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With cardiovascular disease, diabetes mellitus, and neurodegenerative conditions on the rise, understanding their pathogenesis is paramount to tackling this public health crisis. Current research indicates that the primary cause of these diseases is mitochondrial dysfunction in the affected patients. While genetics plays a role in these conditions, lifestyle choices and exposure to toxins also significantly contribute to their development. Unfortunately, early-stage diagnosis can be difficult due to overlapping symptoms with other diseases. Developing innovative therapies that can prevent or reverse the deterioration of metabolic dysfunctions is critical to establishing early intervention. My research focused on investigating molecular targets linked with Friedrich's Ataxia, an inherited metabolic disorder, through conducting functional in-vitro studies using human-derived cell samples, as well as developing inventive animal models created via Xenopus laevis tadpoles to evaluate the effects of environmental stressors. My investigations have uncovered promising treatment options that improve mitochondrial function, mitigate oxidative stress, and elucidate critical mechanisms involved in environmentally induced disruptions to mitochondria. Doctor of Philosophy Metabolic dysfunction is a widespread health issue that affects millions of individuals each day. Its associated disorders, such as cardiovascular disease, diabetes, and neurodegenerative conditions, are rising due to various factors ranging from genetic predispositions to environmental and lifestyle-related risks. Therefore, there's an urgent need to identify this disorder early on and develop innovative treatment options. Considering this growing public health concern, it has become imperative to establish new methods for detecting metabolic dysfunction at its nascent stage while also exploring potential therapeutic interventions. Our research utilized cells derived from affected patients and animal models in devising novel approaches toward understanding the molecular mechanisms underpinning metabolic dysfunction. Our findings revealed several pathways and molecular targets contributing significantly to this condition, which could effectively be leveraged to develop targeted therapeutic strategies to combat its effects. Expanding our knowledge base will enable us to stay updated with emerging insights on treating metabolic dysfunction effectively while substantially improving patient outcomes.

This study aimed to determine if an acute bout of exercise could improve academic performance when compared to sedentary behavior within a 2-hour window before a college exam. The participants of this study completed two bouts of an intervention on two separate occasions, exercise and sedentary, then completed each of the two class exams, followed by a short survey to gain insight on motivation and anxiety. A 2-way ANOVA was used to determine a time or group effect as this study was completed over a 15-week semester and found no significant difference between the group’s exam scores over time, as well as no group effect of the acute bout of exercise on their exam performance. Pre- and post-surveys, as well as post-exam surveys collected data relating to IPAQ, MSLQ, and GRIT which found significant correlations between IPAQ and perceived exam preparedness with P=0.041. As expected in academia, each exam’s scores were positively related to final course grades with P=0.0275 on exam 1 and P=0.0179 on exam 2. Finally, a P=0.048 was found between final course grades and scores from the extrinsic motivations section of the MSLQ on the post-study survey. Results and lessons learned from this pilot study should be used towards creating a larger-scale study in the future. MALS

