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Dissertations / Theses on the topic 'Polymorphisms'

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Published: 4 June 2021

Last updated: 9 June 2025

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1

Karlsson, Sten. "Dynamics of genetic polymorphisms." Doctoral thesis, Norwegian University of Science and Technology, Department of Biology, 2005. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-1992.

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2

Guerra, Sandra. "Gene polymorphisms in SLE." Thesis, King's College London (University of London), 2013. https://kclpure.kcl.ac.uk/portal/en/theses/gene-polymorphisms-in-sle(96ff1bac-bcca-40f1-bfd7-24bc87dc7a25).html.

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Systemic lupus erythematosus (SLE) is an autoimmune disease, with a strong genetic component. It is characterised by hyperactive T and B cells, chronic inflammation and the production of antinuclear autoantibodies. SLE affects mostly women of child baring age, with a 9:1 ratio, women to men and has been reported to be more prevalent in people of non-European ancestry. In the era of genome-wide association studies (GWAS), elucidating the genetic factors present in SLE has been very successful, with over 28 confirmed disease susceptibility loci mapped and a number of candidate genes identified. During this thesis I fine mapped IL18 as it had previously been reported to be associated with SLE, SNP rs360719. After fine mapping and subphenotype analysis in UK and African American cohorts, I was unable to replicate the published association. Although genetic data did not confirm IL18 to be associated with SLE, I demonstrated increased IL-18 serum levels in SLE renal patients compared to SLE patients. I further analysed IL10, another previously associated SLE candidate loci in our current SLE GWAS cohort (4000 cases and 9000 controls) of European ancestry. I again was unable to replicate the previous association, however using other SLE GWAS data showed SNP rs3024505 to be associated in Northern European samples. Further analysing our SLE GWAS, I located IKZF3 as a candidate loci. I identified an associated block of 56 SNPS and located the association to a single SNP rs2941509, p=1.46xlQ-8. Furthermore, I demonstrated an allelic imbalance in this SNP, with the protective G allele being expressed 1.5 times greater than the risk A allele, in controls. These data here demonstrated in this thesis indicates the importance of fine mapping candidate loci and verification of previously associated loci. This thesis contributes to the current knowledge of SLE by demonstrating discrepancies in published association data and showing the importance of larger studies.

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3

Ho, Timothy Boon Leong. "Pathogen polymorphisms of mycobacterium tuberculosis." Thesis, Imperial College London, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.399538.

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4

Zghebeh, Helena. "Cytokine polymorphisms in pre-eclampsia." Thesis, University of Leeds, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.511158.

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5

黎子韻 and Tsz-wan Kristi Lai. "Genetic polymorphisms in ovarian cancer." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2002. http://hub.hku.hk/bib/B31970618.

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6

Tyrer, Jonathan Patrick. "Patterns and networks of polymorphisms." Thesis, University of Sheffield, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.307109.

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7

Barroso, Joana Barbara de Bessa. ""Obesity and inflammation: associated polymorphisms"." Master's thesis, Faculdade de Medicina da Universidade do Porto, 2008. http://hdl.handle.net/10216/23729.

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8

Bondarkova, A. M. "ADRB2 polymorphisms and asthma susceptibility." Thesis, Сумський державний університет, 2013. http://essuir.sumdu.edu.ua/handle/123456789/33568.

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Beta-2-Adrenergic receptors (ADRB2) participate in the physiologic responses of the lung, including bronchodilation and bronchoprotection, through mechanisms such as mucociliary clearance, fluid accumulation and mediator release from mast cells and basophils. Thus, these receptors may also play an important role in the pathophysiology of asthma. The gene encoding ADRB2 is extremely polymorphic, and studies of this gene improves our understanding of asthma and possibly lead to new methods to prevent, diagnose and treat it. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/33568

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9

Lai, Tsz-wan Kristi. "Genetic polymorphisms in ovarian cancer." Hong Kong : University of Hong Kong, 2002. http://sunzi.lib.hku.hk/hkuto/record.jsp?B25176493.

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10

Barroso, Joana Barbara de Bessa. ""Obesity and inflammation: associated polymorphisms"." Dissertação, Faculdade de Medicina da Universidade do Porto, 2008. http://hdl.handle.net/10216/23729.

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11

Genini, Sem. "Establishment of quick-methods to reveal DNA-polymorphisms single strand conformational polymorphism (SSCP) and heteroduplex analysis (HA) /." Zurich : Swiss Federal Institute of Technology, Department of Animal Sciences, Breeding Biology, 2002. http://e-collection.ethbib.ethz.ch/show?type=dipl&nr=50.

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12

Wasfi, Yasmine S. "Apoptosis-related genetic polymorphisms in sarcoidosis /." Connect to full text via ProQuest. IP filtered, 2005.

