Global ETD Search

121	The genomics of Type 1 Diabetes susceptibility regions and effect of regulatory SNPs Beka, Sylvia Enobong January 2016 (has links) Human complex diseases, like Diabetes and Cancer, affect many people worldwide today. Despite existing knowledge, many of these diseases are still not preventable. Complex diseases are known to be caused by a combination of genetic factors, as well as environmental and life style factors. The scope of this investigation covered the genomics of Type 1 Diabetes (T1D). There are 49 human genomic regions that are known to carry markers (disease-associated single nucleotide mutations) for T1D, and these were extensively studied in this research. The aim was to find out in how far this disease may be caused by problems in gene regulation rather than in gene coding. For this, the genetic factors associated with T1D, including the single point mutations and susceptibility regions, were characterised on the basis of their genomic attributes. Furthermore, mutations that occur in binding sites for transcription factors were analysed for change in the conspicuousness of their binding region, caused by allele substitution. This is called SNP (Single nucleotide polymorphism) sensitivity. From this study, it was found that the markers for T1D are mostly non-coding SNPs that occur in introns and non-coding gene transcripts, these are structures known to be involved in gene regulatory activity. It was also discovered that the T1D susceptibility regions contain an abundance of intronic, non-coding transcript and regulatory nucleotides, and that they can be split into three distinct groups on the basis of their structural and functional genomic contents. Finally, using an algorithm designed for this study, thirty-seven SNPs that change the representation of their surrounding region were identified. These regulatory mutations are non-associated T1D-SNPs that are mostly characterised by Cytosine to Thymine (C-T) transition mutations. They were found to be closer in average distance to the disease-associated SNPs than other SNPs in binding sites, and also to occur frequently in the binding motifs for the USF (Upstream stimulatory factor) protein family which is linked to problems in Type 2 diabetes. 616.4
122	A Novel Approach to Identify Candidate Imprinted Genes in Humans Shapiro, Jonathan 21 March 2012 (has links) Many imprinted genes are necessary for normal human development. Approximately 70 imprinted genes have been identified in humans. I developed a novel approach to identify candidate imprinted genes in humans using the premise that imprinted genes are often associated with nearby parent-of-origin-specific DNA differentially methylated regions (DMRs). I identified parent-of-origin-specific DMRs using sodium bisulfite-based DNA (CpG) methylation profiling of uniparental tissues, mature cystic ovarian teratoma (MCT) and androgenetic complete hydatidiform mole (AnCHM), and biparental tissues, blood and placenta. In support of this approach, the CpG methylation profiling led to the identification of parent-of-origin-specific differentially methylated CpG sites (DMCpGs) in known parent-of-origin-specific DMRs. I found new DMRs for known imprinted genes NAP1L5 and ZNF597. Most importantly, I discovered many new DMCpGs, which were associated with nearby genes, i.e., candidate imprinted genes. Allelic expression analyses of one candidate imprinted gene, AXL, suggested polymorphic imprinting of AXL in human blood. Allele Allele-specific DNA Methylation Allele-specific Gene Expression Allele-specific Expression Allele-specific Methylation AnCHM Androgenetic Androgenetic Mole Mole Complete Mole Hydatidiform Mole Complete Hydatidiform Mole Androgenetic Hydatidiform Mole Androgenetic Complete Hydatidiform Mole Biparental Tissue Bisulfite Bisulphite Blood Blood DNA Computational Biology DNA Methylation DNA Methylation Profiling Epigenetic Epi-genetic Epigenomic Epi-genomic Expression Expression Regulation Gene Expression Gene Expression Regulation Genetic Genetic Imprint Genetic Imprinting Genomic Genomic DNA Genomic Imprint Genomic Imprinting Human Imprint Imprinting Teratoma Ovarian Teratoma Cystic Teratoma Mature Teratoma Mature Cystic Teratoma Mature Ovarian Teratoma Cystic Ovarian Teratoma Mature Cystic Ovarian Teratoma MCT Methylation Cytosine Methylation Microarray Neoplasm Ovarian Neoplasm Placenta Profiling Promoter Promoter Region Sodium Bisulfite Sodium Bisulphite Uniparental Tissue WB WBC Imprinted Gene Polymorphic Imprinting Parent-of-origin Parent-of-origin-specific Methylation Parent-of-origin-specific Expression 0369 0307
