Ainda são escassos estudos que avaliem biomarcadores para diferenciação de transtorno depressivo maior (TDM) e transtorno bipolar (TB), principalmente relativo à etiologia desses transtornos e sua relação com os receptores glicocorticoides (GR) e, principalmente, com os receptores mineralocorticoides (MR). Objetivo: Encontrar biomarcadores genéticos e/ou hormonais e observar sua associação entre si e/ou a fatores externos (estresse precoce - EP) para compreender melhor sua fisiopatogenia e auxiliar no diagnóstico diferencial entre TDM e TB. Material e Métodos: Participaram deste estudo N=273 sujeitos, sendo n=113 controles, n=78 unipolares e n=82 bipolares. A triagem diagnóstica de todos os sujeitos foi realizada por meio do MINI PLUS, checagem de história de trauma na infância pela CTQ, avaliação de sintomas depressivos pela GRID-HAM-D21, e demais comorbidades pela BAI, BHS e BSI. Na busca de biomarcador genético, observou-se as frequências genotípicas e alélicas de 3 polimorfismos de receptor de glicocorticoide (GR) (N363S, R22/23K e BclI) e de 2 polimorfismos de MR (MI180V e -2G/C) após realizada a discriminação alélica por reação em cadeia da polimerase quantitativa (qPCR). Foram avaliados de forma intragrupo as variáveis genéticas e endócrinas (e combinadas) e o efeito do EP sobre tais variáveis. Também, as variáveis polimorfismos, níveis hormonais e exposição a EP foram comparadas entre grupos para avaliar se havia diferença de prevalência, de perfil endócrino, ou se havia suscetibilidade maior por parte dos unipolares ou bipolares para alteração dos níveis hormonais e/ou intensidade do quadro depressivo frente a EP ou a determinado genótipo. Resultados: Todos os sujeitos unipolares e bipolares mostraram piora de seus sintomas depressivos frente a EP e seus subtipos, sendo eles unipolares ou bipolares. Como biomarcador hormonal, comparando-se controles x unipolares x bipolares, ou apenas unipolares x\' bipolares, foi possível observar que os níveis de cortisol e os níveis de aldosterona apresentaram-se os altos em unipolares e os baixos mais em bipolares, quando estes pacientes estavam com depressão grave ou gravíssima. Também, bipolares expostos a EP global, abuso físico e emocional mostraram níveis mais baixos de aldosterona que bipolares que não foram expostos. Frente a exposição a esses EP global e abuso físico, os bipolares tenderam a se mostrar mais suscetíveis que os unipolares a alteração dos níveis de aldosterona. Para biomarcador genético, frequência de genótipos ou alelos não diferenciaram unipolares de bipolares. Entretanto, houve maior prevalência do genótipo heterozigoto AG de GR N363S em pacientes depressivos uni e bipolares quando comparados com controles. Combinando-se os biomarcadores genéticos e hormonais, unipolares apresentaram níveis mais baixos de cortisol e de aldosterona quando carregavam genótipo variante GG de MR -2G/C, enquanto bipolares mostraram tendência a redução de cortisol quando carregavam o alelo variante G de MR MI180V. Quando comparados os genótipos por si só, intragrupo, novamente o polimorfismo MR -2G/C mostra influência sobre o fenótipo unipolar. Em unipolares, presença do alelo variante G de MR -2G/C piora significativamente o quadro depressivo, mas o alelo variante G de MI180V mostrou-se protetor frente a EP. Tanto os unipolares frente aos outros 4 polimorfismos, quanto os bipolares frente a todos os polimorfismos estudados, apresentaram piora significativa de seu quadro depressivo se expostos a EP. Bipolares mostraram uma tendência a ser mais suscetíveis que unipolares a alterações endócrinas (aldosterona) quando expostos a EP global e abuso físico. Conclusão: Tendo em vista os vários achados significativos a cerca dos polimorfismos de MR, tanto para unipolar quanto para bipolar, sua influência sobre os níveis de aldosterona e cortisol basais, reforça-se a importância do papel dos receptores MR dentro da etiologia dos transtornos depressivos unipolares