a collective ensemble-technique, combining eight individual classification models. In overall, the method achieves 87.45% accuracy, 71.78% sensitivity and 93.16% specificity. These priliminary results are very promising and shows that EnsembleGASVR methodology significantly outperforms other well-known classification methods for pathogenic mutations.

Les syndromes myélodysplasiques (SMD) sont des hémopathies myéloïdes clonales évoluant vers une leucémie aiguë (LA). Les SMD et LA secondaires, survenant après traitement par chimiothérapie et/ou radiothérapie, ont un pronostic très péjoratif. Cependant seule une partie des sujets exposés aux traitements cytotoxiques développent un SMD secondaire, ce qui suggère une composante génétique dans la susceptibilité individuelle au risque de développer un SMD secondaire. Les objectifs de ce travail ont été d’identifier des polymorphismes génétiques de type SNP (Single Nucleotide Polymorphism) significativement associés à des caractères cliniques et biologiques des SMD tel leur caractère secondaire. Une « puce » à façon a sélectionné 384 SNP de fréquence allélique supérieure à 10 % impliqués dans la réparation de l’ADN, le métabolisme, le transport et la détoxication des xénobiotiques. L’ADN constitutionnel de 65 patients atteints de SMD primaire et secondaire a été recueilli et génotypé pour ces 384 SNP. La seule association significative par test exact de Fisher (p = 0,009 après correction de Benjamini-Hochberg) a été observée pour le caractère secondaire des SMD et la présence de l’allèle variant de MGMT (MéthylGuanine MéthylTransférase) sur deux SNP en déséquilibre de liaison, rs2308321 (Ile143Val) et rs2308327 (Lys178Arg). Nous avons recherché le caractère prédictif de la présence de l’allèle variant de MGMT pour le risque de SMD/LA secondaire chez des patientes ayant reçu un traitement cytotoxique pour un cancer du sein, et ayant développé une LA secondaire. Enfin, nous avons construit des lignées cellulaires stables, isogéniques, exprimant soit la forme sauvage soit la forme variante de MGMT. Les études fonctionnelles par tests de cytotoxicité, co-cultures à long terme et étude des demi-vies des protéines, sous traitement alkylant, montrent respectivement des différences de sensibilité, de prolifération ou de dégradation entre les formes variante et sauvage de MGMT. / Myelodysplastic syndromes (MDS) are clonal hematopoietic disorders evolving toward acute myeloid leukaemia (AML). Therapy-related MDS and AML occur after chemo- and/or radiotherapy for previous cancer and have a very poor outcome. However, only a minimal proportion of patients exposed to anticancer drugs develop secondary MDS, suggesting a genetic component in individual susceptibility. The aim of our study was to identify gene polymorphisms significantly associated with MDS in patients. We have selected 384 SNPs (single nucleotide polymorphisms) with allele frequency >10% in genes involved in DNA repair and drug metabolism and transport. DNA extracts were obtained from blood and cheek samples from a population of 65 MDS patients, and the 384 SNPs were genotyped. We analysed the associations existing between each genotype and several pathological features, especially the treatment-related character of MDS. The Fisher exact test with Benjamini-Hochberg correction for multiple testing was applied for statistical analysis. The only significant association (p = 0.009 after correction) was observed for the treatment-related character of MDS and the presence of a variant allele in MGMT (methylguanine methyltransferase, a gene involved in DNA repair), characterised by two SNPs in complete linkage disequilibrium: rs2308321 (Ile143Val) and rs2308327 (Lys178Arg). An epidemiological study was performed to assess the predictive value of the variant allele in MGMT for the development of secondary acute leukaemia among patients treated for breast cancer. We have constructed isogenic stable cell lines expressing either the wild-type or the variant allele of MGMT. Functional studies (analysis of response to alkylating agents, allele quantification of mixed cultures of wild-type and variant cells and half-lives study of the proteins) show differences in sensitivity to DNA-damaging agents, proliferative capacity and MGMT rate of degradation between the wild-type and the variant MGMT.

