TGF-beta1 plays an important role in the pathogenesis of experimental and clinical glomerulosclerosis and tubufointerstitial fibrosis. Associations have been described between polymorphisms of cytokine and growth factor genes and susceptibility to, or progression of, an increasing number of diseases. In this study, single nucleotide polymorphisms (SNPs) in the TGFbeta1 gene were investigated as possible markers for the progression of chronic renal failure (CRF). One hundred and forty two Caucasian patients with CRF were screened for four TGFB1 SNPs: T-509C in the promoter region; Arg25Pro and Leu10Pro in exon 1 and Thr263Ile in exon 5. There were significant differences between CRF patients and controls in allele frequencies of two of the SNPs (Leu10Pro and C-509T), indicating an association with susceptibility to CRF, We also observed a significant association between rate of progression of CRF (the slope of the reciprocal of serum creatinine v time) and genotype, both at codon 25 (odds ratio 3.77, 95% confidence interval, 2.2 - 6, p < 0.001) and at the -509 promoter site (odds ratio 1.67, 95% confidence interval 1.1-2.5), p < 0.005) in patients with primary nephropathy (excluding PKD). Genotype at codon 25 was also associated with severity of proteinuria (p= 0.038), plasma TGF-B1 protein levels (p = 0,01), and the severity of glomerulosclerosis (p < 0.05). Genotype at C-509T was associated with the level of renal tubular TGF-B1 immunostmning (p = 0.0006) and with renal interstitial inflammatory cellular infiltration (p=0,015). There was a highly significant correlation between the degree of cellular infiltration in renal tissues and tubular TGF-beta1 immunostaining.

The ATP-binding cassette (ABC) transporter superfamily consists of 49 members, to which both Multidrug Resistance Protein 1 (MRP1/gene symbol: ABCC1) and MRP4 (ABCC4) belong. Single nucleotide polymorphisms (SNPs) in drug metabolizing genes have been shown to affect individual responses to drugs and toxins. However, the role of SNPs in modulating the activity of drug transporters, such as MRP1 and MRP4, is poorly characterized. The overall goal of my thesis was to determine the effects of SNPs in the promoter regions of human ABCC1 and ABCC4. For MRP1/ABCC1, two proximal promoter SNPs (-275A>G, -260G>C) were identified in the literature and recreated in vitro, and the activity of the mutant ABCC1 promoter constructs was measured in five human cell lines using a dual luciferase assay. The activity of the -275A>G promoter was comparable to the wild-type ABCC1 promoter. On the other hand, the -260G>C substitution decreased ABCC1 promoter activity in HepG2, MCF-7 and HeLa (40 - 60%) cells. A 1706 bp fragment containing the 5’-flanking and untranslated regions of ABCC4 were isolated from two bacterial artificial chromosome clones and six serially deleted ABCC4 promoter reporter constructs generated. Luciferase assays of the basal promoter constructs of ABCC4 in HEK293T cells revealed the presence of one or more negative regulatory regions between -1706 and -876, between -876 and -641, and one or more positive regulatory regions between -641 and -356, and between -356 and -17. Also, the ABCC4 promoter displayed differential activity in MDCKI and LLC-PK1 cells than in HEK293T cells. One SNP (-523G>C) was identified from an online database and its activity tested. However, -523G>C SNP did not cause any significant change in the ABCC4 promoter activity in both HEK293T and HepG2 cells (80 – 130%). In summary, the data obtained suggest that the promoter SNPs studied may affect the transcriptional activity of ABCC1 or ABCC4, but it seems likely that this is not true in all cell types. / Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2007-09-28 10:03:16.119

