Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Haliotis midae (commonly referred to as perlemoen) is the only one of five endemic species in South Africa that is commercially valued both locally and internationally. Unfortunately, natural perlemoen populations have become a dwindling resource due to commercial exploitation, poaching and the influx of natural threats, such as the West Coast rock lobster, Jasus lalandii. To preserve the natural diversity and sustainability of natural populations as well as commercial stocks, genetic management and improvement of perlemoen is critical. Genetic management requires the utilisation of molecular markers, which aid in the construction of linkage maps and the identification of quantitative trait loci (QTL) associated with economically significant traits. This will allow improvement of commercial stock management in terms of broodstock selection as well as provide valuable insight into natural population dynamics. Single Nucleotide Polymorphisms (SNPs) were selected as the marker of choice due to their successful employment as molecular markers and their wide distribution and abundance within the genomes of various marine species. This study focuses on the characterisation of novel SNPs from transcript sequences generated by Next Generation Sequencing technology. Approximately 40% of the transcripts facilitated the isolation of 105 putative markers, indicating a SNP frequency of ~1% within the H. midae genome. A subset of 24 markers, in addition to 24 previously developed markers, was characterised using the Illumina GoldenGate genotyping assay with the VeraCode technology, a medium to high-throughput genotyping technology. This is the first reported medium- to highthroughput characterisation of SNPs in H. midae. The selected markers were used to determine the efficiency and overall success rate of the GoldenGate platform. Marker characterisation was completed in both natural and commercial populations to determine the utility of these markers for genetic diversity and population structure inference. An 85% genotyping success rate was achieved with the platform. Statistical analysis indicated that the markers developed in this study are suitable for applications including population genetic structure inference, genetic diversity estimation and possibly other downstream applications such as linkage mapping. These markers are considered to be invaluable for future work regarding the genetic management and conservation of H. midae. / AFRIKAANSE OPSOMMING: Haliotis midae (ook bekend as perlemoen) is die enigste van vyf inheemse spesies in Suid-Afrika wat noemenswaardige kommersiële waarde toon plaaslik sowel as internasionaal. Ongelukkig het kommersiële uitbuiting, wildstropery en natuurlike bedreiging (bv. die Weskus kreef Jasus lalandii), wilde perlemoen populasies noemenswaardig verminder. Dus, om natuurlike diversiteit en die voortbestaan van beide wilde en kommersiële populasies te beskerm, is genetiese bestuur en verbetering absoluut noodsaaklik. Genetiese bestuur vereis die gebruik van molekulêre merkers as ’n hulpmiddel in die opstellingvan koppelingskaarte, en die identifisering van die relevante kwantitatiewe eienskap loki (QTL) tipies geassosieer met ekonomies belangrike eienskappe. Die laasgenoemde beoog om kommersiële voorraad bestuur te verbeter, kragtens deur broeidier seleksie sowel as om insig te verskaf m.b.t. wilde bevolking dinamika. Enkel Nukleotied Polimorfismes (SNPs) is gekies as die toepaslike merker vanweë die omvattende toepaslikheid van hierdie merkers binne die genome van verskeie mariene spesies. Hierdie studie fokus op die karakterisering van nuwe SNPs vanuit transkript volgordes ontwikkel deur middel van Volgende Generasie Volgordebepaling (“Next Generation Sequencing”). ’n Beraamde 40% van transkripte het gelei tot die ontwikkeling van 105 potensiëlemerkers, aanduidend van ’n SNP frekwensie van ~1% binne die H. midae genoom. ’n Sub-versameling van 24 merkers, tesame met 24 bestaande merkers, is gekarakteriseer deur die Illumina GoldenGate genotiperings toets met die VeraCode tegnologie, ’n medium tot hoë deurvloei genotiperingstegnologie. Hierdie is die eerste berig van medium tot hoë deurvloei karakterisering van SNPs in H. midae. Die geselekteerde merkers is gebruik om die doeltreffendheid van die GoldenGate platform te bepaal. Merker karakterisering is uitgevoer in beide wilde en kommersiële bevolkings om die effektiewe bruikbaarheid van hierdie merkers m.b.t. genetiese diversiteit, en bevolking struktuur bepaling, te ondersoek. Die platform het ’n 85% genotiperingsukses syfer getoon. Statistiese analise dui daarop dat merkers ontwikkel tydens hierdie studie toepaslik is vir bevolking genetiese struktuur bepaling, genetiese diversiteitberaming en moontlik ook genetiese koppelingskartering. Hierdie merkers word bestempel as onmisbaar vir toekomstige navorsing in genetiese bestuur en bewaring van H. midae.