Prader-Willi Syndrome (PWS) is a genetic disease that results in abnormal hormone levels, developmental delay, intellectual disability, hypogonadism, and excessive appetite. The disease is caused by a de novo genetic deletion in chromosome 15. While many of the deleted genes have been identified, there is little known about their molecular function. There is evidence that a cluster of non-coding RNA genes in the deleted region known as the SNORD116 genes may be the most critical genes deleted in Prader-Willi Syndrome. It is unknown what the SNORD116 genes do at the molecular level, but recent evidence suggests they regulate the expression of other genes involved in the neuroendocrine system. Specifically, the SNORD116 gene is implicated in regulation of NHLH2, a transcription factor gene which plays a key role in development, hormonal regulation, and body weight. In this study we identify phylogenetically conserved regions of SNORD116 and predict interactions with its potential downstream RNA targets. We show that mouse Snord116 post-transcriptionally increases Nhlh2 RNA levels dependent on its 3'UTR and protects it from degradation within 45 minutes of its transcription. Additionally, a single nucleotide variant within Nhlh2 at the predicted Snord116 interaction site may disrupt Snord116's protective effect. This is the first observation of a molecular mechanism for Snord116, identifying its role in RNA stability, and leads us closer to understanding Prader-Willi Syndrome and finding a possible treatment. However, Snord116 in vitro knockdown or paternally inherited in vivo deletion fail to detect differential expression of Nhlh2, likely due to missing the key timepoint of Snord116 regulatory effects on Nhlh2 RNA soon after its transcriptional stimulation, and dependent on leptin signals. Furthermore, the hypothalamic mRNA expression profile of PWS mouse models fed a nutraceutical dietary supplement of conjugated linoleic acid reveals minimal overall changes, while the effect of diet may be stronger than genotype and potentially changes gene expression of metabolic molecular pathways. Doctor of Philosophy Prader-Willi Syndrome is a genetic disease that results in abnormal hormone levels, slow development, intellectual disability, gonad deficiency, and excessive appetite. The disease is caused by a genetic deletion in chromosome 15 that is almost always a spontaneous mutation not inherited from the parents. While many of the deleted genes have been identified, there is little known about what their molecular function is. There is evidence that a cluster of genes in the deleted region known as the SNORD116 genes may be the most critical genes deleted in Prader-Willi Syndrome. It is unknown what the SNORD116 genes do at the molecular level, but recent evidence suggests that it regulates other genes involved in the hormone system. Specifically, the SNORD116 gene is implicated to regulate the levels of NHLH2, a gene which plays a key role in development, hormonal regulation, and body weight. In this study we identify key regions of SNORD116 and predict interactions with its potential downstream targets. We show that SNORD116 increases NHLH2 levels and slows its degradation at the RNA transcript level. This is the first observation of a molecular mechanism for SNORD116 and leads us closer to understanding Prader-Willi Syndrome and finding a possible treatment. However, other mouse models of Snord116 deletion fail to find differences in Nhlh2. This is likely due to missing a brief key timepoint and hormonal signal when Nhlh2 is most subject to Snord116's effects. Furthermore, PWS mouse models fed a supplement intended for weight loss leads to mild overall gene expression changes in the hypothalamus, a brain region that regulates many hormonal signals including appetite and energy balance. The effect of diet may be stronger than genotype in this brain region, with diet potentially changing the activity of metabolic molecular pathways.

Skeletal muscle is a primary contributor to body mass and whole-body energy metabolism. It is an adaptive tissue with the ability to fluctuate in size and mechanical properties in response to stimulus. Health conditions involving chronic elevated inflammation levels often feature metabolic inflexibility and losses in skeletal muscle mass. Mononuclear stem cells, termed satellite cells, are mitotic and serve to donate nuclei to muscle fibers to enable skeletal muscle adaptation. Despite the well-characterized nature of satellite cell activation, proliferation, and differentiation, the underlying mechanisms regulating this process is not fully understood. Recent characterization of cytokines secreted by skeletal muscle in an endocrine type fashion has led to discoveries of inflammatory cytokines influencing satellite cell function. However, how the autocrine production and secretion of these cytokines during proliferation and differentiation in humans and their correlation with myogenic transcription factors is not well understood. Our study used satellite cells cultured from the vastus lateralis of 12 male human research subjects, and ELISA analysis to measure levels of TNF-α and IL-6 across proliferation, early differentiation, and late differentiation. Additionally, mRNA levels of Pax7, MyoD, myogenin, IL-6, TNF-α, and TGF-β were assessed in satellite cells cultured from a subset of two endurance trained and two sedentary individuals from the larger group of 12 human subjects. The novelty of our study is the large number of human research subjects and simultaneous analysis of inflammatory cytokine secretion, mRNA inflammatory cytokine expression, and myogenic transcription factor mRNA expression. Results showed an 83% decrease in IL-6 protein secretion 24 hours after exposure to differentiation media (p-value