As knowledge of the human genome has accelerated, various diseases and individuals’ responses to drugs have been pinpointed to specific DNA variations in one’s genome. Among many different types of variants, the most common and simplest is the single nucleotide polymorphism (SNP) in which a single base substitution occurs. Although there have been considerable improvements in technologies that can reveal a single base difference in a DNA strand, simple and affordable methods that have high detection sensitivity and require small sample volume are expected to facilitate widespread adoption of routine SNP analysis in clinical settings. One such method that meets these requirements is to use nanopore as a single molecule detector, an emerging analytic system that detects changes in current related to molecules occupying a nanometer aperture. This dissertation thus chronicles our endeavors in developing a nanopore-based SNP assay using polymer tagged dideoxynucleotides (ddNTPs). The fundamental principles of this method rely on single base extension (SBE) of a primer by DNA polymerase using polymer tagged ddNTP analogs for allele discrimination and simple electronic readout of an alpha hemolysin (αHL) nanopore current for allele detection at the single molecule level. Using four uniquely tagged ddNTPs, a characteristic current level that is specific to each base is produced, thus identifying the SNP alleles present and the genotype at the site. To demonstrate the feasibility of this approach, four polymer attached ddNTPs, each with a different tag that generates a characteristic current blockade level in the αHL nanopore, were designed and synthesized. To search for a DNA polymerase that can accept these tagged ddNTP analogs as substrates, several candidate DNA polymerases were surveyed and their relative efficiencies for incorporation of the analogs were compared (Chapter 2). To generate a steady and stable blockade event for accurate SNP analysis, two different means of positioning a tag molecule in the αHL nanopore after the SBE reaction have been explored: covalent conjugation of DNA primer to the pore and immobilization of biotinylated primer within the pore by streptavidin. To find a suitable position for primer attachment on the pore, three αHL mutants, each with a different single conjugation point, were constructed. Using these mutants, different DNA-pore conjugates were produced and purified via various chromatography systems (Chapter 3). In the nanopore system, charged molecules such as DNA are electrophoretically driven through the pore under an applied voltage, thereby modulating the ionic current through the nanopore. This current reveals useful information about the structure and dynamic motion of the molecule at the single molecule level. Before performing SNP analysis, we first studied single molecule behaviors of oligonucleotides of different lengths and structures in the αHL pore and their ensuing current signatures in the system (Chapter 4). Finally, harnessed with tools and insights from the nanopore single molecule studies, actual SNP assays were performed in our nanopore system using the polymer tagged ddNTPs and SBE. Chapter 5 discusses the integrated approach where SBE is achieved on a primer-conjugated αHL nanopore and Chapter 6 presents the results using a biotin-streptavidin complex for immobilization of tag molecules in the pore. Overall, this thesis validates adaptation of the nanopore detection system for SNP analysis using the polymer tagged ddNTPs.

<p>Single nucleotide polymorphisms (SNP) in leptin (LEP) and pro-opiomelanocortin (POMC) have been associated with beef carcass quality and yield respectively. Both hormones also play a role in immune performance. Since both of these genes are pleiotrophic, it was important to determine whether selection based on these SNPs would negatively affect immune cell numbers. A SNP in each of these hormones was assessed for effects on immune cell counts and antibody titres in twenty-seven beef cattle herds (n = 556). A commercial rabies vaccine was administered to these animals. Prior to being vaccinated, the types of lymphocytes evaluated included B cells, gamma delta cells, regular and activated CD4 and CD8 cells and numbers of lymphocytes as well as baseline serum antibody titres. On day 21, antibody titres were measured and a booster vaccine was administered. Finally on day 42, antibody titres and lymphocyte types were again counted. Several cell types were significantly associated with the LEP genotype however, no consistent pattern of correlation was observed between LEP genotype (TT, CT or CC) and peripheral blood lymphocyte populations. The number of different lymphocytes significantly associated with LEP genotype increased from two on day 0 to four on day 42. Animals with CT and CC genotypes had significantly higher increased rabies antibody titres in the first 21 days after vaccination than those with TT genotypes. The POMC SNP also did not show a clear pattern of association between lymphocyte subtypes and genotype. There was no difference in response to the rabies vaccination associated with the POMC genotype. Our results suggested that selection at either of the SNPs examined in this research would not detrimentally impact immune function in beef cattle.</p>

<p>Single nucleotide polymorphisms (SNP) in leptin (LEP) and pro-opiomelanocortin (POMC) have been associated with beef carcass quality and yield respectively. Both hormones also play a role in immune performance. Since both of these genes are pleiotrophic, it was important to determine whether selection based on these SNPs would negatively affect immune cell numbers. A SNP in each of these hormones was assessed for effects on immune cell counts and antibody titres in twenty-seven beef cattle herds (n = 556). A commercial rabies vaccine was administered to these animals. Prior to being vaccinated, the types of lymphocytes evaluated included B cells, gamma delta cells, regular and activated CD4 and CD8 cells and numbers of lymphocytes as well as baseline serum antibody titres. On day 21, antibody titres were measured and a booster vaccine was administered. Finally on day 42, antibody titres and lymphocyte types were again counted. Several cell types were significantly associated with the LEP genotype however, no consistent pattern of correlation was observed between LEP genotype (TT, CT or CC) and peripheral blood lymphocyte populations. The number of different lymphocytes significantly associated with LEP genotype increased from two on day 0 to four on day 42. Animals with CT and CC genotypes had significantly higher increased rabies antibody titres in the first 21 days after vaccination than those with TT genotypes. The POMC SNP also did not show a clear pattern of association between lymphocyte subtypes and genotype. There was no difference in response to the rabies vaccination associated with the POMC genotype. Our results suggested that selection at either of the SNPs examined in this research would not detrimentally impact immune function in beef cattle.</p>