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13

Roecklein, Kathryn Ariel. "Melanopsin polymorphisms in seasonal affective disorder /." Download the thesis in PDF, 2005. http://www.lrc.usuhs.mil/dissertations/pdf/Roecklein2005.pdf.

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14

Dinc, Havva. "Alu Insertion Polymorphisms In Anatolian Turks." Master's thesis, METU, 2003. http://etd.lib.metu.edu.tr/upload/1169929/index.pdf.

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In the present study<br>ten autosomal human-specific Alu insertion polymorphisms<br>ACE, APO, A25, B65, D1, FXIIIB, HS4.32, HS4.69, PV92 and TPA25 were analyzed in approximately 100 unrelated individuals from Anatolia. Alu insertion polymorphisms offer several advantages over other nuclear DNA polymorphisms for human evolution studies. The frequencies of the ten biallelic Alu insertions in Anatolians were calculated and all systems were found to be in Hardy-Weinberg equilibrium (p&gt<br>0.05). By combining the results of this study with results of previous studies done on worldwide populations, the genetic distance (Nei&rsquo<br>s DA) between each pair of populations was calculated and neighbor joining trees were constructed. In general, geographically closer populations were found to be also genetically similar. Principal component analysis (PCA) was performed and Anatolia was found to be in the European cluster. As a result of PCA<br>it was concluded that FXIIIB, PV92 and ACE were the variables contributing the most to the explanation of the variation between the populations. Additionally<br>canonical variates analysis (CVA) concluded that the most discriminative markers for the groups of populations were PV92, D1, ACE and HS4.32. Pair-wise Fst values were also calculated between Anatolians and some of the populations for which the data was available. It was concluded that, Anatolians have non-significant pair-wise Fst values with Swiss and French Acadian populations. Lastly, heterozygosity vs. distance from centroid graph was constructed and it was found that Anatolians and India-Hindu had exactly the expected heterozygosity value predicted by the model of Harpending and Ward (1982).

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15

Marsh, Howard Piers. "Genetic polymorphisms in bladder cancer angiogenesis." Thesis, University of Bristol, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.428513.

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16

Cadenas, Alicia M. "Y-chromosome polymorphisms in southern Arabia." FIU Digital Commons, 2006. http://digitalcommons.fiu.edu/etd/1962.

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In order to explore south Arabia's role in the migratory episodes leaving Africa to Eurasia and back, high-resolution Y-chromosome analyses of males from the United Arab Emirates (164), Qatar (72) and Yemen (62) were performed. The distribution of specific haplogroups (E3bl-M35 and J1-M267) and their microsatellite-based age estimates in southern Arabia offer additional insight on their dissemination. With the exception of Yemen, southern Arabia displays high diversity in its Y-haplogroup substructure and share similarities with populations along the eastern coast of the Gulf of Oman, possibly serving as a coastal corridor for migrations. Elevated rates of consanguinity may have had an impact in Yemen and Qatar, which experience deficiencies in their ratios of observed to expected heterozygosity at 15 hypervariable autosomal STR loci. Higher diversity along the Gulf of Oman may be due to trade emanating from the kingdom of Oman involving East Africa, southern Pakistan and western India.

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17

Harcourt, Rebecca Louise. "DNA sequence polymorphisms in Triticeae species." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239617.

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18

Carpen, Jayshan D. "Polymorphisms in the human Period genes." Thesis, University of Surrey, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.441716.

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19

Pong-Wong, Ricardo. "Milk protein polymorphisms in dairy cattle." Thesis, University of Edinburgh, 1996. http://hdl.handle.net/1842/11270.

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This study covered two main areas of major genes affecting quantitative traits: (i) the estimation of their effects with emphasis on the milk protein loci and (ii) the use of genotype information on major genes as part of the selection criteria. In a situation in which only a subset of the population has known genotypes for a major gene, the estimated effects of this gene obtained with a method using performance information on all the individuals (with and without known genotype) were compared with those estimates obtained with a method using information on only individuals with known genotype. The first method used a Gibbs sampling approach to infer genotypes of individuals with unknown value. The results from a simulation study showed that, in absence of selection, both methods yielded unbiased estimates of the major gene effects. However, the inclusion of performance information of individuals without genotype decreased the error variance of the estimates by 12 to 69% of the reduction there would be if all individuals had known genotype, depending on the gene frequency, and the mode of action of the major locus. In the population undergoing selection the use of such information also substantially reduced the bias of estimates. This methodology was applied to estimation of the effects of the β-lactoglobulin and the κ-casein loci on lactation traits (milk yield, fat and protein yield and content), using data from 1452 Holstein Friesian cows of two experimental herds and a MOET nucleus in the UK, and available progeny test of sires. There were no significant effects of these loci on any of the traits considered. To study the use of genotype information as part of the selection criteria, a deterministic model for predicting response to selection when a single locus is segregating was defined. It was used to compare the traditional phenotypic selection with other methods of combining performance information with either the genotype of the major locus or only its Mendelian sampling term (i.e. the effect due to the major locus expressed as deviation from family mean).