123	A Novel Approach to Identify Candidate Imprinted Genes in Humans Shapiro, Jonathan 21 March 2012 (has links) Many imprinted genes are necessary for normal human development. Approximately 70 imprinted genes have been identified in humans. I developed a novel approach to identify candidate imprinted genes in humans using the premise that imprinted genes are often associated with nearby parent-of-origin-specific DNA differentially methylated regions (DMRs). I identified parent-of-origin-specific DMRs using sodium bisulfite-based DNA (CpG) methylation profiling of uniparental tissues, mature cystic ovarian teratoma (MCT) and androgenetic complete hydatidiform mole (AnCHM), and biparental tissues, blood and placenta. In support of this approach, the CpG methylation profiling led to the identification of parent-of-origin-specific differentially methylated CpG sites (DMCpGs) in known parent-of-origin-specific DMRs. I found new DMRs for known imprinted genes NAP1L5 and ZNF597. Most importantly, I discovered many new DMCpGs, which were associated with nearby genes, i.e., candidate imprinted genes. Allelic expression analyses of one candidate imprinted gene, AXL, suggested polymorphic imprinting of AXL in human blood. Allele Allele-specific DNA Methylation Allele-specific Gene Expression Allele-specific Expression Allele-specific Methylation AnCHM Androgenetic Androgenetic Mole Mole Complete Mole Hydatidiform Mole Complete Hydatidiform Mole Androgenetic Hydatidiform Mole Androgenetic Complete Hydatidiform Mole Biparental Tissue Bisulfite Bisulphite Blood Blood DNA Computational Biology DNA Methylation DNA Methylation Profiling Epigenetic Epi-genetic Epigenomic Epi-genomic Expression Expression Regulation Gene Expression Gene Expression Regulation Genetic Genetic Imprint Genetic Imprinting Genomic Genomic DNA Genomic Imprint Genomic Imprinting Human Imprint Imprinting Teratoma Ovarian Teratoma Cystic Teratoma Mature Teratoma Mature Cystic Teratoma Mature Ovarian Teratoma Cystic Ovarian Teratoma Mature Cystic Ovarian Teratoma MCT Methylation Cytosine Methylation Microarray Neoplasm Ovarian Neoplasm Placenta Profiling Promoter Promoter Region Sodium Bisulfite Sodium Bisulphite Uniparental Tissue WB WBC Imprinted Gene Polymorphic Imprinting Parent-of-origin Parent-of-origin-specific Methylation Parent-of-origin-specific Expression 0369 0307
124	Cis-regulatory variation and divergence in Capsella Steige, Kim A. January 2016 (has links) Cis-regulatory changes in e.g. promoters or enhancers that affect the expression of a linked focal gene have long been thought to be important for adaptation. In this thesis, I investigate the selective importance and genomic correlates of cis-regulatory variation and divergence in the genus Capsella, using massively parallel sequencing data. This genus provides an opportunity to investigate cis-regulatory changes in response to polyploidization and mating system shifts, as it harbors three diploid species, the outcrosser Capsella grandiflora and the selfers Capsella orientalis and Capsella rubella, as well as the tetraploid Capsella bursa-pastoris. We first identify cis-regulatory changes associated with adaptive floral evolution in connection with the recent switch to self-fertilization in C. rubella and show that cis-regulatory changes between C. rubella and its outcrossing close relative C. grandiflora are associated with differences in transposable element content. Second, we show that variation in positive and purifying selection is important for the distribution of cis-regulatory variation across the genome of C. grandiflora. Interestingly, the presence of polymorphic transposable elements is strongly associated with cis-regulatory variation in C. grandiflora. Third, we show that the tetraploid C. bursa-pastoris is of hybrid origin and investigate the contribution of both parental species to gene expression. We show that gene expression in the tetraploid