Introdução: Fatores genéticos estão entre os determinantes de obesidade, podendo influenciar a resposta a intervenções em estilo de vida. O impacto de polimorfismos de nucleotídeo único (SNPs) na resposta de biomarcadores a intervenções não é claro. Objetivo: Este estudo examinou as associações de seis SNPs FTO T/A, PPAR Pro12Ala, Apo A1 -75G/A, TNF- -308G/A, IL-6 - 174G/C e AdipoQ 45T/G com mudanças induzidas por uma intervenção em amostra de brasileiros de risco cardiometabólico. Métodos: Em um programa de nove meses de orientações em hábitos alimentares e atividade física, 180 indivíduos com prediabetes ou síndrome metabólica foram genotipados e agrupados segundo a presença do alelo variante de cada SNP e comparados quanto a variáveis antropométricas, metabólicas e inflamatórias. Resultados: A intervenção resultou em redução do consumo calórico, aumento da atividade física, melhora na antropometria e outros biomarcadores. Estratificando pelos SNPs, os principais achados estão contidos em dois artigos. Artigo 1: Houve melhor resposta do perfil glicêmico após a intervenção nos portadores do alelo variante do SNP TNF -308 G/A. Observou-se melhora das variáveis lipídicas nos portadores do alelo variante do SNP IL-6 -174 G/C, enquanto que aqueles com o genótipo referência obtiveram melhora no metabolismo da glicose. Carreadores do SNP AdipoQ 45T/G não obtiveram melhora no perfil lipídico nem no glicêmico.Artigo 2: O alelo variante do FTO T/A associou-se a melhores perfis 9 inflamatório e glicêmico em resposta à intervenção. Portadores do alelo variante do SNP PPAR Pro12Ala obtiveram melhora na pressão arterial, enquanto que indivíduos com o genótipo referência melhoraram o metabolismo lipídico. Carreadores do alelo variante do SNP Apo A1 -75G/A apresentaram melhora no perfil lipídico que, após ajuste para medicação, não se manteve significante. Conclusões: SNPs relacionados à obesidade e comorbidades podem influenciar a resposta de marcadores metabólicos e inflamatórios a intervenções em hábitos de vida em brasileiros. O SNP TNF -308G/A parece favorecer um melhor perfil glicêmico. O SNP IL-6 -174G/C pode conferir efeito benéfico no perfil lipídico, mas não na glicemia. O SNP AdipoQ 45T/G compromete a resposta à intervenção em indivíduos de risco cardiometabólico no nosso meio. O SNP FTO T/A pode favorecer a resposta do metabolismo da glicose e a atenuação da inflamação. O SNP PPAR Pro12Ala pode ter impacto benéfico na pressão arterial, mas não no metabolismo lipídico. Em contraste com a literatura, o SNP Apo A1 -75G/A não parece influenciar resposta dos lípides à intervenção. Mais estudos envolvendo estes SNPs são necessários para possível direcionamento de intervenções a subgrupos específicos de indivíduos de risco. / Introduction: Genetic factors are one of the determinants of obesity and may influence the response to interventions. The impact of single nucleotide polymorphisms (SNPs) in weight loss and inflammatory response to interventions is not clear. Objective: This study examined associations of six polymorphisms FTO T/A, PPAR Pro12Ala, Apo A1 -75G/A, TNF- -308G/A, IL-6 -174G/C and AdipoQ 45T/G with changes induced by lifestyle intervention in Brazilians at cardiometabolic risk. Methods: In a 9-month intervention on diet and physical activity, 180 individuals with prediabetes or metabolic syndrome were genotyped and compared according the presence of variant allele of the SNPs and antrophometric, metabolic and inflammatory variables. Results: The intervention resulted in lower energy intake and greater total physical activity as well as improvement in anthropometry and several biomarkers. Stratified by SNPs, the main findings are covered in two articles. Article 1: Variant allele carriers of TNF -308 G/A SNP decreased plasma glucose after intervention. Lipid profile improved after intervention