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20

Gayden, Tenzin. "Y-chromosome polymorphisms in the Himalayas." FIU Digital Commons, 2006. http://digitalcommons.fiu.edu/etd/3587.

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In the present study, high resolution Y-chromosome SNP analyses were employed to investigate the genetic origins of three distinct groups from Nepal namely, the general population of Kathmandu, Newar, and Tamang, as well as a collection from Tibet. The results suggest that the Tibetans and Nepalese are descendants of Tibeto-Burman speaking groups originating in Northeast Asia. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to Indian Y haplogroup substructure. These results suggest recent gene flow from the Indian subcontinent, a conclusion that is also supported by the admixture analysis. In contrast, while YAP+ , a genetic signature of Central Asian origin, is completely absent in Nepal, it accounts for more than fifty percent of Tibetan Y-chromosome. Low frequencies of haplogroup R lineages in Tibet reflect limited gene flow from India most likely due to the Himalayan mountain range to the south.

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21

Howell, Bruce F. "The Use of Genetic Polymorphisms and Discriminant Analysis in Evaluating Genetic Polymorphisms as a Predictor of Population." Thesis, University of North Texas, 2002. https://digital.library.unt.edu/ark:/67531/metadc3138/.

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Discriminant analysis is a procedure for identifying the relationships between qualitative criterion variables and quantitative predictor variables. Data bases of genetic polymorphisms are currently available that group such polymorphisms by ethnic origin or nationality. Such information could be useful to entities that base financial determinations upon predictions of disease or to medical researchers who wish to target prevention and treatment to population groups. While the use of genetic information to make such determinations is unlawful in states and confidentiality and privacy concerns abound, methods for human “redlining” may occur. Thus, it is necessary to investigate the efficacy of the relationship of certain genetic information to ethnicity to determine if a statistical analysis can provide information concerning such relationship. The use of the statistical technique of discriminant analysis provides a tool for examining such relationship.

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22

Robitaille, Nicole. "Polymorphisme de l'apolipoprotéine E au sein de la population du Lac St-Jean Chibougamau /." Thèse, Chicoutimi : Université du Québec à Chicoutimi, 1994. http://theses.uqac.ca.

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Mémoire (M.Med.Exp.)-- Université du Québec à Chicoutimi, 1994.<br>Ce mémoire a été réalisé à l'Université du Québec à Chicoutimi dans le cadre du programme de maîtrise en médecine expérimentale de l'Université Laval extensionné à l'UQAC. CaQCU Document électronique également accessible en format PDF. CaQCU

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23

Sauer, Sascha. "Technology development for genotyping single nucleotide polymorphisms." [S.l.] : [s.n.], 2001. http://www.diss.fu-berlin.de/2002/102/index.html.

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24

Byström, Jonas. "Eosinophil Cationic Protein : Expression Levels and Polymorphisms." Doctoral thesis, Uppsala University, Department of Medical Sciences, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-2059.

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<p>The eosinophil cationic protein (ECP) is usually associated with the eosinophil granulocyte. In this thesis the presence and production of this protein has been studied in two other cells. The circulating monocyte was found to contain ECP mRNA and small amounts of ECP, one thousand times less than that found in the eosinophil. The production decreased by differentiation of the myelomonoblastic cell line U937 into a macrophage phenotype. Submucosal lung macrophages did not stain for ECP and alveolar macrophages did not contain ECP mRNA. The circulating neutrophil contains ECP at a level hundred fold less than the eosinophil. We found that the protein is located to the primary granules of the neutrophil but could detect no ECP mRNA in the cell. It was shown in vitro that the protein was taken up by the cell and partly transported to the primary granules. The uptake did not seem to be receptor mediated. Upon stimulation of the neutrophils, ECP previously taken up, was re-secreted. </p><p>The ECP protein is heterogeneous both to molecular characteristics and to function. To evaluate if a genetic component is involved, the ECP gene was analysed in 70 individuals. Three single nucleotide polymorphisms (SNP´s) were found, denoted 277(C>T), 434(G>C) and 562(G>C). The two first were located to the mature peptide-coding region and would change the amino acids, arg45cys and arg97thr. The prevalence of the most common SNP, 434, was evaluated in two eosinophil-related diseases, allergy/asthma and Hodgkin Lymphoma (HL). Forty-three HL patients were evaluated and it was found that the 434GG was significantly more prevalent in patients having nodular sclerosis (NS) as compared to other histologies (p=0.03). Erythrocyte sedimentation rate was also related to the 434GG genotype (p=0.009). In 209 medical students 434GG was more common (p=0.002) in those who indicated allergy. The genotype was unrelated to the production of IgE antibodies to allergens. In analysis of 76 subjects with asthma it was found that the 434GG genotype was significantly more common among allergic asthmatics (p=0.04). Asthma and HL-NS are characterized by fibrosis and eosinophils and ECP has been suggested in fibrosis development. </p>

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25

Leviel, Keren Sullivan Patrick F. "Investigation of polymorphisms in schizophrenia relevant genes." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2006. http://dc.lib.unc.edu/u?/etd,305.