is partly explained by cis-regulatory divergence between the parental species. Nonetheless, within C. bursa-pastoris there is a great deal of variation in homeolog expression. In summary, this thesis explores the role of cis-regulatory changes for adaptive morphological changes in connection to a shift in mating system, the role of cis-regulatory divergence between progenitor species for an allopolyploid as well as the impact of positive and purifying selection on cis-regulatory variation within a species. Capsella Shepherd's Purse cis-regulatory changes allele-specific expression mating system shift floral evolution polyploidy positive selection purifying selection transposable elements small RNA methylation transposable element silencing distribution of fitness effects
125	Diabetes mellitus 2. typu a Alzheimerova demence: studium společných patogenetických faktorů / Study of Common Pathogenetic Factors of Alzheimer Disease and Type 2 Diabetes Mellitus Vacínová, Gabriela January 2014 (has links) Alzheimer's disease (AD) and type 2 diabetes mellitus (T2DM) are aging-associated diseases that have rising prevalence in all industrialized countries. AD is a neurodegenerative disease characterized by progressive loss of cognitive functions. It is a complex disease which formation involves both genetic factors and environmental factors. The most important marker associated with this disease is the risk allele ε4 in APOE gene. From the latest genome-wide association study emerged another ten candidate genes. As the most significant from those genes appears the minority G allele of rs744373 polymorphism in the gene BIN1. AD is connected with many metabolic and immune disorders. To the markers of interest belongs also the new parameter visfatin which can act as a pro-inflammatory cytokine. T2DM is a chronic disease characterized by raised levels of blood glucose, which is also characterized by neurological disorders. In the case of both of these diseases can be found a large number of metabolic disorders. One of the most important disorders is insulin resistance. This thesis consists of two parts - the biochemical and genetic one. The biochemical part of the thesis studies the visfatin level in patients with AD and healthly control and studies whether visfatin is related to AD. In this part of the...
126	Establishment of a Y-chromosome specific extraction method for the separation of Y-chromosomal haplotypes from male DNA mixtures Rothe, Jessica 05 June 2014 (has links) Die Haplotypspezifische Extraktion (HSE) bietet für die Analyse von männlichen Mischprofilen einen neuen und direkteren Lösungsansatz, in dem die haploiden Y-chromosomalen DNS-Komponenten der einzelnen Individuen bereits vor der Analyse der individual spezifischen Marker separiert werden können und dadurch eine wirkliche physische Trennung erreicht wird. Die HSE verwendet Y-chromosomalen SNPs für die Erstellung allelspezifische Extraktionssonden, die nun gezielt nur die Marker der extrahierten DNS Komponente bzw. einer Person separieren sollen. Dabei werden im Hybridisationsschritt der HSE selektive nur komplett hybridisierte Sonden durch eine Polymerase verlängert. Während der Elongation erfolgt eine Biotinylierung des neu entstehenden Stranges, welcher dann selektiv durch Streptavidin markierte Eisenkügelchen extrahiert werden kann. Erste Durchführungen einer HSE zeigten nur eine sehr schwache bis keine Anreicherung. Während der Optimierung verschiedener Parameter wurde die Schlüsselstellung des Sondendesigns in der HSE-Technik deutlich. Die Ergebnisse zeigten, dass die neu entwickelten Sonden den Trennungserfolg der Mischprobe enorm verbessern und in einigen Fällen sogar zum Ausschluss des konkurrierenden Allels führten. Ein Vergleich der HSE Ergebnisse mit den simulierten Sondenparametern der getesteten Sonden ergab, dass der Extraktionserfolg der Sonde maßgeblich durch das Zusammenspiel von Sondenlänge und GC-Gehalt bestimmt wird. Durch dieses neu gewonnene Verständnis über den Einfluss der einzelnen Sondenparameter auf den Trennungserfolg der Mischprobe, können für künftige HSE Anwendungen Sonden effizienter erstellt und deren Wirksamkeit vorhergesagt werden. Zusätzlich konnte das neu entwickelte Vorhersage-Model der Sondenspezifität auch für weitere