e bipolares, e a forma diferente de funcionamento do MR para a distinção entre TDM e TB / There are still few studies assessing biomarkers for differentiation of major depressive disorder (MDD) and bipolar disorder (TB), mainly related to the etiology of these disorders and its relationship with glucocorticoid receptors (GR) and, manily, with mineralocorticoid receptors (MR). Aim: Finding genetic and / or hormonal biomarkers and observing their association to each other and / or external factors (early-life stress - ELS) for better comprehend their pathophysiology and, then, assisting in differential diagnosis between MDD and TB. Material and Methods: A total of N = 273 subjects composed the study sample, being n = 113 control, n = 78 unipolar, and n = 82 bipolar subjects. The diagnostic screening of all subjects was performed applying MINI PLUS, for history of ELS, CTQ; assessment of depressive symptoms, GRID-HAM-D21; and assessment of other comorbidities, BAI, BHS, and BSI. Researching for genetic biomarker, genotypic and allelic frequencies of 3 GR polymorphisms (N363S, R22 / 23K and BclI) and 2 MR polymorphisms (MI180V and -2G/C) were evaluated after allelic discrimination by quantitative polymerase chain reaction (qPCR). Genetic and endocrine variables (and their combination), and the effect of ELS over these variables were assessed intragrups. Also, polymorphisms, hormonal levels and history to ELS were compared between groups to assess whether there was difference in prevalence, endocrine profile, or whether there was greater susceptibility on the part of unipolar or bipolar for alteration of hormonal levels and / or severity of depressive symptoms considering history of ELS and/or a specific genotype. Results: All unipolar and bipolar subjects showed worsening of their depressive symptoms in the presence of ELS and its subtypes. As hormonal biomarker, comparing unipolar x bipolar x control subjects, or comparing unipolar x bipolar, cortisol and aldosterone levels were higher in unipolar subjects, and lower in bipolar subjects, when these patients presented severe or very severe depressive symptoms. Also, bipolar subjects\' exposed to global ELS, physical and emotional abuse showed lower basal levels of aldosterone than did bipolar who were not exposed to ELS. Concerning global ELS and physical abuse, bipolar tended to be more susceptible than unipolar for aldosterone levels to change. For genetic biomarker, frequency of genotypes or alleles did not distinguished unipolar from bipolar sample. However, there was a higher prevalence of GR N363S heterozygous genotype (AG) in unipolar and bipolar depressive patients when compared to controls. Combining the genetic and hormonal biomarkers, unipolar had lower levels of cortisol and aldosterone when carrying GG variant genotype of MR-2G / C, while bipolar showed tendency to reduce cortisol when carrying the variant G allele of MR MI180V. When comparing the genotypes (intragroup), again, MR-2G/C polymorphism shows influence on the unipolar phenotype. In unipolar, the presence of the variant G allele of MR-2G / C significantly worsens the depressive condition, unlike variant G allele of MI180V has shown to be protective against ELS. Both the unipolar compared to the other 4 polymorphisms, and the bipolar ones against all polymorphisms studied, presented a significant worsening of their depressive condition if exposed to ELS. Bipolar tend to be more susceptible than unipolar to endocrine changes (aldosterone) when exposed to global ELS and physical abuse. Conclusion: Considering the several significant findings regarding MR polymorphisms, for both unipolar and bipolar subjects, and their influence on basal aldosterone and cortisol levels, we highlight importance of the role of MR receptors within the etiology of depressive unipolar and bipolar disorders, and different way of MR functioning in each disorder for assisting the distinction between MDD and TB