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Thesis (M.S.)--University of North Carolina at Chapel Hill, 2006.<br>Title from electronic title page (viewed Oct. 10, 2007). "... in partial fulfillment of the requirements for the degree of Master of Science in the Department of Genetics." Discipline: Genetics; Department/School: Medicine.

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26

Bashiardes, Evy. "Gene polymorphisms, gene expression and atherosclerotic plaques." Thesis, Imperial College London, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.420882.

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27

Mathias, Neal. "Y chromosome DNA polymorphisms and human evolution." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333355.

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28

Hubner, Richard Anthony. "Low penetrance polymorphisms and colorectal neoplasia susceptibility." Thesis, Institute of Cancer Research (University Of London), 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.499095.

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29

Hogben, Alexandra Leigh. "Diurnal preference, clock gene polymorphisms and personality." Thesis, University of Surrey, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.527006.

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30

Heathcote, Kirsten. "Polymorphisms of the human TGF-β1 gene". Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.603934.

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Experimental evidence has implicated a function for TGF-β1 in many pathological processes, including atherosclerosis, cancer, fibrotic diseases and osteoporosis. In this study 1115 bp of the TGF-β1 promoter, the 5' untranslated region and exons 1, 2 and 3 were screened by single stranded conformational polymorphism analysis. Four polymorphisms were identified in the TGF-β1 gene at -800 and -509 of the promoter and at +869 (codon 10) and +914 (codon 25) of exon 1. A simple non-radioactive assay was developed for each of these polymorphisms and also for a polymorphism located at +1628 (exon 5, codon 263) which was reported in the literature. These polymorphisms were analysed in a study of postmenopausal female twins and the -800, -509 and +869 polymorphisms were associated with the concentration of TGF-β1 in the serum detected by ELISA. The TGF-β1 promoter polymorphisms (-509 and -800) were associated with increased and decreased serum TGF-β1 respectively in the twin study. These promoter isoforms were assayed <I>in vitro</I> to establish whether there was a functional effect of the polymorphisms on the basal activity of the TGF-β1 promoter. However, the activity of the TGF-β1 promoter was weak, and in the cell line studied no difference in activity between the isoforms of the TGF-β1 promoter was observed. The five TGF-β1 polymorphisms were analysed in 457 subjects recruited to the St. George's Heart Disease study. None of the polymorphisms showed any association with either coronary artery disease or hypertension in this study. However, strong linkage disequilibrium was observed at the TGFB1 locus and haplotypes of the locus were also considered in this study. The haplotype G(-800)C(-509)T(+869)G(+914)C(+1628) arose more frequently in the control subjects than the coronary artery disease cases (p=0.024), suggesting that it may be cardioprotective. The -509 and -800 TGF-β1 promoter polymorphisms were analysed in subjects of a breast cancer study. Subjects homozygous for the -800A allele appeared to have an increased risk for breast cancer in this study (relative risk 3.9, 95% confidence interval 0.90-17), but few homozygotes were observed and this risk was not insignificant.

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31

阮陳健貞 and Kian-cheng Tan-Un. "Chinese B thalassaemia: DNA polymorphisms andspecific mutations." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1986. http://hub.hku.hk/bib/B31230970.

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32

Wheatley, Amanda Patricia. "#beta#â†2-adrenoceptor polymorphisms and asthma." Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.326540.

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33

Lanchbury, J. S. S. "Studies of genetic polymorphisms in human populations." Thesis, University of Newcastle Upon Tyne, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.371918.

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34

Hennig, Branwen Johanna Wanda. "Genetic polymorphisms and early-onset periodontal diseases." Thesis, University of Newcastle Upon Tyne, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.311107.

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35

Payne, Katie Emma. "β₃ integrin gene polymorphisms and gene regulation". Thesis, University of Leeds, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.413197.

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36

Reynard, Mark. "Cytokine gene polymorphisms and their clinical relevance." Thesis, University College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.404568.

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37

Brown, Jason John. "Polymorphisms of the equine Major Histocompatibility Complex." Thesis, University of Liverpool, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.406666.

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38

Baresic, A. "Structural analysis of single amino acid polymorphisms." Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1344177/.