Extraktionsorte außerhalb des Y-Chromosoms bestätigt werden. Weiterhin konnte durch die Kombination verschiedener Sonden in einer Multiplex HSE mehrerer Y-chromosomaler Marker gleichzeitig getrennt. / Haplotype-specific extraction (HSE) allows the separation of diploid samples in their haploid components and offers in forensic a new straight forward method to separate Y-chromosomal mixed profiles, consisting of haplotype markers like short tandem repeats (STRs). The advantage of the HSE approach in mixture analysis is the real physical separation of the individual DNA components before the amplification of the STR markers. In order to use the HSE technique for the separation of male DNA mixtures, Y-chromosomal extraction probes were designed to single nucleotide polymorphisms (SNPs), which have been specific for one contributor of the male DNA mixtures. During extraction only complete matched probes are extended by a polymerase which results in the incorporation of biotinylated nucleotides. The synthesized and biotin labeled strand is separated by streptavidin coated magnetic beads. Finally, samples were analyzed by PCR coupled capillary electrophoresis for the detection of the extracted STR markers. First tests of a Y-chromosomal specific extraction showed only little till no enrichment of the targeted alleles. Therefore optimization tests of different parameters were carried out, which revealed the probe design as the key factor of successful HSE. A comparison between simulated probe parameters and their extraction success in HSE showed that the HSE probe efficiency mainly depends of the relation of probe length and GC-contents. Because of the new gained knowledge about the influence of the probe-design on the separation success, probes for future HSE application can be developed faster and cost-effective. The new prediction model for probe-specificity was also successful tested for the extraction of other genome-loci. Furthermore, a multiplex HSE approach was used to separate several STR markers simultaneously in one extraction reaction and therefore achieved the separation of one contributor Y-chromosomal haplotype. Haplotypspezifische Extraktion allelspezifische Sonden Mischspuren dbSNPs Sondendesign ASER haplotype-specific extraction dbSNP forensic DNA mixture probe design mixed profiles allele-specific probes ASER 570 Biowissenschaften, Biologie 32 Biologie WC 4460 ddc:570
127	Microfluidic bead-based methods for DNA analysis Russom, Aman January 2005 (has links) With the completion of the human genome sequencing project, attention is currently shifting toward understanding how genetic variation, such as single nucleotide polymorphism (SNP), leads to disease. To identify, understand, and control biological mechanisms of living organisms, the enormous amounts of accumulated sequence information must be coupled to faster, cheaper, and more powerful technologies for DNA, RNA, and protein analysis. One approach is the miniaturization of analytical methods through the application of microfluidics, which involves the manipulation of fluids in micrometer-sized channels. Advances in microfluidic chip technology are expected to play a major role in the development of cost-effective and rapid DNA analysis methods. This thesis presents microfluidic approaches for different DNA genotyping assays. The overall goal is to combine the potential of the microfluidic lab-on-a-chip concept with biochemistry to develop and improve current methods for SNP genotyping. Three genotyping assays using miniaturized microfluidic approaches are addressed. The first two assays are based on primer extension by DNA polymerase. A microfluidic device consisting of a flow-through filter chamber for handling beads with nanoliter liquid volumes was used in these studies. The first assay involved an allelespecific extension strategy. The microfluidic approach took advantage of the different reaction kinetics of matched and mismatched configurations at the 3’-ends of a primer/template complex. The second assay consisted of adapting pyrosequencing technology, a bioluminometric DNA sequencing assay based on sequencing-bysynthesis, to a microfluidic flow-through platform. Base-by-base sequencing was performed in a microfluidic device to obtain accurate SNP