In the world today there is a massive dependency on fossil fuels as they are currently used to provide around 80% of the world’s energy. This is hugely detrimental to the environment and is a major contributory factor in climate change. Biofuel is a renewable energy source that is already being used to lessen some of the fossil fuel dependency. 2nd generation biofuels, by using non-food parts of plants, circumvent the food vs fuel argument, and by using farming waste or surplus can also avoid changing land use problems. Additionally liquid biofuels can use existing infrastructure for storage and delivery, and also fit into current lifestyles. Cost-effective 2nd generation biofuel production is directly affected by the presence of the polymer lignin in plant biomass, as it has been shown to impede enzymatic sugar release (saccharification) that is used for biofuel production. The work undertaken in this project developed a high-throughput methodology for the assessment of straw lignin content and composition across a large population of elite varieties in the economically important cereal crop, barley. Saccharification yield was also measured across the same population along with a number of other agronomically important traits, such as thousand-grain weight, biomass, mechanical stem properties and height. The data provided by these measurements allowed correlations between traits to be identified and their strength gauged. Genome wide association studies (GWAS) were also carried out and identified influential regions of the genome for each trait. The results revealed varying levels of association between measured traits and lignin content and monomeric constituents. Importantly a negative connection was shown between lignin content and saccharification yield, with lignin content being responsible for approximately 1/5th of the variation seen. Interestingly there was no correlation between lignin content and mechanical stem properties, an important factor in the agronomically important trait, lodging. GWAS results revealed a number of genomic regions that were influential across several traits indicating regions that would be difficult to separate through breeding due to their close proximities. However, unique QTL were identified for saccharification yield and lignin content providing candidates for breeding or genetic manipulation to improve the crop for biofuel production.

Orientador: Jayme Augusto de Souza Neto / Resumo: Dengue é a arbovirose de maior crescimento nos últimos anos, repercutindo em impactos sociais e econômicos devido às altas taxas de morbidade e mortalidade desencadeadas pela infecção. O vírus dengue tem como principal vetor o mosquito Aedes aegypti. Por apresentar hábito hematofágico, antropofílico, de rápido desenvolvimento, é um excelente transmissor do vírus. Medidas de controle estão restritas à eliminação do mosquito vetor, uma vez que um tratamento específico ou uma vacina não estão disponíveis à população. E uma característica que determina a disseminação de doenças é a alta competência vetorial de seus mosquitos vetores, a qual tem sido associada à fatores genéticos do mosquito e ambientais. Sabe-se que a variabilidade genética dos mosquitos é um dos fatores que pode determinar o sucesso da relação mosquito-patógeno específico. Com isso, no presente trabalho foram estudadas as competências vetoriais de mosquitos Aedes aegypti da cidade de Botucatu infectados com DENV-2 e DENV-4 a fim de entender melhor a competência vetorial desses mosquitos. Além disso, foram feitas tentativas para selecionar linhagens resistentes e susceptíveis desses mosquitos infectados com ambos os sorotipos. Os mosquitos infectados com DENV-2 foram genotipados pela metodologia de SNP chip e posteriormente foram realizadas análises de estudo global do genoma (GWAS) afim de encontrar fatores genéticos relacionados com os diferentes fenótipos susceptív... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Dengue is the arboviruses with the greatest growth in recent years, with social and economic impacts due to the high morbidity and mortality rates triggered by the infection. Dengue has as main vector the mosquito Aedes aegypti. Because of the haematophagic habit, been antropophilic, fast development, Aedes aegypti mosquitoes are excellent transmitter of the dengue virus. Control measures are restricted to vector mosquito elimination since a specific treatment or vaccine is not available to the population. The characteristic that determinates the diseases dissemination is the high vector competence of the mosquitoes, which has been associated with mosquito genetic and environmental factors. It is known that the genetic variability of mosquitoes is one of the