in variant allele carriers of IL-6 -174 G/C, while individuals with reference genotype had better plasma glucose response. Variant allele carriers of AdipoQ 45T/G did not improve lipid and glycemic profile. Article 2: Only variant allele carriers of FTO T/A decreased fasting plasma glucose and C-reactive protein concentration after intervention. Blood pressure reduced after intervention in variant allele carriers of the PPAR Pro12Ala, while the reference genotype increased Apo A1. Apparent favorable response of lipid profile to intervention in variant allele carriers of Apo A1 -75G/A was not maintained after adjustments for lipid-lowering medication. Conclusions: SNPs associated with obesity and comorbidities may influence the response of metabolic and inflammatory markers after lifestyle intervention. The TNF -308G/A may predispose a better response of glucose metabolism. The IL-6 -174 G/C SNP may confer a beneficial effect on lipid profile but not in glucose metabolism. Our findings reinforce unfavorable effects of the AdipoQ 45T/G SNP in lipid and glucose metabolism after lifestyle intervention in Brazilians at cardiometabolic risk. FTO T/A SNP induces a favorable impact on inflammatory status and glucose metabolism. The reference genotype of PPAR Pro12Ala seems to favor a better lipid profile, while the variant allele to decrease blood pressure. In contrast to literature, our data did not support benefits on lipid profile of the variant allele of Apo A1 -75G/A SNP. Further studies of these SNPs are needed to direct interventions to specific subgroups of at-risk individuals.

Introdução: no contexto das doenças crônicas não transmissíveis (DCNT), vários estudos associam a presença de determinados polimorfismos de nucleotídeo único (SNP) ao risco de desfechos metabólicos, como a obesidade e a dislipidemia. Objetivo: avaliar a presença de SNP associados à adiposidade corporal e ao metabolismo lipídico sobre o índice de massa corporal (IMC), o consumo alimentar, o perfil lipídico e a concentração plasmática de biomarcadores inflamatórios em indivíduos adultos participantes do estudo de base populacional (ISA-Capital). Métodos: 244 indivíduos adultos de ambos os gêneros (idade entre 20-59 anos) participaram do estudo, no qual foram realizadas as avaliações antropométricas e do consumo alimentar por meio do questionário de 24 horas (R24h) e a coleta de sangue para avaliação da concentração de biomarcadores inflamatórios. O índice de qualidade da dieta revisado (IQDR) foi utilizado no estudo. Foi realizada a genotipagem de oito genes e 13 SNP (FTO rs9939609, rs8050136, rs9930506; LDLR rs688, rs5925; APOB rs693, rs1367117, APOA5 rs662799; LIPC rs2070895, rs1800588; FADS1 rs174546; MYRF rs174537 e ELOVL2 rs953413) pelo sistema TaqMan Open Array. A partir dos resultados da genotipagem, foi elaborado um escore de risco genético (ERG). Resultados: foi verificada associação negativa entre o consumo de vegetais totais (P=0,004) e vegetais verdes-escuros e alaranjados e leguminosas (P=0,002) e leite e derivados (P=0,009) com o IMC. O consumo de cereais totais (P=0,029) e de carboidratos totais (P=0,011) mostrou interação negativa para o ERG, enquanto o consumo de carnes, ovos e leguminosas teve interação positiva (P=0,028) ao influenciar o IMC. As concentrações plasmáticas de HDL-c tiveram associação negativa (P=0,026) com o IQDR e associação positiva (P=0,007) com o componente Gord_AA (valor energético proveniente da gordura sólida, álcool e açúcar de adição). Foi encontrada interação significativa entre o consumo de óleos (lipídios insaturados) (P=0,019) e de Gord_AA (P<0,001). Concentrações plasmáticas de HDL-c e de LDL-c são significativamente menores nos carreadores do alelo variante T para os SNP que correspondem às atividades das enzimas dessaturases (FADS1 e MYRF). As concentrações do ácido oleico foram