From a fresh data science perspective, this thesis discusses the prediction of coronary artery disease based on Single-Nucleotide Polymorphisms (SNPs) from the Ontario Heart Genomics Study (OHGS). First, the thesis explains the k-Nearest Neighbour (k-NN) and Random Forest learning algorithms, and includes a complete proof that k-NN is universally consistent in finite dimensional normed vector spaces. Second, the thesis introduces two dimensionality reduction techniques: Random Projections and a new method termed Mass Transportation Distance (MTD) Feature Selection. Then, this thesis compares the performance of Random Projections with k-NN against MTD Feature Selection and Random Forest for predicting artery disease. Results demonstrate that MTD Feature Selection with Random Forest is superior to Random Projections and k-NN. Random Forest is able to obtain an accuracy of 0.6660 and an area under the ROC curve of 0.8562 on the OHGS dataset, when 3335 SNPs are selected by MTD Feature Selection for classification. This area is considerably better than the previous high score of 0.608 obtained by Davies et al. in 2010 on the same dataset.

Advances in molecular methods for analyzing DNA, RNA and proteins in humans as well as in other animals, plants, fungi, bacteria or viruses have greatly increased the resolution with which we can study life’s complexity and dynamics on earth. While genomic, transcriptomic and proteomic laboratory tools for molecular diagnosis of disease are rapidly becoming more comprehensive, the access to such advanced yet often expensive and centralized procedures is limited. There is a great need for rapid and comprehensive diagnostic methods in low-resource settings or contexts where a person can not or will not go to a hospital or medical laboratory, yet where a clinical analysis is urgent. In this thesis, results from development and characterization of novel technologies for DNA and protein microarray analysis are presented. Emphasis is on methods that could provide rapid, cost-effective and portable analysis with convenient readout and retained diagnostic accuracy. The first study presents a magnetic bead-based approach for DNA microarray analysis for a rapid visual detection of single nucleotide polymorphisms. In the second work, magnetic beads were used as detection reagents for rapid differential detection of presence of pestiviral family members using a DNA oligonucleotide microarray with read-out by means of a tabletop scanner or a digital camera. In paper three, autoimmune responses from human sera were detected on a protein autoantigen microarray, again by means of magnetic bead analysis. Here, special emphasis was made in comprehensively comparing the performance of the magnetic bead detection to common fluorescence-based detection. In the fourth study, an immunochromatographic lateral flow protein microarray assay is presented for application in the classification of contagious pleuropneumonia from bovine serum samples. The analysis could be performed within 10 minutes using a table top scanner, and the performance of the assay was shown to be comparable to that of a cocktail ELISA. In the fifth paper, the lateral flow microarray framework is investigated in further detail by means of experiments and numerical simulation. It was found that downstream effects play an important role, and the results further suggest that the downstream binding profiles may find use in simple affinity evaluation. / QC 20100713

La presente tesis, titulada “Genes, peoples and languages in Central Africa”, examina los patrones de diversidad genética en poblaciones del oeste de Africa central, más específicamente, poblaciones Bantús y Pigmeas de Gabon y Camerún, dos zonas vitales para la comprensión de la expansión Bantú. Se han analizado más de 800 muestras a nivel del cromosoma Y con el fin de caracterizar genéticamente a estas poblaciones, y establecer la relación genética entre ellas. Los resultados han demostrado que la expansión Bantú homogeneizó el acervo genético de las poblaciones Bantús, eliminando la diversidad pre-Bantú, mientras que diversificó aquel de las poblaciones Pigmeas, introduciendo linajes Bantus. Además, se ha visto que el flujo de linajes paternos parece haber tenido una única dirección: de Bantus a Pigmeos. Estos resultados contrastan con aquellos obtenidos para linajes maternos (DNA mitocondrial) en estas zonas, donde se ha observado un considerable flujo genético de Pigmeos a Bantus, sugiriendo un posible sesgo sexual en la tasa de mestizaje entre poblaciones Bantus y Pigmeas. Un hallazgo interesante es la presencia de un linaje no-africano en estas poblaciones de África subsahariana. / The present thesis titled “ Genes, peoples and languages in Central Africa” examines the genetic diversity patterns in populations from west central Africa, more specifically, in Bantu and Pygmy populations from Gabon and Cameroon, two key areas in the understanding of the Bantu expansion. More than 800 samples have been analysed at the Y chromosome level in order to genetically characterise these populations and establish the genetic relationship between them. The results have shown that the Bantu expansion largely homogenised the gene pool of Bantu populations, erasing the pre-Bantu diversity, while it diversified that of Pygmy groups, introducing Bantu lineages into their gene pool. Furthermore, gene flow of paternal lineages seems to have taken place mainly in one direction; from Bantus to Pygmies. These results contrast with those found in studies of maternal (mtDNA) lineages in these areas, where considerable gene flow from Pygmy to Bantu populations have been observed, suggesting possible sex-biased admixtures rates between Bantu and Pygmy populations. An interesting finding, is the significant presence of a non-African lineage in these sub-Saharan populations.