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Understanding genetic variation is the basis for prevention and diagnosis of inherited disease. In the `next generation sequencing' era with rapidly accumulating variation data, the focus has shifted from population-level analyses to individuals. This thesis is centred on the problem of gathering, storing and analysing mutation data to understand and predict the effects single amino acid mutations will have on protein structure and function. I present analysis of a subset of mutations and a new predictive method implemented to expand the coverage of the structural effects by our pipeline. I characterised a subset of pathogenic mutations: `compensated pathogenic deviations'. These are mutations which cause disease in humans, but the mutant residues are found as native residues in other species. During evolution, they are presumed to spread through populations by coevolving with another, neutralising mutation. When compared with uncompensated mutations, they often cause milder structural disruptions, prefer less conserved structural environments and are often found on the protein surface. I describe the development of a new analysis to test the eeffects of mutations by predicting residues involved in protein-protein interfaces where the structure of the complex is unknown. Two machine learning methods (multilayer perceptrons and, in particular, random forests) show an improvement over previously published protein-protein interface predictors. This new method further increases the ability of the SAAPdb analysis pipeline to show the effects of mutations on protein structure and function. Furthermore, it is a template for building prediction-based structural analysis methods for the pipeline, where available structural data are insufficient. In summary this thesis examines mutations from both an evolutionary and a disease perspective. In addition, a novel method for predicting protein interaction regions is developed thus expanding the existing pipeline and furthering our ability to understand mutations and use them in a predictive context.

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39

Singh, Ravi Kumar. "Platelet reactivity, polymorphisms and premature myocardial infarction." Thesis, University of Leicester, 2005. http://hdl.handle.net/2381/29880.

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I have carried out a detailed assessment of platelet function and reactivity in 205 subjects that suffered a premature MI (at a mean age 42.3 +/- 5.7) and 200 age and sex matched controls, to two endogenous platelet agonists adenosine diphosphate (ADP) and thrombin receptor activating peptide (TRAP). I have further analysed the effect on platelet function of polymorphisms in two platelet receptors (GPIIbIIIa C196T and GPIaIIa G873A), which have been proposed as genetic risk factors for MI. Platelet reactivity to several concentrations of ADP and TRAP, measured as degree of fibrinogen binding by flow cytometry, showed marked inter-individual variation (4-5 fold) in both cases and controls. There was a strong correlation between the ADP and TRAP responses and experimental analysis suggested that this was because the TRAP response is substantially mediated via the ADP receptor.;Expression of the GPIaIIa receptor on the platelet surface showed up to 10-fold variation between subjects. The G837A polymorphism in the GP1a gene had a marked effect on GPIaIIa expression (accounting for about one-fifth of the variation) but did not influence the risk of MI (odd ratio 1.12 (95%CI 0.86-1.46)). Expression of the GPIIbIIIa receptor in both the resting state and after agonist stimulation was not affected by C196T polymorphism in the GPIIIa gene and did not influence risk of MI (odds ratio=0.94 (0.61-1.45)).;Of the emerging risk factors, fibrinogen (p<0.001) and Lp(a) (p = 0.016) were higher in the cases. There were significant effect of the G455A polymorphism in the fibrinogen beta chain gene and the C93T polymorphism in the apolipoprotein (a) gene on fibrinogen and Lp(a) levels, respectively.

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40

Greene, Jennifer A. "Toll-like Receptor Polymorphisms and Cerebral Malaria." Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1270153850.

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41

Yoshida, Kanako. "Analysis of DNA polymorphisms for human identification." Kyoto University, 2000. http://hdl.handle.net/2433/181418.

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42

Lau, Chi Chiu. "Hepatitis B virus and single nucleotide polymorphisms." HKBU Institutional Repository, 2007. http://repository.hkbu.edu.hk/etd_ra/810.

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43

Williams, Neil Ray. "PCR-based polymorphisms in bermudagrass (Cynodon spp.)." [Gainesville, Fla.] : University of Florida, 2003. http://purl.fcla.edu/fcla/etd/UFE0001484.

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44

Wong, Li-Chuen. "IL-10 promoter polymorphisms in atopic dermatitis." Thesis, The University of Sydney, 2002. https://hdl.handle.net/2123/27849.

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Atopic dermatitis (AD) is one of the many clinical manifestations of atopy. It is one of the most common chronic inflammatory skin diseases with increasing prevalence over the last century. The aetiology of this disease is multifactorial with a complex interaction of genetic, environmental and immunologic factors.

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45

Clark, Daniel N. "Promoter Polymorphisms in Interferon Regulatory Factor 5." BYU ScholarsArchive, 2013. https://scholarsarchive.byu.edu/etd/4058.