maiores nos indivíduos com genótipo CT/TT no gene da FADS1 e AG/GG no gene da ELOVL2 em relação aos genótipos selvagens. Apenas os carreadores do alelo T tanto em FADS1 quanto em MYRF tiveram concentrações de ácido linoleico e linolênico superiores em relação aos genótipos selvagens. Por outro lado, as concentrações de ácido araquidônico, de ácido docosapentaenoico (DPA), de ácidos graxos saturados e de poli-insaturados totais foram menores nos indivíduos carreadores dos alelos variantes para os três polimorfismos avaliados. O conteúdo de ácido eicosapentaenoico (EPA) foi menor nos carreadores do alelo T dos genes FADS1 e MYRF, enquanto o conteúdo de ácido esteárico foi menor apenas nos carreadores do alelo G do gene ELOVL2, sendo que nestes indivíduos as concentrações plasmáticas do conteúdo total de ácidos monoinsaturados foram significativamente maiores quando comparados ao genótipo selvagem (AA). Observou-se também que a atividade estimada da enzima estearoil CoA dessaturase (SDC_18) é maior nos genótipos CT/TT da FADS1 e da ELOVL2. Contudo, a estimativa da atividade da enzima delta-5 dessaturase (D5D) foi estatisticamente menor na presença do alelo polimórfico para os três SNP estudados (FADS1 CT/TT; MYRF GT/TT; ELOVL2 AG/GG). Apenas para os carreadores do alelo T da FADS1 (CT/TT), a estimativa da atividade da enzima delta-6 dessaturase (D6D) foi estatisticamente menor em relação ao genótipo selvagem CC. Conclusões: a presença dos SNP estudados na população de São Paulo mostraram associações em relação ao aumento do risco para adiposidade corporal e dislipidemias, podendo também apresentar associações com a qualidade da dieta dos participantes. Nesse sentido, a aplicação do IQDR junto com o ERG pode ser uma ferramenta útil na identificação de associações entre gene-nutriente e o impacto nas doenças metabólicas. / Introduction: excess weight and changes in lipid profile may be associated with environmental factors, such as diet quality, and non-modifiable factors, such as genetic inheritance. In the context of chronic noncommunicable diseases (NCDs), several studies associate the presence of certain single nucleotide polymorphisms (SNP) to the risk of metabolic outcomes, such as obesity and dyslipidemia. Objective: to evaluate the presence of SNP associated with body fat and lipid metabolism on body mass index (BMI), dietary intake, lipid profile and plasma concentration of inflammatory biomarkers in adult individuals participating in the population-based study (ISA-Capital). Methods: 244 adult subjects of both genders (ages 20-59 years) participated in the study, in which the anthropometric traits were evaluated, and food consumption evaluations were performed using the 24- hour questionnaire (R24h) and blood collection for evaluation of concentration of inflammatory biomarkers. The Brazilian healthy eating index revised (BHEIR) was used in the study. Genotyping of eight genes and 13 SNP (FTO rs9939609, rs8050136, rs9930506; LDLR rs688, rs5925; APOB rs693, rs1367117, APOA5 rs662799; LIPC rs2070895, rs1800588; FADS1 rs174546; MYRF rs174537 and ELOVL2 rs953413) were performed by the TaqMan Open Array system. From the results of the genotyping, a genetic risk score (GRS) was elaborated. Results: there was a negative association between the consumption of total vegetables (p = 0.004) and dark green and orange vegetables and legumes (p = 0.002), milk and dairy (p=0.009) with BMI. Total cereal consumption (p = 0.029) and total carbohydrates (p = 0.011) showed negative interaction for GRS (categories 3 to 5), while meat, egg and legume consumption had a positive interaction (p = 0.028) influence BMI. Of the BHEIR components, plasma HDL-c concentrations were negatively associated (p = 0.026) with the BHEIR and positive association (p = 0.007) with the SoFAAS component (energy value from solid fat, alcohol