Genome wide association studies (GWAS) have identified the H1 microtubule associated protein tau (MAPT) haplotype single nucleotide polymorphisms as leading common risk variants for Parkinson's disease (PD), progressive supranuclear palsy (PSP) and corticobasal degeneration (CBD). Gene expression studies have demonstrated haplotype-specific increases in expression of MAPT exon 3-containing transcripts from the protective H2 allele compared to the H1. The difference in alternative splicing between the haplotypes likely contributes risk or protection in the absence of protein coding variants. Here, we investigate the regulation of MAPT exon 3 alternative splicing by common, risk-associated, non-coding, haplotype-specific single nucleotide polymorphisms (SNPs) through a combination of in silico analysis of the MAPT locus, in vitro gene expression and biochemistry studies. Comparative sequence analysis of whole-locus genomic H1 and H2 MAPT (143 kb) vectors showed they capture over 86% of the MAPT sequence diversity. We generated and expressed haplotype-hybrid H1 and H2 MAPT vectors in a human neuroblastoma cell culture model and demonstrated that a functional SNP rs17651213 near the exon 3 5' splice site regulates exon 3 inclusion in a haplotype-specific manner. Using RNA-electrophoretic mobility shift assays (RNA-EMSA), we showed differential RNA-protein complex formation at the H1 and H2 sequence variants of SNP rs17651213. We further identified candidate trans-acting splicing factors interacting with functional SNP rs17651213 sequences by RNA-protein pull-down experiment and mass spectrometry. Finally, gene knockdown of candidate splice factors identified by mass spectrometry demonstrated a role for hnRNP F and hnRNP Q in the haplotype-specific regulation of exon 3 inclusion. In this study, we have dissected the MAPT locus to identify sequences regulating the allele-specific alternative splicing of exon 3 and provided mechanistic insights into how common non-coding H1/H2 MAPT haplotype-specific SNPs may contribute to the risk/protection of neurodegeneration at a complex genetic locus.

Made available in DSpace on 2016-06-02T20:20:37Z (GMT). No. of bitstreams: 1 6268.pdf: 2312191 bytes, checksum: f16c107fdc91ed439efa845247c55dc4 (MD5) Previous issue date: 2014-06-30 / Financiadora de Estudos e Projetos / This thesis has been divided into three chapters for better understanding of the experiments. The first chapter refers to a brief Literature Review, with the main concepts and justifications for this work. The second chapter discusses the strategy of positional and functional candidate genes for traits of feed efficiency in Nelore cattle, and the third chapter presents a genome-wide association study for feed efficiency traits in the same population. Feed efficiency is an important production trait in beef cattle production systems. The aim of this study was to identify genes/QTLs associated with feed efficiency traits in Nelore cattle genotypes using the Illumina BeadChip BovineHD (770K) of 593 Nelore steers. The traits analyzed were: average daily weight gain (ADG), dry matter intake (DMI), feed conversion (FC), feed efficiency (FE), residual feed intake (RFI), efficiency of maintenance (EM), efficiency gain (EG), partial efficiency of growth (PEG) and relative growth rate (RGR). The first strategy discussed in this work, using candidate genes, investigated the association of Neurogenic differentiaton 1 (NEUROD1), Kv channel interacting protein 4 (KCNIP4), and Vascular endothelial