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The promoter region of interferon regulatory factor 5 (IRF5) contains the rs2004640 T or G single nucleotide polymorphism (SNP) and a CGGGG indel. Both of these polymorphisms have been implicated as genetic risk factors for several autoimmune diseases, including systemic lupus erythematosus, whose pathology involves altered apoptosis and cytokine signaling. The polymorphisms' overall effect is to increase IRF5 levels. IRF5 is a transcription factor of several cytokines, including interferon, and is pro-apoptotic. Thus an alteration of cytokine levels and apoptosis signaling due to high IRF5 levels is the proposed source of autoimmune risk. Each of IRF5's four first exons (1A, 1B, 1C, 1D) has its own promoter and responds to specific stimuli. rs2004640 is a T or G polymorphism; T is the risk allele. The SNP creates a sequence-specific recognition site for the spliceosome, making exon 1B spliceable. Analysis of the 1B promoter showed putative p53 binding site. IRF5 and p53 are pro-apoptotic transcription factors, and the p53 site may provide a positive feedback loop. Apoptosis levels were altered in cells with the rs2004640 risk T/T allele when treated with DNA damaging agents (extrinsic apoptosis), but not when activating death receptors (intrinsic apoptosis). The 1B promoter was the only one to activate expression after inducing DNA damage in a luciferase reporter assay, and this activation was abolished after mutating the p53 site. The exon 1A promoter contains either three or four copies (4X) of CGGGG; the 4X variant is the risk allele. The 1A promoter is constitutively active and is responsive to the Toll-like receptor 7 agonist imiquimod. RNA folding analysis revealed a hairpin encompassing exon 1B. Mutational analysis showed that the hairpin shape decreased translation five-fold in a luciferase reporter assay. Cells with the CGGGG or rs2004640 risk allele exhibited higher levels of IRF5 mRNA and protein, but demonstrated no change in mRNA stability. Quantitative PCR in cell lines with either risk polymorphism demonstrated decreased usage of exons 1C or 1D, although no other correlated splicing events were observed. Also, several mRNA splice variants of IRF5 were sequenced. The risk polymorphisms altered cytokine signaling as well. Expression of interferon, Toll-like receptor, and B cell receptor pathways were affected by a risk haplotype which includes the rs2004640 SNP. The CGGGG polymorphism decreased the levels of CC-chemokine receptor 7. Specific transcription factor binding sites define promoter activity and thus first exon usage and transcription levels. Translation levels are affected by mRNA folding. Overall, the rs2004640 SNP and the CGGGG indel cause high levels of IRF5. High IRF5 expression causes altered cytokine and apoptosis signaling, and may bias the immune system toward autoimmunity.

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46

Gutierrez, Cortes Nicolas. "Expression métabolique des polymorphismes mitochondriaux : mutations pathogènes et haplogroupes." Thesis, Bordeaux 2, 2011. http://www.theses.fr/2011BOR21877/document.

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Les mitochondries, organelles intracellulaires des eucaryotes, fournissent par les oxydations phosphorylantes l'essentiel de l'énergie nécessaire aux différents travaux cellulaires sous la forme d'ATP grâce à un couplage entre la chaîne respiratoire et l’ATPsynthase. Ces réactions du métabolisme énergétique sont assurées par des complexes enzymatiques constitués de sous-unités codées à la fois par l'ADN nucléaire et par l'ADN mitochondrial. Il a été montré que des défauts dans l'activité de ces complexes pouvaient être responsables de l’apparition de pathologies regroupées sous le nom de cytopathies d’origine mitochondriale. Un des problèmes fondamentaux qui se pose lors de l’étude des mécanismes conduisant aux pathologies mitochondriales est de comprendre l’influence de l’ADN mitochondrial sur le métabolisme de la mitochondrie. En effet, la mitochondrie possède son propre ADN, et les mutations de cet ADN sont classées selon leur impact sur le métabolisme mitochondrial : des mutations pathogènes, qui ont des répercussions négatives sur ce métabolisme, et des polymorphismes, qui sont considérés comme étant neutres.Pour étudier l’influence de l’ADNmt sur le métabolisme énergétique, j’ai utilisé deux modèles d’étude : des cybrids portant des mutations de l’ADNmt retrouvées chez des patients atteints de surdité non-syndromique, et des cybrids portant des polymorphismes caractéristiques de l’haplogroupe J.Les résultats obtenus nous indiquent clairement que la différence entre des mutations pathogènes et des polymorphismes n’est pas aussi importante que ce qui était jusqu’à alors supposé. En effet, elle dépend d’un ensemble de facteurs tels que (i) le fonds génétique nucléaire et mitochondrial, (ii) de facteurs environnementaux. Car sous l’influence de ces différents facteurs une mutation considérée comme pathogène peut devenir neutre, et un polymorphisme considéré comme neutre peut devenir pathogène<br>Mitochondria, intracellular organelles of eukaryotic organisms, provide most of the necessary energy for cellular activity through oxidative phosphorylation, synthesizing ATP (energy source for the cell) by a coupling between the respiratory chain and the ATPsynthase. These energy metabolism reactions are carried out by enzymatic complexes constituted by sub-units coded by both nuclear and mitochondrial DNA. It has been shown that activity defects in these complexes could be responsible for a group of pathologies under the name of mitochondrial cytopathies.One of the fundamental issues of the study of the mechanisms that lead to mitochondrial cytopathies is the understanding of the influence that mitochondrial DNA has over mitochondrial metabolism. Indeed, mitochondria have their own DNA, and mutations in this DNA are classified according to their impact on mitochondrial metabolism: pathological mutations, which have negative consequences on mitochondrial metabolism, and polymorphisms, which are considered to be neutral.In order to study the influence of mtDNA on energy metabolism, I used two different models: cybrid cells carrying mtDNA mutations found in non-syndromic hearing loss patients, and cybrid cells carrying polymorphisms defining haplogroup J.The results gathered in these studies show that the difference between pathological mutations and polymorphisms is not as big as previously believed. Indeed, it depends on several factors, such as the nuclear and mitochondrial genetic backgrounds, as well as the environmental factors, because under the influence of these factors a mutation considered as pathological may become neutral, and a polymorphism considered neutral may become pathological