Single nucleotide polymorphisms (SNPs) have been increasingly popular for a wide range of genetic studies. A high-throughput genotyping technologies usually involves a statistical genotype calling algorithm. Most calling algorithms in the literature, using methods such as k-means and mixturemodels, rely on elliptical structures of the genotyping data; they may fail when the minor allele homozygous cluster is small or absent, or when the data have extreme tails or linear patterns. We propose an automatic genotype calling algorithm by further developing a linear grouping algorithm (Van Aelst et al., 2006). The proposed algorithm clusters unnormalized data points around lines as against around centroids. In addition, we associate a quality value, silhouette width, with each DNA sample and a whole plate as well. This algorithm shows promise for genotyping data generated from TaqMan technology (Applied Biosystems). A key feature of the proposed algorithm is that it applies to unnormalized fluorescent signals when the TaqMan SNP assay is used. The algorithm could also be potentially adapted to other fluorescence-based SNP genotyping technologies such as Invader Assay. Motivated by the SNP genotyping problem, we propose a partial likelihood approach to linear clustering which explores potential linear clusters in a data set. Instead of fully modelling the data, we assume only the signed orthogonal distance from each data point to a hyperplane is normally distributed. Its relationships with several existing clustering methods are discussed. Some existing methods to determine the number of components in a data set are adapted to this linear clustering setting. Several simulated and real data sets are analyzed for comparison and illustration purpose. We also investigate some asymptotic properties of the partial likelihood approach. A Bayesian version of this methodology is helpful if some clusters are sparse but there is strong prior information about their approximate locations or properties. We propose a Bayesian hierarchical approach which is particularly appropriate for identifying sparse linear clusters. We show that the sparse cluster in SNP genotyping datasets can be successfully identified after a careful specification of the prior distributions.

The SLC30A2 zinc transporter has been investigated due to its important role in zinc secretion into human milk. SLC30A2 is expressed in mammary epithelial cells, and the presence of genetic variations in this transporter could cause low zinc transport into the milk, leading to Transient Neonatal Zinc Deficiency (TNZD) in newborns. Through bioinformatics analysis 22 SNPs were identified. Therefore, we aim to identify the functional changes caused by 4 SNPs. By subcloning the SLC30A2 open reading frames into the Gateway expression plasmid tagged with red and green fluorescent proteins (mCherry, tGFP). Four SNPs were introduced by mutagenesis and tagged with mCherry. We transfected individual plasmids into mammary epithelial cells (HC11) and observed cellular targeting using epifluorescent imaging. The most common variants located to secreting endosomes and membrane in HC11 cells. Incorrect targeting of SLC30A2 causes mislocalization. It may be possible to identify mothers carrying risk genotypes for infant zinc deficiency.

The SLC30A2 zinc transporter has been investigated due to its important role in zinc secretion into human milk. SLC30A2 is expressed in mammary epithelial cells, and the presence of genetic variations in this transporter could cause low zinc transport into the milk, leading to Transient Neonatal Zinc Deficiency (TNZD) in newborns. Through bioinformatics analysis 22 SNPs were identified. Therefore, we aim to identify the functional changes caused by 4 SNPs. By subcloning the SLC30A2 open reading frames into the Gateway expression plasmid tagged with red and green fluorescent proteins (mCherry, tGFP). Four SNPs were introduced by mutagenesis and tagged with mCherry. We transfected individual plasmids into mammary epithelial cells (HC11) and observed cellular targeting using epifluorescent imaging. The most common variants located to secreting endosomes and membrane in HC11 cells. Incorrect targeting of SLC30A2 causes mislocalization. It may be possible to identify mothers carrying risk genotypes for infant zinc deficiency.

Single nucleotide polymorphisms (SNPs) have been increasingly popular for a wide range of genetic studies. A high-throughput genotyping technologies usually involves a statistical genotype calling algorithm. Most calling algorithms in the literature, using methods such as k-means and mixturemodels, rely on elliptical structures of the genotyping data; they may fail when the minor allele homozygous cluster is small or absent, or when the data have extreme tails or linear patterns. We propose an automatic genotype calling algorithm by further developing a linear grouping algorithm (Van Aelst et al., 2006). The proposed algorithm clusters unnormalized data points around lines as against around centroids. In addition, we associate a quality value, silhouette width, with each DNA sample and a whole plate as well. This algorithm shows promise for genotyping data generated from TaqMan technology (Applied Biosystems). A key feature of the proposed algorithm is that it applies to unnormalized fluorescent signals when the TaqMan SNP assay is used. The algorithm could also be potentially adapted to other fluorescence-based SNP genotyping technologies such as Invader Assay. Motivated by the SNP genotyping problem, we propose a partial likelihood approach to linear clustering which explores potential linear clusters in a data set. Instead of fully modelling the data, we assume only the signed orthogonal distance from each data point to a hyperplane is normally distributed. Its relationships with several existing clustering methods are discussed. Some existing methods to determine the number of components in a data set are adapted to this linear clustering setting. Several simulated and real data sets are analyzed for comparison and illustration purpose. We also investigate some asymptotic properties of the partial likelihood approach. A Bayesian version of this methodology is helpful if some clusters are sparse but there is strong prior information about their approximate locations or properties. We propose a Bayesian hierarchical approach which is particularly appropriate for identifying sparse linear clusters. We show that the sparse cluster in SNP genotyping datasets can be successfully identified after a careful specification of the prior distributions.

Thesis (M.Sc.). / Written for the Dept. of Neurology and Neurosurgery. Title from title page of PDF (viewed 2009/06/29). Includes bibliographical references.