growth factor C (VEGFC) genes, with production traits in the same population. Our results are in according to literature that indicate NEUROD1, KCNIP4 and VEGFC as candidate genes for feed efficiency; and this study is the first to suggest the NEUROD1 gene as a candidate for gene backfat thickness, body weigth and metabolic weight in Nelore cattle. In the genome-wide association study some QTL regions identified in this study minimally overlapped with QTL regions previously reported for feed efficiency in Bos Taurus cattle, and harbor genes with biological functions related to metabolic processes, lipid and protein metabolism, energy generation and growth. A comparison with published results indicates that different QTL and genes may be involved in the control of feed efficiency in this population of Nelore cattle. The validation of the results obtained in this work in independent populations may contribute to elucidation of the mechanisms will involved in the variation of feed consumption and specific improvement in Nelore programs. / Esta tese foi dividida em três capítulos para melhor compreensão dos experimentos realizados. O primeiro capítulo refere-se a uma breve Revisão de Literatura, com os principais conceitos e justificativas para a realização deste trabalho. O segundo capítulo aborda a estratégia de genes candidatos posicionais e funcionais para características de eficiência alimentar na raça Nelore e o terceiro capítulo apresenta um estudo de associação genômica ampla para características de eficiência alimentar na mesma população. A eficiência alimentar é uma característica produtiva importante em sistemas de produção de bovinos de corte. O objetivo deste estudo foi identificar genes/QTLs associados com características de eficiência alimentar em bovinos da raça Nelore utilizando genótipos do Illumina BovineHD BeadChip (770K). As características analisadas foram: ganho de peso médio diário (GMD), consumo de matéria seca (CMS), conversão alimentar (CA), eficiência alimentar (EA), consumo alimentar residual (CAR), eficiência da mantença (EM), eficiência de ganho (EG), eficiência parcial de crescimento (EPC) e taxa de crescimento relativo (TCR). A primeira estratégia abordada neste trabalho, a de genes candidatos, investigou a associação dos genes Neurogenic differentiaton 1 (NEUROD1), Kv channel interacting protein 4 (KCNIP4), e Vascular endothelial growth factor C (VEGFC), com características produtivas nesta mesma população. Nossos resultados corroboram com resultados da literatura que indicam os genes KCNIP4 e VEGFC como genes candidatos para eficiência alimentar; e este estudo é o primeiro a sugerir o gene NEUROD1 como gene candidato para espessura de gordura subcutânea, peso médio e peso metabólico em bovinos da raça Nelore. No estudo de associação genômica, algumas regiões de QTL identificadas foram sobrepostas minimamente com regiões de QTL relatadas anteriormente para eficiência alimentar em bovinos Bos taurus, e abrigam genes com funções biológicas relacionadas com processos metabólicos, metabolismo lipídico e proteíco, geração de energia e crescimento. A comparação com os resultados publicados indicam que diferentes QTL e genes podem estar envolvidos no controle da eficiência alimentar nesta população de bovinos da raça Nelore. A validação dos resultados obtidos neste trabalho em populações independentes pode contribuir para elucidação dos mecanimos envolvidos na variação do consumo alimentar e para programas de melhoramento específicos para a raça Nelore.