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47

Torkko, Kathleen Carroll. "Vitamin D receptor gene polymorphisms and prostate cancer /." Connect to full text via ProQuest. IP filtered, 2005.

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Thesis (Ph.D. in Epidemiology) -- University of Colorado at Denver and Health Sciences Center, 2005.<br>Typescript. Includes bibliographical references (leaves 95-118). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

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48

Chu, Sok-fan. "Association between [beta]-Chemokine gene polymorphisms and tuberculosis." Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B35736136.

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49

Schwonbeck, Susanne. "Analyse von Single-Nucleotide-Polymorphisms an Glas-Oberflächen." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=974115568.

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50

Schwonbeck, Susanne. "Analyse von Single Nucleotide Polymorphisms an Glas-Oberflächen." Phd thesis, Universität Potsdam, 2004. http://opus.kobv.de/ubp/volltexte/2005/221/.

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Ziel der vorliegenden Arbeit war die Entwicklung einer SNP-Genotypisierungsmethode mit auf Mikroarrays immobilisierten PCR-Produkten. Für die Analyse wurde ein faseroptischer Affinitätssensor bzw. ein Durchfluss-Biochip-Scanner mit integrierter Fluoreszenzdetektion verwendet. An den immobilisierten Analyten (PCR-Produkten) wurde eine Fluoreszenzoligonukleotidsonde hybridisiert und anschließend die Dissoziation der Sonde im Fluss verfolgt. Die Diskriminierung von Wildtyp- und Mutanten-DNA erfolgte durch die kinetische Auswertung der Dissoziationskurven sowie durch die Analyse der Fluoreszenzintensität. <br> <br> Die Versuche am faseroptischen Affinitätssensor zeigten, dass DNA-DNA-Hybride sowohl von Oligonukleotiden als auch von PCR-Produkten ein typisches Dissoziationsverhalten aufweisen, wobei fehlgepaarte Hybride eine signifikant schnellere Dissoziation zeigen als perfekt passende Hybride. Dieser Geschwindigkeitsunterschied lässt sich durch den Vergleich der jeweiligen kinetischen Geschwindigkeitskonstanten kD quantitativ erfassen. </p> <p>Da die Kopplung des Analyten an der Chipoberfläche sowie die Hybridisierungs- und Dissoziationsparameter essentiell für die Methodenentwicklung war, wurden die Parameter für ein optimales Spotting und die Immobilisierung von PCR-Produkten ermittelt. Getestet wurden die affine Kopplung von biotinylierten PCR-Produkten an Streptavidin-, Avidin- und NeutrAvidin-Oberflächen sowie die kovalente Bindung von phosphorylierten Amplifikaten mit der EDC/Methylimidazol-Methode. Die besten Ergebnisse sowohl in Spotform und -homogenität als auch im Signal/Rausch-Verhältnis wurden an NeutrAvidin-Oberflächen erreicht. </p> <p>Für die Etablierung der Mikroarray-Genotypisierungsmethode durch kinetische Analyse nach einem Hybridisierungsexperiment wurden Sondenlänge, Puffersystem, Spotting-Konzentration des Analyten sowie Temperatur optimiert. Das Analysensystem erlaubte es, PCR-Produkte mit einer Konzentration von 250 ng/µl in einem HEPES-EDTA-NaCl-Puffer auf mit NeutrAvidin beschichtete Glasträger zu spotten. In den anschließenden Hybridisierungs- und Dissoziationsexperimenten bei 30 °C konnte die Diskriminierung von homocygoter Wildtyp- und homocygoter Mutanten- sowie heterocygoter DNA am Beispiel von Oligonukleotid-Hybriden erreicht werden. </p> <p>In einer Gruppe von 24 homocygoten Patienten wurde ein Polymorphismus im SULT1A1-Gen analysiert. Sowohl durch kinetische Auswertung als auch mit der Analyse der Fluoreszenzintensität wurde der Genotyp der Proben identifiziert. Die Ergebnisse wurden mit dem Referenzverfahren, der Restriktionschnittstellenanalyse (PCR-RFLP) validiert. Lediglich ein Genotyp wurde falsch bestimmt, die Genauigkeit lag bei 96%. </p> <p>In einer Gruppe von 44 Patienten wurde der Genotyp eines SNP in der Adiponectin-Promotor-Region untersucht. Nach Vergleich der Analysenergebnisse mit denen eines Referenzverfahrens konnten lediglich 14 der untersuchten Genotypen bestätigt werden. Ursache für die unzureichende Genauigkeit der Methode war vor allem das schlechte Signal/Rausch-Verhältnis.