Diabetes mellitus is a major public health concern. Although the accessible novel drugs, techniques, and surgical intervention has improved the survival rate of individuals with diabetes, the prevalence of diabetes is still rising. Type 2 diabetes (T2D) is a result of chronic insulin resistance (IR) and loss of β-cell mass and function. Therefore, the search for naturally occurring, low-cost, and safe compounds that could enhance insulin sensitivity and protect functional β-cell mass can be an effective strategy to prevent this disease. Kaempferol, a flavonol present in various medicinal herbs and edible plants, has been shown to elicit various pharmacological activities in preclinical studies. However, studies investigating the effect of kaempferol on diabetes are limited. In this dissertation, I explored the anti-diabetic potential of dietary intake of kaempferol in diet-induced obese mice and insulin-deficient diabetic mice. First, kaempferol was supplemented in the diet to determine whether it can prevent IR and hyperglycemia in high fat (HF) diet-induced obese mice or STZ-induced obese diabetic mice. To evaluate its efficacy for treating diabetes, kaempferol was administrated once daily via oral gavage to diet-induced obese and insulin-resistant mice or lean STZ-induced diabetic mice. The results demonstrated that long-term oral administration of kaempferol prevents HFD-induced metabolic disorders in middle-aged obese mice. Oral administration of kaempferol improved glucose intolerance and insulin sensitivity, and this effect was associated with increased Glut4 and AMPKa expression in muscle and adipose tissues. Consistent with our findings from the in iii vitro study in C2C12 muscle cell line, these findings suggest that kaempferol may reduce IR at the molecular level by improving glucose metabolism in peripheral tissues. In the second study, dietary kaempferol supplementation prevented hyperglycemia and glucose intolerance by protecting β-cell against the induced damage in obese STZ-induced diabetic mice. In the third study, the administration of kaempferol by oral gavage significantly ameliorated hyperglycemia and glucose intolerance and reduced the incidence of diabetes from 100 % to 77.8% in lean STZinduced diabetic mice. This kaempferol effect was associated with reduced hepatic glucose production, the primary contributor to hyperglycemia, and increased glucose oxidation in the muscle of diabetic mice. Kaempferol treatment restored hexokinase activity in the liver and skeletal muscle and reduced pyruvate carboxylase (PC) activity and glycogenolysis in the liver. Unlike its effect on T2D mice, kaempferol effect in lean STZ-induced diabetic mice was not associated with changes in plasma insulin levels. In the last study, we found that administration of kaempferol by oral gavage significantly improved blood glucose control by suppressing hepatic glucose production and improving glucose intolerance in obese insulin-resistant mice. Similar to its effect in old obese mice, kaempferol enhanced whole-body insulin sensitivity. Kaempferol increased Akt and hexokinase activity and decreased PC activity in the liver. However, kaempferol did not exert any changes in glucose metabolism or insulin sensitivity when administered to healthy lean mice. Overall, findings from these studies provide new insight into the role of kaempferol in the regulation of glucose homeostasis and suggest that kaempferol may be a naturally occurring anti-diabetic compound by improving insulin sensitivity, improving glucose regulation and metabolism, and preserving functional β-cell mass. Ph. D.

The pathogen Francisella tularensis subsp. tularensis has been classified as a Center for Disease Control (CDC) select agent. However, little is still known of what makes the bacteria cause dis-ease, especially the highly virulent type A1 strains. The work in this dissertation focused on type A1 strains from the Inzana laboratory, including a wildtype virulent strain TI0902, an avirulent chemical mutant strain TIGB03 with a Single Nucleotide Polymorphism in the wbtK gene, and several complemented mutants, [wbtK+]TIGB03, with dramatic differences in virulence and growth rates. One of the complemented clones (Clone12 or avp-[wbtK+]TIGB03-C12) was aviru-lent, but protected mice against challenge of a lethal dose of TI0902 and was considered as a possible vaccine strain. Whole genome sequencing was performed to identify genetic differences between the virulent, avirulent and protective strains using both Roche/454 and Illumina next-generation sequencing technologies. Additionally, RNASeq analysis was performed to identify differentially expressed genes between the different strains. This comprehensive genomic analysis revealed the critical role of transposable elements in inducing genomic instability resulting in large du-plications and deletions in the genomes of the chemical mutant and the complemented clones that in turn affect gene dosage and expression of genes known to regulate virulence. For exam-ple, whole genome sequencing of the avirulent chemical mutant TIGB03 revealed a large 75.5 kb tandem duplication flanked by transposable elements, while the genome of a virulent Clone01 (vir-[wbtK+]TIGB03-C1) lost one copy of the 75.5 kb tandem duplicated region but gained a tandem duplication of another large 80kb region that contains a virulence associated transcription factor SspA. RNAseq data showed that the dosage effect of this extra region in Clone1 suppresses expression of MglA regulated genes. Since MglA regulates genes that are known to be crucial for virulence, including the well-studied Francisella Pathogenicity Island (FPI), these results suggest that gene dosage effects arising from large duplications can trigger unknown virulence mechanisms in F. tularensis subsp. tularensis. These results are important especially when designing live vaccine strains that have repeated insertion elements in their genomes. Ph. D.