factors that can determine the success of the specific mosquito-pathogen relationship. In the present study, the vector competence of Aedes aegypti mosquitoes from Botucatu city infected with DENV-2 and DENV-4 were compared in order to understand the vector competence of these specific mosquitoes. In addition, we tried to do resistant and susceptible strains selections of these mosquitoes infected with both serotypes. And mosquitoes infected with DENV-2 were genotyped by the SNP chip methodology and later analyzes were carried out to study the genome (GWAS) in order to find genetic factors related to the different susceptible and resistant phenotypes of them. As results we observed different vector competence of the same ... (Complete abstract click electronic access below) / Doutor

Submitted by Letícia Tiemi Egami Oda (leticia.e.o@gmail.com) on 2018-11-19T14:17:39Z No. of bitstreams: 1 Tese DR LTEO-corrigida final.pdf: 2530249 bytes, checksum: 4783af91c3819b7b7b372559ab20f01a (MD5) / Approved for entry into archive by ROSANGELA APARECIDA LOBO null (rosangelalobo@btu.unesp.br) on 2018-11-21T10:42:03Z (GMT) No. of bitstreams: 1 oda_lte_dr_bot.pdf: 2530249 bytes, checksum: 4783af91c3819b7b7b372559ab20f01a (MD5) / Made available in DSpace on 2018-11-21T10:42:03Z (GMT). No. of bitstreams: 1 oda_lte_dr_bot.pdf: 2530249 bytes, checksum: 4783af91c3819b7b7b372559ab20f01a (MD5) Previous issue date: 2018-05-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Dengue é a arbovirose de maior crescimento nos últimos anos, repercutindo em impactos sociais e econômicos devido às altas taxas de morbidade e mortalidade desencadeadas pela infecção. O vírus dengue tem como principal vetor o mosquito Aedes aegypti. Por apresentar hábito hematofágico, antropofílico, de rápido desenvolvimento, é um excelente transmissor do vírus. Medidas de controle estão restritas à eliminação do mosquito vetor, uma vez que um tratamento específico ou uma vacina não estão disponíveis à população. E uma característica que determina a disseminação de doenças é a alta competência vetorial de seus mosquitos vetores, a qual tem sido associada à fatores genéticos do mosquito e ambientais. Sabe-se que a variabilidade genética dos mosquitos é um dos fatores que pode determinar o sucesso da relação mosquito-patógeno específico. Com isso, no presente trabalho foram estudadas as competências vetoriais de mosquitos Aedes aegypti da cidade de Botucatu infectados com DENV-2 e DENV-4 a fim de entender melhor a competência vetorial desses mosquitos. Além disso, foram feitas tentativas para selecionar linhagens resistentes e susceptíveis desses mosquitos infectados com ambos os sorotipos. Os mosquitos infectados com DENV-2 foram genotipados pela metodologia de SNP chip e posteriormente foram realizadas análises de estudo global do genoma (GWAS) afim de encontrar fatores genéticos relacionados com os diferentes fenótipos susceptível e resistente dos mosquitos. Como resultados observou-se diferentes competências vetoriais dos mesmos mosquitos infectados com diferentes sorotipos. Os mosquitos infectados com DENV-2 foram aproximadamente 70% susceptíveis, e mosquitos infectados com DENV-4 aproximadamente 70% foram resistentes, possuindo assim competências vetoriais opostas. Já no estudo da seleção dos fenótipos foi possível uma seleção de 80% até a geração F3 de mosquitos infectados com DENV-2, apesar do número baixo de indivíduos nas seleções. Os mosquitos infectados com DENV-4 não obtiveram uma taxa de seleção muito elevada, visto que as seleções foram feitas só até a geração F-2. Os resultados das análises de GWAS mostraram possíveis associações dos SNPs com os fenótipos estudados, apesar de não serem estatisticamente significantes para a correção de Bonferroni. Com isso, concluímos que a diferença vetorial é bastante dependente do sorotipo viral; para as análises de seleção e formação de linhagem é necessário um maior número de indivíduos nas primeiras infecções; e no estudo GWAS apesar da associação não ter sido significativa, devido ao baixo número de indivíduos, e dos parâmetros de correção estatística não serem ideais para indivíduos de uma única população, acredita-se que as associação encontradas de alguns SNPs com os fenótipos estudados sejam verdadeiras. / Dengue is the arboviruses with the greatest growth in recent years, with social and economic impacts due to the high morbidity and mortality rates triggered by the infection. Dengue has as main vector the mosquito Aedes aegypti. Because of the haematophagic habit, been antropophilic, fast development, Aedes aegypti mosquitoes are excellent transmitter of the dengue virus. Control measures are restricted to vector mosquito elimination since a specific treatment