Submitted by Thaysa Buss Carvalho (thata_carv@hotmail.com) on 2018-03-06T20:09:50Z No. of bitstreams: 1 Dissertação (versão final - Pós).pdf: 3710550 bytes, checksum: bab583912c5fbf652bf225a988df911b (MD5) / Approved for entry into archive by ROSANGELA APARECIDA LOBO null (rosangelalobo@btu.unesp.br) on 2018-03-08T18:01:27Z (GMT) No. of bitstreams: 1 carvalho_tb_me_bot.pdf: 3710550 bytes, checksum: bab583912c5fbf652bf225a988df911b (MD5) / Made available in DSpace on 2018-03-08T18:01:27Z (GMT). No. of bitstreams: 1 carvalho_tb_me_bot.pdf: 3710550 bytes, checksum: bab583912c5fbf652bf225a988df911b (MD5) Previous issue date: 2018-02-23 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A doença de Chagas (DC), causada pelo protozoário Trypanosoma cruzi (T. cruzi), ainda é considerada como um problema de saúde pública em muitos países da América Latina. De acordo com a Organização Mundial da Saúde, estima-se que entre seis a sete milhões de pessoas no mundo estejam infectadas. Indivíduos na fase crônica da doença podem ser classificados como assintomáticos ou sintomáticos (estes, desenvolvendo as formas clínicas cardíaca, digestiva ou mista). Os assintomáticos correspondem a 70% dos indivíduos nessa fase e, embora apresentem sorologia positiva para anticorpos anti T-cruzi, não desenvolvem manifestações clínicas da doença. O motivo pelo qual alguns pacientes permanecem assintomáticos, e outros desenvolvem sintomas severos, ainda é desconhecido. Fatores genéticos do hospedeiro são bastante relevantes e podem explicar a heterogeneidade encontrada em pacientes que vivem com a doença em áreas endêmicas. Diante disso, o presente trabalho teve como objetivo avaliar SNPs (Single Nucleotide Polymorphisms) no gene TNF-α (rs1800629) e ACAT-1 (rs1044925) em indivíduos com DC crônica e verificar se os mesmos estão relacionados com a susceptibilidade para manifestação de formas clínicas sintomáticas com uso da técnica PCR-RFLP. Foram genotipadas 124 amostras para o gene TNF-α e 135 para o gene ACAT-1. Foi observada associação significativa da presença do alelo A do gene TNF- α em indivíduos sintomáticos em relação aos assintomáticos (p = 0,045). Também houve associação significativa entre o alelo G (p = 0,008) e o genótipo GG (p = 0,001) do gene TNF-α e os genótipos AA (p = 0,047) e AC (p = 0,016) do gene ACAT-1 nos indivíduos assintomáticos em relação aos sintomáticos. Nossos resultados sugerem que a presença do alelo A do gene TNF-α possa estar relacionada com a presença de manifestações clínicas sintomáticas na fase crônica da doença e o alelo G, bem como, genótipo GG possam estar associados com ausência de sintomas clínicos em indivíduos nessa fase. A respeito do SNP do gene ACAT-1, nossos dados sugerem efeito protetor dos genótipos AA e AC segundo apresentação de sintomas da doença na fase crônica, o que representa dado inédito em chagásicos. / Chagas disease (CD), caused by the protozoan Trypanosoma cruzi (T. cruzi), is still considered a public health problem in many Latin America countries. According to the World Health Organization, it is estimated that between six and seven million people worldwide are infected. Disease’s chronic phase individuals may be classified as asymptomatic or symptomatic (these, developing as clinical cardiac, digestive or mixed forms). Asymptomatic individuals account for 70% of the patients at this stage and, although they have positive serology for anti-T-cruzi antibodies, they do not develop it’s clinical manifestations. The reason why some patients remain asymptomatic, and others develop severe symptoms, is still unknown. Host’s genetic factors are quite relevant and may explain the heterogeneity found in patients living with the disease in endemic areas. The objective of this study was to evaluate SNPs in the TNF-α (rs1800629) and ACAT-1 (rs1044925) genes in individuals with chronic CD and to verify if the polymorphisms are related to the susceptibility to manifestation of symptomatic clinical forms using the PCR-RFLP technique. Were genotyped 124 samples for the TNF-α gene and 135 for the ACAT-1 gene. Significant association for the presence of the A allele of the TNF-α gene was observed for symptomatic individuals in relation to the asymptomatic ones (p = 0.045). There was also a significant association between the G allele (p = 0.008) and the GG genotype (p = 0.001) of the TNF-α gene and the AA (p = 0.047) and AC (p = 0.016) genotypes of the ACAT-1 gene for asymptomatic patients. Our results suggests that the presence of the TNF-α gene A allele may be related to the presence of symptomatic clinical manifestations in the chronic phase of the disease and the G allele as well as the GG genotype may be associated with absence of clinical symptoms in individuals at this stage. Regarding the ACAT-1 gene SNP, our data suggests a protective effect of AA and AC genotypes according to the to the presentation of chronic disease symptoms, which is an unprecedented finding in chagasic patients. / CAPES: 1578310