Chickens from lines that have been divergently selected for either low (LWS) or high (HWS) body weight at 56 days of age for more than 57 generations serve as unique models to study eating disorders. The LWS have different severities of anorexia while all HWS become obese. Over the past decade our groups has demonstrated that these lines have differential food intake threshold responses to a range of intracerebroventricular (ICV) injected neurotransmitters. The major brain region regulating homeostatic regulation of appetite is the hypothalamus, and hence this dissertation was focused on understanding how the hypothalamus is different between LWS and HWS lines. Experiments 1 and 2 were performed as follows: whole hypothalamus as well as individual hypothalamic nuclei, respectively, were collected from 5 day-old chicks that had been fasted for 180 min or had free access to food. The hypothalamic nuclei included those primarily associated with appetite including the lateral hypothalamus, paraventricular nucleus (PVN), ventromedial hypothalamus, dorsomedial nucleus, and arcuate nucleus (ARC). Total RNA was isolated, reverse transcribed, and real time PCR performed. Hypothalamic expression of anorexigenic factors was greater in LWS than HWS, those factors including calcitonin, corticotropin-releasing factor receptor 1, leptin receptor, neuropeptide S, melanocortin receptor 3 (MC3R), and mesotocin. The gene expression data from individual hypothalamic nuclei revealed that mesotocin from the PVN may play an important role in the inhibition of appetite in the LWS. Experiment 3 was then designed to evaluate the effects of stress on food intake: besides the differences in hypothalamic gene expression between the lines, they also have different feeding responses when stressed: ICV injection of neuropeptide Y (0.2 nmol, NPY) did not increase food intake in LWS on day 5 after stress exposure. Experiment 4 was thus designed to study the molecular mechanisms underlying conditional feeding responses to exogenous NPY after stress in the LWS. The melanocortin system (AgRP and MC3R) changed in the hypothalamus after stress in the LWS, and hence may be responsible for the loss of responsiveness to exogenous NPY in stressed LWS. Experiment 5 was designed to evaluate whether hypothalamic differences exist at the protein level: label-free liquid chromatography coupled to tandem-mass spectrometry was used to measure the abundance of proteins in the hypothalamus. Hypothalamus was obtained from fed and 180 minute-fasted 5 day-old male LWS and HWS chicks. Proteins involved in energy metabolism were different between the lines. Differences were also found in proteins involved in GABA synthesis and uptake as well as protein ubiquitination. In conclusion, these results suggest that different feeding behaviors of LWS and HWS may be due to differences in gene and protein expression in the hypothalamus. Ph. D.

Energy balance includes energy intake and energy expenditure. Either excessive food intake or insufficient physical activity will increase the body mass and cause obesity, a worldwide health problem. In the US, more than two-thirds of people are obesity or overweight. Conversely, it is well accepted that reducing energy intake can increase the life span and the resistance to age-related diseases. MicroRNAs are highly conserved non-coding RNA molecules with a length of 21-23 nucleotides. Recent studies show that numerous microRNAs are associated with the regulation of oxidative stress, inflammation, insulin signaling, apoptosis, and angiogenesis that relate to obesity. However, the role of microRNAs in the regulation of energy balance in central nervous system remains unknown, especially within the hypothalamus, a primary site of energy balance control. In this project, microRNA, and mRNA were profiled using microarray technology. Furthermore, quantitative proteomics were used to identify differential protein levels during fasting, and in a genetically obese mouse model, Mice were given either a 24-hour fast, or ad libitum access to food. Hypothalamic RNA and microRNA samples were analyzed by microarray, using both the Affymetrix and Toray 3D mRNA and microRNA platforms. No microRNAs were found to be differentially expressed between two treatments, whereas numerous mRNAs were significantly regulated by fasting, including 7 cell cycle related genes. Hypothalamic protein samples from WT and N2KO mice treated either to ad lib feeding or 24-hour fasting were analyzed by MSE quantitative proteomics. Over 650 proteins were identified with some proteins showing significantly different abundances between or among the four groups. Between ad lib fed WT and N2KO mice, 53 proteins were differentially expressed, with some of these linked to neurodegeneration, NAD synthesis, and the citrate acid cycle (TCA). Overall, the results of this study suggest that while microRNA-mediated mechanisms are not significant modulators of hypothalamic gene expression upon a 24 hour fast, cell cycle gene expression changes represent a major contributor to the fasting response. Moreover, Nlhl2 might play an important role in the neurodegeneration and mitochondrial metabolism. Ph. D.