or vaccine is not available to the population. The characteristic that determinates the diseases dissemination is the high vector competence of the mosquitoes, which has been associated with mosquito genetic and environmental factors. It is known that the genetic variability of mosquitoes is one of the factors that can determine the success of the specific mosquito-pathogen relationship. In the present study, the vector competence of Aedes aegypti mosquitoes from Botucatu city infected with DENV-2 and DENV-4 were compared in order to understand the vector competence of these specific mosquitoes. In addition, we tried to do resistant and susceptible strains selections of these mosquitoes infected with both serotypes. And mosquitoes infected with DENV-2 were genotyped by the SNP chip methodology and later analyzes were carried out to study the genome (GWAS) in order to find genetic factors related to the different susceptible and resistant phenotypes of them. As results we observed different vector competence of the same mosquitoes infected with different serotypes. Mosquitoes infected with DENV-2 were approximately 70% susceptible, and mosquitoes infected with DENV-4 were approximately 70% resistant, thus the opposing vector competence. In the selection study it was possible to select 80% up to the F3 generation of mosquitoes infected with DENV-2, despite the low number of individuals in the selections. Mosquitoes infected with DENV-4 did not obtain a very high selection rate, since the selections were made only up to the F-2 generation. The results of the GWAS analysis showed possible associations of the SNPs with the studied phenotypes, although they were not statistically significant for the Bonferroni correction. With this, we conclude that the vector competence difference is quite dependent on the viral serotype; for the analysis of selection and formation of lineage is necessary a greater number of individuals in the first infections; and in the GWAS study, although the association was not significant because of the low number of individuals, and the statistical correction parameters are not ideal for individuals from the same population, it is believed that the association of some SNPs with the studied phenotypes is true.

Proteins are the primary functional units of biology and the direct targets of most drugs, yet there is limited knowledge of the genetic factors determining inter-individual variation in protein levels (protein quantitative trait loci (pQTLs)). Limitations in high-throughput proteomic measurement technology have meant well-powered genome-wide association studies for large number of proteins so far have lagged behind many of the other "omic" studies such as transcriptomics and metabolomics. This is made more challenging by the complexity of human plasma, characterised by high dynamic range spanning several magnitudes of concentrations and a large number of low abundance proteins. By using an expanded high-throughput multiplex aptamer-based proteomic assay with more than twice the proteome coverage of previous studies, I am able to greatly expand on existing knowledge on genetic determinants of human plasma proteins through testing 10.6 million DNA variants against levels of 2,994 proteins in 3,301 individuals. I identify 1,927 genetic associations with 1,478 proteins, replicating many previous associations as well as gaining novel insights into the genetic architecture of the human plasma proteome. I use several approaches to highlight the application of pQTLs to biology and disease. I show several examples linking distant pQTLs to biologically plausible genes and demonstrate the mediation of distant pQTL by local protein levels, highlighting the role of protein-protein interactions. In addition, I find epistatic effects of genetically determined phenotypes (blood group and secretor status) on protein levels. Through linking previous disease associations, I show that disease associated variants are enriched for pQTLs and I provide insights into possible mechanisms underpinning some of the disease loci. Finally, I identify causal roles for protein biomarkers in disease through multivariable Mendelian randomisation (MR) analysis, leveraging on the simultaneous measurement of multiple functionally related proteins in a locus to account for potential pleiotropic effects. Whereas MR studies of plasma proteins have been constrained by availability of few suitable genetic instruments, the data generated here remedy this bottleneck by furnishing an extensive toolkit. Overall, the work within this thesis foreshadows major advances in post-genomic science through increasing application of novel bioassay technologies to major population biobanks.