Schizophrenia (SCZ) is a debilitating disorder with a prevalence of approximately 1 % worldwide. SCZ is known to have a high degree of genetic and clinical heterogeneity and is a major health problem worldwide. The integrin-β 3 subunit gene (ITGB3) gene at 17q21.32 has been implicated in psychiatric disorders. We therefore hypothesized that ITGB3 gene polymorphisms might also play a role in SCZ and age at onset (AAO) of SCZ. We investigated the genetic associations of 23 single-nucleotide polymorphisms (SNPs) of the ITGB3 gene with AAO in SCZ in two Caucasian samples (2,166 cases and 2,525 controls) using linear regression analysis and meta-analysis. We observed four ITGB3-SNPs associated with AAO in SCZ in a non-Genetic Association Information Network (GAIN) sample (p < 10-3). Three of these four SNPs were replicated in the GAIN sample. The SNP rs16941771 was most significantly associated with AAO (p = 7.47 × 10-5). Meta-analysis showed that 6 of 23 SNPs were associated with AAO. The haplotype analysis also supports the association of ITGB3 with AAO. Three disease-associated SNPs were located at species-conserved regions, indicating functional importance. This is the first report which shows that ITGB3 variants are associated with AAO in SCZ, providing direct evidence of the use of AAO as an intermediate phenotype to dissect the complex genetics of SCZ.

Schizophrenia (SCZ) is a debilitating disorder with a prevalence of approximately 1 % worldwide. SCZ is known to have a high degree of genetic and clinical heterogeneity and is a major health problem worldwide. The integrin-β 3 subunit gene (ITGB3) gene at 17q21.32 has been implicated in psychiatric disorders. We therefore hypothesized that ITGB3 gene polymorphisms might also play a role in SCZ and age at onset (AAO) of SCZ. We investigated the genetic associations of 23 single-nucleotide polymorphisms (SNPs) of the ITGB3 gene with AAO in SCZ in two Caucasian samples (2,166 cases and 2,525 controls) using linear regression analysis and meta-analysis. We observed four ITGB3-SNPs associated with AAO in SCZ in a non-Genetic Association Information Network (GAIN) sample (p < 10-3). Three of these four SNPs were replicated in the GAIN sample. The SNP rs16941771 was most significantly associated with AAO (p = 7.47 × 10-5). Meta-analysis showed that 6 of 23 SNPs were associated with AAO. The haplotype analysis also supports the association of ITGB3 with AAO. Three disease-associated SNPs were located at species-conserved regions, indicating functional importance. This is the first report which shows that ITGB3 variants are associated with AAO in SCZ, providing direct evidence of the use of AAO as an intermediate phenotype to dissect the complex genetics of SCZ.

High-throughput genomics projects have resulted in a rapid accumulation of protein sequences. Therefore, computational methods that can predict protein functions and functional sites efficiently and accurately are in high demand. In addition, prediction methods utilizing only sequence information are of particular interest because for most proteins, 3-dimensional structures are not available. However, there are several key challenges in developing methods for predicting protein function and functional sites. These challenges include the following: the construction of representative datasets to train and evaluate the method, the collection of features related to the protein functions, the selection of the most useful features, and the integration of selected features into suitable computational models. In this proposed study, we tackle these challenges by developing procedures for benchmark dataset construction and protein feature extraction, implementing efficient feature selection strategies, and developing effective machine learning algorithms for protein function and functional site predictions. We investigate these challenges in three bioinformatics tasks: the discovery of transmembrane beta-barrel (TMB) proteins in gram-negative bacterial proteomes, the identification of deleterious non-synonymous single nucleotide polymorphisms (nsSNPs), and the identification of helix-turn-helix (HTH) motifs from protein sequence.