Nescient Helix Loop Helix 2 (Nhlh2) is a member of the basic helix-loop-helix transcription factor family. Mice with a targeted deletion of Nhlh2, called N2KO mice, show adult onset obesity in both males and females. Nhlh2 regulates other genes by binding to the E-box in the promoter region of these genes. This transcription factor regulates many other transcription factors including MC4R and PC1/3 which are associated with human obesity. The Nhlh2 promoter has been analyzed for putative transcription factors binding sites. These putative binding sites have been tested to be the regulators of Nhlh2 by transactivation assays with mutant promoters, Electrophoretic Shift Assay (EMSA), and Chromatin Immunoprecipitation Assay (ChIP) as methods to investigate the DNA-protein binding. The results of these experiments showed that the Nhlh2 promoter has five Signal Transducer and Activator of Transcription 3 (Stat3) binding site motifs at -47, -65, -80, -281, -294 and two Nuclear Factor Kappa-Light-Chain-Enhancer of Activated B Cells (NFκB) binding site motifs at -67 and -135. While NFκB acts as a negative regulator of Nhlh2, this research showed that Stat3 acts as a regulator for the Nhlh2 basal expression and leptin stimulation. The ChIP assay using chromatin from mouse hypothalamus and antibodies against Stat3 and the NFκB subunits P50, P65, and c-Rel demonstrated that all of these antibodies were able to pull down the part of the Nhlh2 promoter containing the binding sites of Stat3 and NFκB. The EMSA results not only demonstrated that NFκB and Stat3 binding site motifs are real binding sites, but also exists the possibility of a relationship between these transcription factors to regulate Nhlh2 expression with leptin stimulation. An effort in analyzing the human NHLH2 3'UTR showed that one of the SNPs located at position 1568 in the NHLH2 mRNA (NHLH2A1568G) which converts adenosine to guanine might have the potential to decrease the mRNA stability. For more investigation about this SNP, the mouse Nhlh2 tail was cloned into 2 different vectors and these vectors were subjected to site directed mutagenesis to create the 3'UTR SNP that convert A to G. One of these vectors used luciferase as a reporter gene for expression while the other one was used to measure Nhlh2 mRNA stability. These vectors were transfected into hypothalamic cell line N29/2 to test the effect of this SNP on Nhlh2 expression. This study demonstrated that this SNP down regulated luciferase expression and also decreased Nhlh2 mRNA stability. Taken together, this study demonstrated that Nhlh2 could be regulated transcriptionally by both NFκB and Stat3 transcription factors and post-transcripitionally by the 3'UTR SNP that converts adenosine to guanine. Ph. D.