and addition sugar). Significant interaction was observed between the consumption of oils (unsaturated lipids) (p = 0.019) and SoFAAS (p <0.001). About the enzymes associated with biosynthesis of omega 3 and polyunsaturated fatty acids 6, plasma HDL-c and LDL-c plasma concentrations are significantly lower in carriers of the T variant allele for SNP that correspond to the activities of desaturases (FADS1 and MYRF). Oleic acid concentrations were statistically higher in individuals with CT / TT genotypes in the FADS1 and AG / GG gene in the ELOVL2 gene in relation to wild genotypes. In addition, only the T allele carriers in both FADS1 and MYRF had higher concentrations of linoleic and linolenic acid than wild genotypes. The concentrations of arachidonic acid, docosapentaenoic acid (DPA), saturated fatty acids and total polyunsaturated fatty acids were lower in the carriers of the variant alleles for the three evaluated polymorphisms. The eicosapentaenoic acid (EPA) content was lower in the T allele carriers of the FADS1 and MYRF genes, while the stearic acid content was lower only in the G allele carriers of the ELOVL2 gene, where in these individuals the plasma concentrations of the total content of monounsaturated acids were significantly higher when compared to the wild-type (AA) genotype. It was also observed that the estimated activity of the stearoyl CoA desaturase enzyme (SDC_18) is higher in the CT / TT genotypes of FADS1 and ELOVL2. However, the estimate of the activity of the enzyme delta-5 desaturase (D5D) was statistically lower in the presence of the polymorphic allele for the three SNP studied (FADS1 CT/ TT; MYRF GT / TT; ELOVL2 AG / GG). Only for the FADS1 (CT / TT) allele carriers, the estimate of the activity of the enzyme delta-6 desaturase (D6D) was statistically lower than the wild-type CC genotype. Conclusions: the presence of SNP studied in the population of São Paulo showed associations in relation to the increased risk for body fatness and dyslipidemia and may also present associations with the quality of the participants\' diet. In this sense, the application of BHEIR together with GRS may be a useful tool in the identification of genenutrient associations and the impact on metabolic diseases.

Introdução: Fatores genéticos estão entre os determinantes de obesidade, podendo influenciar a resposta a intervenções em estilo de vida. O impacto de polimorfismos de nucleotídeo único (SNPs) na resposta de biomarcadores a intervenções não é claro. Objetivo: Este estudo examinou as associações de seis SNPs FTO T/A, PPAR Pro12Ala, Apo A1 -75G/A, TNF- -308G/A, IL-6 - 174G/C e AdipoQ 45T/G com mudanças induzidas por uma intervenção em amostra de brasileiros de risco cardiometabólico. Métodos: Em um programa de nove meses de orientações em hábitos alimentares e atividade física, 180 indivíduos com prediabetes ou síndrome metabólica foram genotipados e agrupados segundo a presença do alelo variante de cada SNP e comparados quanto a variáveis antropométricas, metabólicas e inflamatórias. Resultados: A intervenção resultou em redução do consumo calórico, aumento da atividade física, melhora na antropometria e outros biomarcadores. Estratificando pelos SNPs, os principais achados estão contidos em dois artigos. Artigo 1: Houve melhor resposta do perfil glicêmico após a intervenção nos portadores do alelo variante do SNP TNF -308 G/A. Observou-se melhora das variáveis lipídicas nos portadores do alelo variante do SNP IL-6 -174 G/C, enquanto que aqueles com o genótipo referência obtiveram melhora no metabolismo da glicose. Carreadores do SNP AdipoQ 45T/G não obtiveram melhora no perfil lipídico nem no glicêmico.Artigo 2: O alelo variante do FTO T/A associou-se a melhores perfis 9 inflamatório e glicêmico em resposta à intervenção. Portadores do alelo variante do SNP PPAR Pro12Ala obtiveram