scoring data on nanoliter volumes. This thesis also presents the applications of monolayer of beads immobilized by microcontact printing for chip-based DNA analysis. Single-base incorporation could be detected with pyrosequencing chemistry on these monolayers. The third assay developed is based on a hybridization technology termed Dynamic Allele-Specific Hybridization (DASH). In this approach, monolayered beads containing DNA duplexes were randomly immobilized on the surface of a microheater chip. DNA melting-curve analysis was performed by dynamically heating the chip while simultaneously monitoring the DNA denaturation profile to determine the genotype. Multiplexing based on single-bead analysis was achieved at heating rates more than 20 times faster than conventional DASH provides. / QC 20101008 Genetics single nucleotide polymorphism DNA analysis SNP microfluidics pyrosequencing beads lab on a chip hybridization DASH microsystem micro totat analysis system allele-specific extension DASH microcontact printing Genetik Clinical genetics Klinisk genetik
128	The Impact of Genome-Wide Supported Schizophrenia Risk Variants in the Neurogranin Gene on Brain Structure and Function Walton, Esther, Geisler, Daniel, Hass, Johannes, Liu, Jingyu, Turner, Jessica, Yendiki, Anastasia, Smolka, Michael N., Ho, Beng-Choon, Manoach, Dara S., Gollub, Randy L., Rößner, Veit, Calhoun, Vince D., Ehrlich, Stefan 06 February 2014 (has links) (PDF) The neural mechanisms underlying genetic risk for schizophrenia, a highly heritable psychiatric condition, are still under investigation. New schizophrenia risk genes discovered through genome-wide association studies (GWAS), such as neurogranin (NRGN), can be used to identify these mechanisms. In this study we examined the association of two common NRGN risk single nucleotide polymorphisms (SNPs) with functional and structural brain-based intermediate phenotypes for schizophrenia. We obtained structural, functional MRI and genotype data of 92 schizophrenia patients and 114 healthy volunteers from the multisite Mind Clinical Imaging Consortium study. Two schizophrenia-associated NRGN SNPs (rs12807809 and rs12541) were tested for association with working memory-elicited dorsolateral prefrontal cortex (DLPFC) activity and surface-wide cortical thickness. NRGN rs12541 risk allele homozygotes (TT) displayed increased working memory-related activity in several brain regions, including the left DLPFC, left insula, left somatosensory cortex and the cingulate cortex, when compared to non-risk allele carriers. NRGN rs12807809 non-risk allele (C) carriers showed reduced cortical gray matter thickness compared to risk allele homozygotes (TT) in an area comprising the right pericalcarine gyrus, the right cuneus, and the right lingual gyrus. Our study highlights the effects of schizophrenia risk variants in the NRGN gene on functional and structural brain-based intermediate phenotypes for schizophrenia. These results support recent GWAS findings and further implicate NRGN in the pathophysiology of schizophrenia by suggesting that genetic NRGN risk variants contribute to subtle changes in neural functioning and anatomy that can be quantified with neuroimaging methods. Allele Antipsychotika Neuroleptika Funktionelle Magnetresonanztomographie Haplotyp Phänotyp Schizophrenie Genotyp Arbeitsgedächtnis TU Dresden Publikationsfonds Alleles Antipsychotics Functional magnetic resonance imaging Haplotypes Phenotypes Schizophrenia Variant genotypes Working memory Technical University Dresden Publication funds ddc:610 rvk:XA 10000
129	Molecular Marker Applications in Oat (Avena Sativa L.) Breeding and Germplasm Diagnostics Benazir Katarina, Marquez 27 May 2014 (has links) The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars. oat (Avena sativa L.) DNA fingerprinting genotyping-by-sequencing (GBS) graphical genotyping single nucleotide polymorphism (SNP) quantitative trait loci (QTL) pedigree haplotype intra-cultivar variation cultivar genomic heterogeneity KBioscience's Allele-Specific PCR (KASP)