Submitted by Daniella Sodre (daniella.sodre@ufpe.br) on 2015-04-17T15:24:58Z No. of bitstreams: 2 TESE Manuela de Souza.pdf: 8389907 bytes, checksum: 5002b2436d9b695b176799e52ad52b6a (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Made available in DSpace on 2015-04-17T15:24:58Z (GMT). No. of bitstreams: 2 TESE Manuela de Souza.pdf: 8389907 bytes, checksum: 5002b2436d9b695b176799e52ad52b6a (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2013-04-19 / FACEPE / Doenças neuropsiquiátricas afetam cerca de 450 milhões de pessoas em todo mundo e dentre estas patologias os Transtornos do Humor (TH) e Doença de Alzheimer (DA) são as mais comuns. Em relação à sua etiologia as doenças neuropsiquiátricas são resultados de variações em um grupo de genes e de fatores ambientais. Pesquisas recentes vêm mostrando associação positiva entre variações genéticas em genes envolvidos nos sistemas de neurotransmissores com o desenvolvimento de doenças neuropsiquiátricas. Por isso, os estudos sobre polimorfismos genéticos, nas doenças psiquiátricas são de grande importância para a compreensão dos mecanismos moleculares envolvidos e podem auxiliar no diagnóstico das mesmas. Neste cenário, mutações encontradas no DNA têm sido amplamente estudadas, a fim de elucidar aspectos genéticos relacionados às neuropatologias. Os polimorfismos do tipo SNPs (Polimorfismo de Base Única) e INDELs (inserções e deleções de fragmentos de DNA) têm se destacado devido as fortes associações com os TH e DA. Diversos métodos de biologia molecular têm sido utilizados para detectar estes tipos de polimorfismos, os experimentos moleculares geram grande quantidade de dados a serem analisados, fazendo-se necessário a utilização de ferramentas computacionais para se extrair informações a partir desses dados gerados. Assim, o objetivo desse estudo foi o uso de bioinformática e de genotipagem em larga escala na busca de novos polimorfismos genético em TH e aplicação de ferramentas computacionais em banco de dados de GWAS referente à DA. Para obter os resultados referentes à TH optamos por utilizar o software CLCbio Workbench®, sequenciamento automatizado mega Bace 1000 e experimentos preliminares da técnica de DNA pooling. Já para a DA, utilizamos o teste de associação e método de regressão linear do software PLINK e o pacote genetics da linguagem de programação R, para correlacionar os níveis da proteína βamiloide no plasma e líquido cefalorraquidiano e um total de 598.821 SNPs, ambos os dados oriundos do banco de dados ADNI (Alzheimer’s Disease Neuroimaging Initiative). Após uma sequência de passos in silico identificamos variações anteriormente descritas e novos polimorfismos candidatos à fisiopatologia dos TH, na fase de validação dessas variações, por meio de sequenciamento, falsos positivos foram frequentemente identificados, sendo descartados após a verificação na cadeia complementar. Apenas o SNP rs14068, localizado no exon 2 do gene GABRA5 foi validado em amostras de pacientes com TH. No estudo referente à DA, 5 SNPs nas regiões dos genes TOMM40, PAMR1, TRIM9 e CCDC112 e 3 SNPs em regiões de intron atingiram associação significativa, levantando a possibilidade de estejam relacionados a fisiopatologia da DA.