From a fresh data science perspective, this thesis discusses the prediction of coronary artery disease based on Single-Nucleotide Polymorphisms (SNPs) from the Ontario Heart Genomics Study (OHGS). First, the thesis explains the k-Nearest Neighbour (k-NN) and Random Forest learning algorithms, and includes a complete proof that k-NN is universally consistent in finite dimensional normed vector spaces. Second, the thesis introduces two dimensionality reduction techniques: Random Projections and a new method termed Mass Transportation Distance (MTD) Feature Selection. Then, this thesis compares the performance of Random Projections with k-NN against MTD Feature Selection and Random Forest for predicting artery disease. Results demonstrate that MTD Feature Selection with Random Forest is superior to Random Projections and k-NN. Random Forest is able to obtain an accuracy of 0.6660 and an area under the ROC curve of 0.8562 on the OHGS dataset, when 3335 SNPs are selected by MTD Feature Selection for classification. This area is considerably better than the previous high score of 0.608 obtained by Davies et al. in 2010 on the same dataset.

>Magister Scientiae - MSc / As human beings we are curious about our origin and ancestry. A curiosity has led to an investigation of human evolution and expansion across the world by means of population genetics and phylo-genetics by evaluating a region in Southern Africa that is largely unknown. The objective of this study was to develop a quick, inexpensive and accurate hierarchical diagnostic screening system of the MtDNA phylogenetic tree, AI-SNPs in the mtDNA genome by using High Resolution Melting analysis to evaluate the population composition and ancestral haplogroups of Southern African populations in Limpopo. The admixture between the ‘Khoesan’ hunter-gatherers, herders and the Bantu speaking populations led to population growth and expansion in Limpopo. This has contributed to populations settling in Limpopo and has thus shaped the ancestral contemporary populations. No research on these individuals residing in Limpopo has been done before, thus an investigation of their ancestral origin was necessary. A total of 760 saliva samples were collected from individuals residing in Limpopo. Only 500 saliva samples were extracted by means of an optimized salting out technique. Five hundred extracted genomic samples were genotyped by means of a quick, inexpensive High-resolution melting analysis. Of the 500 samples, the genotyping results showed 95 individuals derived for the L3 haplogroup which gives a 19% ratio of individuals screened with Multiplex 1. Only 56 individuals were derived for the L1 haplogroup, which gives a percentage of 11%. A total of 249 individuals were derived for the L0 haplogroup, making up a 50% of the total individuals genotyped. Only 100 samples were derived for L0a, making up 20% of individuals screened with Multiplex 1. Of the 95 samples derived for the L3 haplogroup, the results showed 87 individuals to be ancestral for both M and N, making up 91.57% of individuals screened with Multiplex 2. http://etd.uwc.ac.za/. In population genetics using SNPs to infer population history and ancestral origin has become significant, this study allowed researchers to evaluate population groups by investigating their genetic markers and the application of the results allowed for downstream analyses. Finally, this study provides a quick and simple screening method for the selection of lineages that are of interest for further studies.

No description available.