</p> <p> Zusammenfassend kann gesagt werden, dass das in dieser Arbeit entwickelte Analysesystem für die Genotypisierung von Einzelpunktmutationen geeignet ist, homocygote Patientenproben zuverlässig zu analysieren. Prinzipiell ist das auch bei heterocygoter DNA möglich. Da nach aktuellem Kenntnisstand eine SNP-Analysemethode an immobilisierten PCR-Produkten noch nicht veröffentlicht wurde, stellt das hier entwickelte Verfahren eine Alternative zu bisher bekannten Mikroarray-Verfahren dar. Als besonders vorteilhaft erweist sich der reverse Ansatz der Methode. </p> <p>Der hier vorgestellte Ansatz ist eine kostengünstigere und weniger hoch dimensionierte Lösung für Fragestellungen beispielsweise in der Ernährungswissenschaft, bei denen meist eine mittlere Anzahl Patienten auf nur einige wenige SNPs zu untersuchen ist. Wenn es gelingt, durch die Weiterentwicklung der Hardware bzw. weiterer Optimierung, eine Verbesserung des Signal/Rausch-Verhältnisses und damit die Diskriminierung von heterocygoter DNA zu erreichen, kann diese Methode zukünftig bei der Analyse von mittelgroßen Patientengruppen alternativ zu anderen Genotypisierungsmethoden verwendet werden.<br>The aim of this thesis was the development of a SNP genotyping method involving PCR products immobilised on microarrays. For the analysis a fibre optic affinity biosensor and a flow-through biochip scanner were used. Fluorescent probes were hybridized with the immobilised PCR products. In order to start the dissociation process the surface was rinsed with buffer and the fluorescence intensity was measured. <br><br> Two different cases were studied: First, the full-matched DNA hybrid (wildtyp single strand with complementary wildtype single strand), second the mis-matched hybrid (wildtype single strand and mutant single strand). After determinating the reaction rates (kD) as kinetic parameter the kD values of both cases were compared. The experiments showed a significant difference in the kD value of the full- and the mis-match hybrids. Therefore, mutant and wildtype DNA were discriminated by kinetic analysis of the dissociation process and analysis of the fluorescence intensity. <br><br> To set up the complete analysis process the reaction parameters like coupling of the PCR products had to be optimised. Both affininty coupled (streptavidin, neutravidin, avidin - biotin) and covalent methods (EDC/methylimidazol) were carried out. Best results in spot homogeinity and spot appearance were obtained with coupling of biotinylated PCR products on neutravidin coated chip surfaces. Additionally, the length of the probe, the spotting concentration, the spotting buffer and the reaction temperature were optimised. In the optimised analysis PCR products (250 µg/µl) were spotted onto neutravidin coated surfaces. The hybridisation <br><br> and dissociation processes were carried out at 30°C. A HEPES-EDTA-NaCl buffer was used for spotting, diluting of the fluorescent probe and rinsing the microarray surface. A fluorescent probe was used with 13 nucleotides in length. The mis- or full-matching base indicating the polymorphism was located in the center position of the probe. <br><br> The analysis system was tested with the genomic DNA of a group of 24 homocygote individuals with a SNP in the SULT1A1 gene region. The hybridisation and dissociation processes were carried out and the reaction rates were determinated. Subsequently after the analysis in the flow-through biochip scanner the fluorescence intensity of the <br><br> spots were measured. The results showed very good comparability with results of a PCR-RFLP analysis (one false genotype). Additionally, a group of 44 heterocygote DNA samples with one SNP in the adiponectin promotor region were also genotyped. Compared to a reference method only 14 genotypes were correctly determined. This was mostly due to a low signal-noise-ratio and needs to be further investigated. <br><br> Besides the problem in analysing heterocygote DNA samples the developed analysis system is very useful for genotyping SNP in homocygote DNA samples. The successful analysis of heterocygote sample is principally possible and with further investigations/optimisation, a better analysis should be possible. <br><br> The most important advantage of the developed method is the reverse approach of binding PCR products at the surface instead of oligonucleotides. This allows the parallel genotyping of several individuals. Other advantages include low costs and medium sized dimensions in terms of throughput.

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