Made available in DSpace on 2018-08-01T21:35:21Z (GMT). No. of bitstreams: 1 tese_12338_Tese - Paulo Cilas Morais Lira Junior.pdf: 2589044 bytes, checksum: 296741ac94e07c977802b7850599cabc (MD5) Previous issue date: 2018-03-19 / O câncer de ovário (CaOV) configura como um câncer letal. Fatores genéticos contribuindo para o risco de desenvolvimento do CaOV têm sido investigados através dos estudos de associação ampla do genoma (GWAS), identificando loci de risco em diferentes regiões dos cromossomos, dentre eles o locus 8q21. Nesse estudo, realizamos uma análise funcional sistemática de nove SNPs candidatos para a causalidade ao CaOV no locus proximal ao gene CHMP4C. Após a caracterização da região para prováveis elementos regulatórios e genes associados, testamos os nove SNPs candidatos para atividade alelo específica para regiões com atividade de enhancer, como também testes para identificar prováveis fatores de transcrição. O SNP candidato localizado na região codificante do gene CHMP4C foi testado para instabilidade da proteína. Três SNPs foram identificados com funcionalidade alelo específica: rs35094336, rs137960856, rs1116683632. Este estudo elucidou o campo funcional da região 8q21 associado ao CaOV e identificou SNPs funcionais como possíveis mecanismos de associação ao risco de desenvolvimento da doença.

Genetics has been successful in associating DNA sequence variants to both dichotomous and continuous traits in a variety of organisms, from plant and farm animal studies to human disease. With the advent of high-throughput genotyping, there has been an almost routine gen- eration of genome-wide association studies (GWAS) between human disease traits and genomic regions. Despite this success, a particular frustration is that the majority of associated loci are in non-coding regions of the genome and thus interpretation is hard. To improve characterisation of non-coding regions, molecular as- says can be used as a phenotype, and subsequently be used to explain how genetics alter molecular mechanisms. In this thesis, the inter- play of three molecular assays that are involved in regulating gene expression is studied. On 60 individuals, several assays are performed: FAIRE-chip, CTCF- seq, RNA-seq and DNA-seq. In the first part, the discovery and characteristics of FAIRE-QTLs is presented. The identified FAIRE-QTLs show strong overlap with other molecular QTLs, histone modifications, and transcription factors. The second part consists of the integration of genome-wide molecu- lar assays in a human population to reconstruct the human epigenome. Each of the molecular assays is associated with each of the other assays to discover phenotype-to-phenotype correlations. Furthermore, QTL data are used to dissect the causality for these phenotype-to-phenotype correlations in a system genetic manner. The third part presents a comprehensive view of CTCF binding on the X chromosome, and its implications for X-chromosome inactivation. A novel X chromosome-wide CTCF effect is observed. Using the gender of each of the cell lines, observations are made about which CTCF sites are dosage-compensated, active on both chromosomes, or are only bound in females.

The first genetic CAD risk locus to be identified by genome-wide association studies, single nucleotide polymorphisms (SNPs) at 9p21.3 predispose to increased risk of CAD. By bioinformatics scan analysis of the 9p21.3 locus; we interrogated the 59 linked SNPs over the 53,202bp to identify putative transcription factor-binding consensus sequences. We hypothesize that some genetic polymorphisms at the 9p21.3 locus are functional and will disrupt specific regulatory sequences within enhancers. Here, I investigated how polymorphisms affect TEAD-dependent regulation at the 9p21.3 locus, and also how polymorphisms affect GATA factor-dependent regulation at the 9p21.3 locus, using cultured HEK293 and primary human aortic smooth muscle cells (HAoSMCs) to transfect the pGL3-promoter plasmid constructs containing the reference or risk variant sequences (rs10611656, rs4977757, rs10757269, rs9632885). We showed by luciferase reporter assay that the risk allele of the SNPs disrupt activation by various TEAD transcription factors. We also performed electrophoretic mobility shift assay (EMSA) to test for allele-specific transcription factor binding that affect the family of TEAD transcription factors and the GATA factors. EMSA showed binding of TEAD3 and TEAD4, and differential binding for both GATA genotypes, and luciferase reporter assay confirmed that TEAD3 and TEAD4 activate the non-risk but not the risk allele, and for GATA factors no significant activation was shown. Our investigations lead us to conclude that rs10811656 and rs4977757 are functional and disrupt specific TEAD regulatory sequences within enhancers