melhora na pressão arterial, enquanto que indivíduos com o genótipo referência melhoraram o metabolismo lipídico. Carreadores do alelo variante do SNP Apo A1 -75G/A apresentaram melhora no perfil lipídico que, após ajuste para medicação, não se manteve significante. Conclusões: SNPs relacionados à obesidade e comorbidades podem influenciar a resposta de marcadores metabólicos e inflamatórios a intervenções em hábitos de vida em brasileiros. O SNP TNF -308G/A parece favorecer um melhor perfil glicêmico. O SNP IL-6 -174G/C pode conferir efeito benéfico no perfil lipídico, mas não na glicemia. O SNP AdipoQ 45T/G compromete a resposta à intervenção em indivíduos de risco cardiometabólico no nosso meio. O SNP FTO T/A pode favorecer a resposta do metabolismo da glicose e a atenuação da inflamação. O SNP PPAR Pro12Ala pode ter impacto benéfico na pressão arterial, mas não no metabolismo lipídico. Em contraste com a literatura, o SNP Apo A1 -75G/A não parece influenciar resposta dos lípides à intervenção. Mais estudos envolvendo estes SNPs são necessários para possível direcionamento de intervenções a subgrupos específicos de indivíduos de risco. / Introduction: Genetic factors are one of the determinants of obesity and may influence the response to interventions. The impact of single nucleotide polymorphisms (SNPs) in weight loss and inflammatory response to interventions is not clear. Objective: This study examined associations of six polymorphisms FTO T/A, PPAR Pro12Ala, Apo A1 -75G/A, TNF- -308G/A, IL-6 -174G/C and AdipoQ 45T/G with changes induced by lifestyle intervention in Brazilians at cardiometabolic risk. Methods: In a 9-month intervention on diet and physical activity, 180 individuals with prediabetes or metabolic syndrome were genotyped and compared according the presence of variant allele of the SNPs and antrophometric, metabolic and inflammatory variables. Results: The intervention resulted in lower energy intake and greater total physical activity as well as improvement in anthropometry and several biomarkers. Stratified by SNPs, the main findings are covered in two articles. Article 1: Variant allele carriers of TNF -308 G/A SNP decreased plasma glucose after intervention. Lipid profile improved after intervention in variant allele carriers of IL-6 -174 G/C, while individuals with reference genotype had better plasma glucose response. Variant allele carriers of AdipoQ 45T/G did not improve lipid and glycemic profile. Article 2: Only variant allele carriers of FTO T/A decreased fasting plasma glucose and C-reactive protein concentration after intervention. Blood pressure reduced after intervention in variant allele carriers of the PPAR Pro12Ala, while the reference genotype increased Apo A1. Apparent favorable response of lipid profile to intervention in variant allele carriers of Apo A1 -75G/A was not maintained after adjustments for lipid-lowering medication. Conclusions: SNPs associated with obesity and comorbidities may influence the response of metabolic and inflammatory markers after lifestyle intervention. The TNF -308G/A may predispose a better response of glucose metabolism. The IL-6 -174 G/C SNP may confer a beneficial effect on lipid profile but not in glucose metabolism. Our findings reinforce unfavorable effects of the AdipoQ 45T/G SNP in lipid and glucose metabolism after lifestyle intervention in Brazilians at cardiometabolic risk. FTO T/A SNP induces a favorable impact on inflammatory status and glucose metabolism. The reference genotype of PPAR Pro12Ala seems to favor a better lipid profile, while the variant allele to decrease blood pressure. In contrast to literature, our data did not support benefits on lipid profile of the variant allele of Apo A1 -75G/A SNP. Further studies of these SNPs are needed to direct interventions to specific subgroups of at-risk individuals.