Cranberry common bean (Phaseolus vulgaris L.) is planted worldwide and consumed as a critical food source of human protein, fibre, carbohydrates, and minerals. Marsh spot (MS) is a physiogenic disorder which severely impacts seed quality in common beans. Previous studies indicate that MS involves a nutritional disorder caused by Mn deficiency. However, the inheritance and genetic mechanism of MS resistance are still not fully understood. To investigate the genetics of MS resistance, a population of 138 recombinant inbred lines (RILs) was developed from a bi-parental cross between a susceptible cultivar Messina and a resistant cultivar Cran09. The population and its two parents were evaluated for MS resistance during five consecutive years from 2015 to 2019 in both sandy and heavy clay soils in Morden, Manitoba, Canada. The severities of MS were rated and subsequently converted to MS resistance index (MSRI) and MS incidence (MSI). Statistical analyses indicated that MSI and MSRI were highly correlated (r = 0.96-0.99) and had high broad-sense heritability (H²) of 86.5% and 83.2%, respectively. Joint segregation analysis (JSA) of 18 phenotypic datasets from five years and two soil types showed that MS resistance was controlled by four major genes with genetic interactions - one of which may suppress the additive effect of the other three genes. To identify the quantitative trait loci (QTL) and the candidate genes associated with the MS resistance, the 138 RILs and the two parents were sequenced using genotyping by sequencing approach. A total of 52,676 SNPs were detected. After further filtering with a threshold of minor allele frequency > 0.01 and call rate > 20%, 2,061 SNPs were retained and then imputed for genetic map construction and QTL mapping. A genetic map consisting of 2,058 SNP markers on 11 linkage groups or chromosomes was constructed, which covered 1,004 recombination blocks with a total length of 6,449 cM and an average block of 6.42 cM. Three linkage map-based QTL-mapping models ICIM-ADD, ICIM-EPI, and GCIM and one genome-wide association study (GWAS) model RTM-GWAS for 18 phenotypic datasets from different years and soil types were used for identification of QTL. A total of 36 QTL, including 21 of additive and 15 of epistatic effects, were identified. Functional gene annotation analysis revealed 151 Mn-related candidate genes across the common bean reference genome and 17 of them harbored the six QTL discovered in this study. In conclusion, MS resistance in common bean is a highly heritable trait and controlled by several major and minor genes. The results of JSA and QTL mapping advance the current understanding of the genetic mechanisms of MS resistance in cranberry common bean, and provide additional resources for application in genomics-assisted breeding and potential isolation and functional characterization of the candidate genes.

Many countries in the global south - which harbour the majority of the world’s biodiversity - face serious resource limitations and a lack of access to affordable sequencing services. Furthermore, biodiversity research and monitoring of non-model, threatened and/or cryptic species often relies on low-quality non-invasive genetic samples. In situ conservation genomics approaches optimised for field conditions and low-quality DNA can help empower local researchers and meet their needs. To do so, however, accessible and reproducible sequencing and genotyping alternatives are needed. I designed a SNP panel as a field-friendly genotyping approach for two species of Amazonian primates using both high- and low-quality DNA samples, and two different sequencing platforms, Illumina and Nanopore. I used 14 high-quality genomes to identify a set of 210 SNPs that allow for identification of species (twelve SNPs), sex (twelve SNPs) and individual identity (186 SNPs) in two species of tamarins, Leontocebus weddelli and Saguinus imperator. Primers, adapters and indexes were designed in a Genotyping-in-Thousands by sequencing approach that is compatible with both sequencing platforms. This approach is based on sequencing multiplexed PCR products of a few hundred target SNPs to genotype thousands of individuals in a single sequencing run. In an effort to make conservation genomics more accessible, the reproducible pipeline to obtain the informative SNPs is being modulated with Snakemake, a workflow management system. / Muchos países en el sur global - los cuales poseen la mayoría de la biodiversidad mundial - enfrentan serias limitaciones de recursos y una falta de acceso a servicios económicos de secuenciación. Con frecuencia, la investigación y el monitoreo de biodiversidad y especies no-modelo, amenazadas y/o crípticas, dependen de muestras genéticas no-invasivas de baja calidad. La genómica de la conservación in situ optimizada para condiciones de campo y ADN de baja calidad puede empoderar a investigadorxs locales y ayudarles a responder a sus necesidades. Para ello, sin embargo, se requieren alternativas accesibles y reproducibles de secuenciación y genotipado. Diseñé un panel de SNPs como una aproximación de genotipado apta para el campo y dirigida a dos especies de primates amazónicos con el uso de ADN de baja y alta calidad, y dos plataformas de secuenciación (Illumina y Nanopore). Usé 14 genomas de alta calidad para encontrar 210 SNPs que permiten la identificación de la especie (doce SNPs), del sexo (doce SNPs) y de la identidad individual (186 SNPs) en dos especies de pichicos, Leontocebus weddelli y Saguinus imperator. Los cebadores, adaptadores e índices fueron diseñados con un enfoque de Genotyping-in-Thousands by sequencing (Genotipado en los miles por secuenciación) que es compatible con ambas plataformas de secuenciación. Este método está basado en la secuenciación de productos de PCR multiplexados de unos cientos de SNPs para genotipar miles de individuos en una sola corrida de secuenciación. En un intento de mejorar la accesibilidad de la genómica de la conservación, el proceso reproducible para obtener a los SNPs informativos está siendo modulado con Snakemake, un sistema de manejo de flujos de trabajo.

No description available.