Penalized regression methods are becoming increasingly popular in genome-wide association studies (GWAS) for identifying genetic markers associated with disease. However, standard penalized methods such as the LASSO do not take into account the possible linkage disequilibrium between adjacent markers. We propose a novel penalized approach for GWAS using a dense set of single nucleotide polymorphisms (SNPs). The proposed method uses the minimax concave penalty (MCP) for marker selection and incorporates linkage disequilibrium (LD) information by penalizing the difference of the genetic effects at adjacent SNPs with high correlation. A coordinate descent algorithm is derived to implement the proposed method. This algorithm is efficient and stable in dealing with a large number of SNPs. A multi-split method is used to calculate the p-values of the selected SNPs for assessing their significance. We refer to the proposed penalty function as the smoothed MCP (SMCP) and the proposed approach as the SMCP method. Performance of the proposed SMCP method and its comparison with a LASSO approach are evaluated through simulation studies, which demonstrate that the proposed method is more accurate in selecting associated SNPs. Its applicability to real data is illustrated using data from a GWAS on rheumatoid arthritis. Based on the idea of SMCP, we propose a new penalized method for group variable selection in GWAS with respect to the correlation between adjacent groups. The proposed method uses the group LASSO for encouraging group sparsity and a quadratic difference for adjacent group smoothing. We call it smoothed group LASSO, or SGL for short. Canonical correlations between two adjacent groups of SNPS are used as the weights in the quadratic difference penalty. Principal components are used to reduced dimensionality locally within groups. We derive a group coordinate descent algorithm for computing the solution path of the SGL. Simulation studies are used to evaluate the finite sample performance of the SGL and group LASSO. We also demonstrate its applicability on rheumatoid arthritis data.

Indiana University-Purdue University Indianapolis (IUPUI) / Alzheimer’s Disease (AD) is one of the most common forms of dementia and is known to have a strong genetic component, but known genetic loci do not fully account for the observed genetic heritability of late onset AD. This genetic complexity is further complicated by disease heterogeneity, with non-uniform presentation and progression of AD neuropathology. Endophenotypes lie upstream of observed AD clinical outcomes and downstream of genetic contributors, allowing for a biological understanding of genetic effects. Understanding the genetic architecture of AD endophenotypes can aid in breaking down AD genetic complexity and heterogeneity. In this study we utilized a variety of models to evaluate the genetic contributors to pathological change and heterogeneity in the top markers of AD pathology: amyloid, tau, neurodegeneration, and cerebrovascular (A/T/N/V framework). Additional composite quantitative measures of cognitive performance were used to relate to downstream AD presentation. These biomarkers allow the investigation of genetic effects contributing to the disease over the stages of disease progression from amyloid deposition to neurofibrillary tangle formation, disruption of metabolism, brain atrophy, and finally to clinical outcomes. First, we performed genome-wide association studies (GWAS) for AD endophenotypes at baseline using a cross-sectional regression model. This method identified sixteen novel or replicated loci, with six (SRSF10, MAPT, XKR3, KIAA1671, ZNF826P, and LOC100507506) associated across multiple A/T/N biomarkers. Cross-sectional data was further utilized to identify three genetic loci (BACH2, EP300, PACRG-AS1) that showed disease stage specific interaction effects. We built upon those results by performing a longitudinal association analysis with linear-mixed effects modeling. Gene enrichment analysis of these results identified 19 significant genetic regions associated with linear longitudinal change in AD endophenotypes. To further break down longitudinal heterogeneity, a latent class mixed model approach was utilized to identify subgroups of longitudinal progression within cognitive and MRI measures, with 16 genetic loci associated with membership in different classes. The genetic patterns of these subgroups show biological relevance in AD. The methods and results from this study provide insight into the complex genetic architecture of AD endophenotypes and a foundation to build upon for future studies into AD genetic architecture. / 2022-11-26