130	Understanding impulsivity : molecular genetic and environmental influences White, Melanie Jade January 2008 (has links) Features of impulsivity underlie multiple psychological disorders. The body of work examining impulsivity has largely focussed on self-report measurement and has incorporated psychological constructs without reference to the broader biological factors that may influence impulsive behaviour. Two studies were conducted to examine whether environmental stress and genetic status associated with dopaminergic and serotonergic function (DRD2, ANKK1 and 5HT2AR genotypes) were predictive of dimensions of impulsivity and risky behaviour (alcohol use). The two studies used a multi-method approach in a non-clinical community sample of young adults (aged 17-25 years). Dopamine is integral to the two leading theories of impulsive personality, Gray's Reinforcement Sensitivity Theory and Cloninger's Psychobiological model of personality. Dopamine plays a crucial role in reward reinforcement circuits in the brain. The A1 allele of the ANKK1 gene (also referred to as TaqIA of the DRD2 gene region) and the CC genotype of the C957T polymorphism of the DRD2 gene have both been associated with reduced D2 dopamine receptor density in key structures linked to brain reward. In addition, a strong body of evidence implicates their involvement in a number of clinical disorders associated with impulsivity. Serotonin function has also been associated with impulsivity in Cloninger's theory and there is also evidence of associations of two polymorphisms of the 2A serotonin receptor gene (5HT2AR T102C and -1438A/G SNPs) with impulsivity. Acute and chronic forms of stress are also important correlates of impulsive behaviour and the two studies directly examined the relationship between genotype, stress and impulsivity. Study 1 (N=180) utilised a cross-sectional design and examined interactions between these polymorphisms and chronic stress exposure on key impulsivity dimensions of reward sensitivity, Novelty Seeking and rash impulsiveness. Participants completed psychological questionnaires measuring chronic stress, dimensions of impulsivity, mood and substance use and provided mouth swab samples of buccal mucosal cells for DNA analysis. The study confirmed the association between A1 and CC allelic status and chronic stress being associated with harm avoidance and sensitivity to punishment. This suggests a role for both dopamine and background stress in impulsive behaviour. Study 2 (N=73) built upon this questionnaire research in the laboratory by utilising experimental psychological paradigms of impulsive behaviour and experimentally manipulating acute stress. Study 2 employed a mixed experimental design with a sub-sample of those studied in the cross-sectional sample. These behavioural paradigms included pre- and post- stress induction administration of the Card Arranging Reward Responsiveness Objective Test (capturing behavioural approach in the presence of reward cues, presumed to reflect reward sensitivity) and post-induction delay discounting and response inhibition measures. Study 2 confirmed the role of one of the two dopamine-related polymorphisms, with those with A1+ allelic status demonstrating lower reward responsiveness prior to rest or stress induction, which was overcome in the second administration of this task, independent of environment. A1+ allelic individuals also demonstrated significantly poorer response inhibition independent of stress, further confirming the association between A1+ allelic status and impulsivity. Those with CC allelic status showed an increase in reward responsiveness only in the stress induction condition. Together, results from the two studies inform the development of a multidimensional model of impulsivity that captures gene-environment influences on discrete aspects of impulsive personality and behaviour. Further refinement of this model may lead to the development of more effective customised prevention and treatment interventions for clinically disordered impulsivity. The implications of dopaminergic systems and stress in understanding disorders such as ADHD and substance dependence are discussed. impulsivity reward punishment reinforcement sensitivity theory psychobiological model personality reward deficiency theory molecular genetics dopamine serotonin receptor gene A1 allele TaqIA C957T T102C -1438A/G chronic stress acute stress psychosocial stressor

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