Introdução: no contexto das doenças crônicas não transmissíveis (DCNT), vários estudos associam a presença de determinados polimorfismos de nucleotídeo único (SNP) ao risco de desfechos metabólicos, como a obesidade e a dislipidemia. Objetivo: avaliar a presença de SNP associados à adiposidade corporal e ao metabolismo lipídico sobre o índice de massa corporal (IMC), o consumo alimentar, o perfil lipídico e a concentração plasmática de biomarcadores inflamatórios em indivíduos adultos participantes do estudo de base populacional (ISA-Capital). Métodos: 244 indivíduos adultos de ambos os gêneros (idade entre 20-59 anos) participaram do estudo, no qual foram realizadas as avaliações antropométricas e do consumo alimentar por meio do questionário de 24 horas (R24h) e a coleta de sangue para avaliação da concentração de biomarcadores inflamatórios. O índice de qualidade da dieta revisado (IQDR) foi utilizado no estudo. Foi realizada a genotipagem de oito genes e 13 SNP (FTO rs9939609, rs8050136, rs9930506; LDLR rs688, rs5925; APOB rs693, rs1367117, APOA5 rs662799; LIPC rs2070895, rs1800588; FADS1 rs174546; MYRF rs174537 e ELOVL2 rs953413) pelo sistema TaqMan Open Array. A partir dos resultados da genotipagem, foi elaborado um escore de risco genético (ERG). Resultados: foi verificada associação negativa entre o consumo de vegetais totais (P=0,004) e vegetais verdes-escuros e alaranjados e leguminosas (P=0,002) e leite e derivados (P=0,009) com o IMC. O consumo de cereais totais (P=0,029) e de carboidratos totais (P=0,011) mostrou interação negativa para o ERG, enquanto o consumo de carnes, ovos e leguminosas teve interação positiva (P=0,028) ao influenciar o IMC. As concentrações plasmáticas de HDL-c tiveram associação negativa (P=0,026) com o IQDR e associação positiva (P=0,007) com o componente Gord_AA (valor energético proveniente da gordura sólida, álcool e açúcar de adição). Foi encontrada interação significativa entre o consumo de óleos (lipídios insaturados) (P=0,019) e de Gord_AA (P<0,001). Concentrações plasmáticas de HDL-c e de LDL-c são significativamente menores nos carreadores do alelo variante T para os SNP que correspondem às atividades das enzimas dessaturases (FADS1 e MYRF). As concentrações do ácido oleico foram maiores nos indivíduos com genótipo CT/TT no gene da FADS1 e AG/GG no gene da ELOVL2 em relação aos genótipos selvagens. Apenas os carreadores do alelo T tanto em FADS1 quanto em MYRF tiveram concentrações de ácido linoleico e linolênico superiores em relação aos genótipos selvagens. Por outro lado, as concentrações de ácido araquidônico, de ácido docosapentaenoico (DPA), de ácidos graxos saturados e de poli-insaturados totais foram menores nos indivíduos carreadores dos alelos variantes para os três polimorfismos avaliados. O conteúdo de ácido eicosapentaenoico (EPA) foi menor nos carreadores do alelo T dos genes FADS1 e MYRF, enquanto o conteúdo de ácido esteárico foi menor apenas nos carreadores do alelo G do gene ELOVL2, sendo que nestes indivíduos as concentrações plasmáticas do conteúdo total de ácidos monoinsaturados foram significativamente maiores quando comparados ao genótipo selvagem (AA). Observou-se também que a atividade estimada da enzima estearoil CoA dessaturase (SDC_18) é maior nos genótipos CT/TT da FADS1 e da ELOVL2. Contudo, a estimativa da atividade da enzima delta-5 dessaturase (D5D) foi estatisticamente menor na presença do alelo polimórfico para os três SNP estudados (FADS1 CT/TT; MYRF GT/TT; ELOVL2 AG/GG). Apenas para os carreadores do alelo T da FADS1 (CT/TT), a estimativa da atividade da enzima delta-6 dessaturase (D6D) foi estatisticamente menor em relação ao genótipo selvagem CC. Conclusões: a presença dos SNP estudados na população de São Paulo mostraram associações em relação ao aumento do risco para adiposidade corporal e dislipidemias, podendo também apresentar associações com a qualidade da dieta dos participantes. Nesse sentido, a aplicação do IQDR junto com o ERG pode ser uma ferramenta útil na identificação de associações entre gene-nutriente e o impacto nas doenças metabólicas. / Introduction: excess weight and changes in lipid profile may be associated with environmental factors, such as diet quality, and non-modifiable factors, such as genetic inheritance. In the context of chronic noncommunicable diseases (NCDs), several studies associate the presence of certain single nucleotide polymorphisms (SNP) to the risk of metabolic outcomes, such as obesity and dyslipidemia. Objective: to evaluate the presence of SNP associated