Background: The high incidence of mutations and cytogenetic abnormalities in patients with myelodysplastic syndrome (MDS) suggests the involvement of DNA repair mechanism defects in the pathogenesis of this disorder. The first part of this work was focused on monitoring of gene expression of DNA repair genes in MDS patients and on their alterations during disease progression. In the second part, next generation sequencing was used to detect single nucleotide polymorphisms (SNPs) and mutations in DNA repair genes and their possible association with MDS development was evaluated. Methods: Expression profiling of 84 DNA repair genes was performed on bone marrow CD34+ cells of patients with MDS. Screening cohort consisted of 28 patients and expression of selected genes was further validated on larger cohort of 122 patients with all subtypes of MDS. Paired samples were used for monitoring of RAD51 and XRCC2 gene expression during disease progression. Immunohistochemical staining for RAD51 recombinase protein was done on samples acquired by trephine-biopsy. Targeted enrichment resequencing of exonic parts of 84 DNA repair genes was performed on the screening cohort of MDS patients. Real-time PCR was used for genotyping of selected SNPs in the population study. Results: RAD51 and XRCC2 genes showed...

Conduct disorder (CD) is a psychiatric syndrome in childhood and adolescence that is one of the most common childhood disorders with continuously increasing prevalence but uncertain pathogenesis. We performed a genome-wide, family-based association study of CD using P2BAT/FBAT software. The data is gathered from Collaborative Study on the Genetics of Alcoholism (COGA) and International Multi-Center ADHD Genetics Project (IMAGE). Using COGA data, we identified 20 markers which showed suggestive associations (p<10-3) with CD. Nine of them are located in known genes. Two genes, ADAM10 and CAMK2A, which had been reported associated with Alzheimer's disease (AD), bipolar disorder, and depression, were of more concern. Using IMAGE sample, our results were well replicated. This study identified several CD associated genetic variants, especially two novel candidate genes. These findings may serve as a resource for replication in other populations to elucidate the potential role of these genetic variants in CD.

Alzheimer's disease (AD), the most common form of dementia, is a chronic neurodegenerative disease. The HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 (HACE1) gene is expressed in human brain and may play a role in the pathogenesis of neurodegenerative disorders. Till now, no previous study has reported the association of the HACE1 gene with the risk and age at onset (AAO) of AD; while few studies have checked the proportional hazards assumption in the survival analysis of AAO of AD using Cox proportional hazards model. In this study, we examined the associations of 14 single nucleotide polymorphisms (SNPs) in the HACE1 gene with the risk and the AAO of AD using 791 AD patients and 782 controls. Multiple logistic regression model identified one SNP (rs9499937 with p = 1.8×10) to be associated with the risk of AD. For survival analysis of AAO, both classic Cox regression model and Bayesian survival analysis using the Cox proportional hazards model were applied to examine the association of each SNP with the AAO. The hazards ratio (HR) with its 95% confidence interval (CI) was estimated. Survival analysis using the classic Cox regression model showed that 4 SNPs were significantly associated with the AAO (top SNP rs9499937 with HR=1.33, 95%CI=1.13-1.57, p=5.0×10). Bayesian Cox regression model showed similar but a slightly stronger associations (top SNP rs9499937 with HR=1.34, 95%CI=1.11-1.55) compared with the classic Cox regression model. Using an independent family-based sample, one SNP rs9486018 was associated with the risk of AD (p=0.0323) and the T-T-G haplotype from rs9786015, rs9486018 and rs4079063 showed associations with both the risk and AAO of AD (p=2.27×10 and 0.0487, respectively). The findings of this study provide first evidence that several genetic variants in the HACE1 gene were associated with the risk and AAO of AD.