with body fat and lipid metabolism on body mass index (BMI), dietary intake, lipid profile and plasma concentration of inflammatory biomarkers in adult individuals participating in the population-based study (ISA-Capital). Methods: 244 adult subjects of both genders (ages 20-59 years) participated in the study, in which the anthropometric traits were evaluated, and food consumption evaluations were performed using the 24- hour questionnaire (R24h) and blood collection for evaluation of concentration of inflammatory biomarkers. The Brazilian healthy eating index revised (BHEIR) was used in the study. Genotyping of eight genes and 13 SNP (FTO rs9939609, rs8050136, rs9930506; LDLR rs688, rs5925; APOB rs693, rs1367117, APOA5 rs662799; LIPC rs2070895, rs1800588; FADS1 rs174546; MYRF rs174537 and ELOVL2 rs953413) were performed by the TaqMan Open Array system. From the results of the genotyping, a genetic risk score (GRS) was elaborated. Results: there was a negative association between the consumption of total vegetables (p = 0.004) and dark green and orange vegetables and legumes (p = 0.002), milk and dairy (p=0.009) with BMI. Total cereal consumption (p = 0.029) and total carbohydrates (p = 0.011) showed negative interaction for GRS (categories 3 to 5), while meat, egg and legume consumption had a positive interaction (p = 0.028) influence BMI. Of the BHEIR components, plasma HDL-c concentrations were negatively associated (p = 0.026) with the BHEIR and positive association (p = 0.007) with the SoFAAS component (energy value from solid fat, alcohol and addition sugar). Significant interaction was observed between the consumption of oils (unsaturated lipids) (p = 0.019) and SoFAAS (p <0.001). About the enzymes associated with biosynthesis of omega 3 and polyunsaturated fatty acids 6, plasma HDL-c and LDL-c plasma concentrations are significantly lower in carriers of the T variant allele for SNP that correspond to the activities of desaturases (FADS1 and MYRF). Oleic acid concentrations were statistically higher in individuals with CT / TT genotypes in the FADS1 and AG / GG gene in the ELOVL2 gene in relation to wild genotypes. In addition, only the T allele carriers in both FADS1 and MYRF had higher concentrations of linoleic and linolenic acid than wild genotypes. The concentrations of arachidonic acid, docosapentaenoic acid (DPA), saturated fatty acids and total polyunsaturated fatty acids were lower in the carriers of the variant alleles for the three evaluated polymorphisms. The eicosapentaenoic acid (EPA) content was lower in the T allele carriers of the FADS1 and MYRF genes, while the stearic acid content was lower only in the G allele carriers of the ELOVL2 gene, where in these individuals the plasma concentrations of the total content of monounsaturated acids were significantly higher when compared to the wild-type (AA) genotype. It was also observed that the estimated activity of the stearoyl CoA desaturase enzyme (SDC_18) is higher in the CT / TT genotypes of FADS1 and ELOVL2. However, the estimate of the activity of the enzyme delta-5 desaturase (D5D) was statistically lower in the presence of the polymorphic allele for the three SNP studied (FADS1 CT/ TT; MYRF GT / TT; ELOVL2 AG / GG). Only for the FADS1 (CT / TT) allele carriers, the estimate of the activity of the enzyme delta-6 desaturase (D6D) was statistically lower than the wild-type CC genotype. Conclusions: the presence of SNP studied in the population of São Paulo showed associations in relation to the increased risk for body fatness and dyslipidemia and may also present associations with the quality of the participants\' diet. In this sense, the application of BHEIR together with GRS may be a useful tool in the identification of genenutrient associations and the impact on metabolic diseases.

Magister Scientiae - MSc / Initially, a pilot study was carried out in order to reconstruct the major paternal and maternal lineages of the Muslim population living in the Cape metropolitan area. The Study has shown the ability of molecular genetic tools to give insight into the origins and history of local communities. The study was also used as a point of reference for the Strand Muslim Community project. Genetic variations of the Y-chromosome and mitochondrial DNA for the pilot study were analyzed using the RFLP technique. The SNaPshot mini-sequencing technique was used to genotype single nucleotide polymorphisms (SNP) on the Y-chromosome and mitochondrial DNA in 115 males from the Strand Muslim community. / South Africa