Mutations in the melanocortin 4 receptor (MC4R) are the most frequent cause of monogenetic forms of human obesity. Despite its importance, the MC4R signaling pathways and transcriptional regulation that underly the melanocortin pathway are far from being fully understood. The transcription factor Nescient Helix Loop Helix 2 (Nhlh2), is known to influence the melanocortin pathway. It regulates the transcription of genes by binding to the E-Box binding sites present in the promoter region. Here in this dissertation, Nhlh2's role as a transcriptional regulator of Mc4r and the effects of deletion of Nhlh2 on peripheral energy expenditure, glucose homeostasis and fatty acid oxidation are reported. To investigate the transcriptional mechanisms of Mc4r and the involvement of Nhlh2, gene expression analysis, DNA-protein binding, transactivation assays, and SiRNA induction were used. We show that Nhlh2 regulates the transcription of Mc4r by binding to the three E-Boxes present on the promoter at -553, -361 and +47. Further, SiRNA knockdown of Nhlh2 in the N29/2 cell line depresses Mc4r expression which suggests the requirement of Nhlh2 for Mc4r transcription. Development of adult onset obesity in the absence of evident hyperphagia questions the ability of mice which lacks Nhlh2 (N2KO) to utilize energy substrate efficiently. To test the effect of deletion of Nhlh2 in N2KO, body composition analysis, tissue specific characterization, fatty acid oxidation and glucose and insulin homeostasis were assessed. N2KO mice have a higher fat content than WT at the age of 12 weeks. There are architectural differences in adipose tissue of N2KO. White adipose tissue (WAT) shows infiltration of macrophages, and increased mRNA and serum levels of interleukin 6 which suggests the presence of a systemic inflammatory state in the N2KO mice. Sympathetic nervous system tone is reduced in both brown adipose tissue (BAT) and WAT, as evidenced by gene expression analysis, and this may be because of overall reduced melanocortinergic tone in N2KO mice. N2KO mice have an impaired glucose tolerance on the basis of their late glucose clearance on glucose (non-significant) and insulin (significant) challenges. Fatty acid oxidation (FAO) is higher in red fibers of skeletal muscle, and the respiratory exchange ratio (RER) is lower in N2KO, which is indicative of using fat as a preferential energy source. Increased expression of genes involved in the lipid metabolism in skeletal muscle and liver supports the RER and FAO, and are indicative of high turnover of lipids in N2KO. Findings from these studies implicate Nhlh2 as a transcriptional regulator of Mc4r which has a direct relevance to the ever increasing epidemic of obesity. Characterization of N2KO mice sheds light on the adult onset obesity phenotype. Knowledge gained from these findings will help us understand the monogenetic form of obesity more completely and could lead to the design of improved pharmacological therapies that target Nhlh2 or Mc4r or modify physical activity behavior. Ph. D.

Growing evidence suggests that obesity and associated metabolic dysregulation occurs in concert with chronic low-grade inflammation. Toll-like receptors (TLR) are transmembrane receptors that play an important role in innate immunity and the induction of inflammatory responses. Our laboratory has observed that TLR4 expression is elevated in the skeletal muscle of obese humans and is associated with reduced fatty acid (FA) oxidation and increased lipid synthesis. Additionally, activation of this pathway by lipopolysaccharide (LPS), ex vivo, results in a shift in substrate metabolism favoring glucose as an energy substrate and preferential storage of FA in intracellular lipid depots. The purpose of this study was to examine the effects of saturated vs. monounsaturated FA on TLR4 transcription and signaling using ex vivo and in vivo models. C2C12 myotubes were incubated in FA-enriched growth medium with varying ratios of palmitate and oleate for 12 hours. Following FA treatment, cells were either collected for measures of mRNA and protein levels of TLR4 or challenged with LPS (500 ng/mL) for 2 hours to assess TLR4 mediated changes in interleukin-6 (IL-6) and glucose and fatty acid metabolism. TLR4 mRNA and protein content were increased in stepwise fashion with higher palmitate concentration (p

Interleukin-1 receptor associated kinase -1 is a protein kinase pivotal in mediating signals for innate immune responses. Here, I report that IRAK-1 also regulates cell-mediated immune responses. NFATc2 (nuclear factor of activated T cells) was found to be associated with IRAK-1 in T cells in vitro and its activity was elevated in the absence of IRAK-1. In addition, IRAK-1-/- mice had increased naturally occurring regulatory T cells and inducible regulatory T cells as well as Th1 responses as compared to WT mice. The findings suggest that activated T cells might employ IRAK-1 to mediate the regulation of acquired immunity. Therefore, IRAK-1 may participate in direct signaling cross talk between the innate and the acquired immunity. Master of Science

The purpose of this study was to develop a SNaPshot® assay to simultaneously discriminate between the dystrophic and wild type (wt) alleles in mdx mice. The mdx mouse is an animal model for Duchenne muscular dystrophy (DMD), a severe and fatal muscle wasting disease. To evaluate possible treatments and to carry out genetic studies, it is essential to distinguish between mice that carry the mutant dystrophic or wt allele(s). The current Amplification-Resistant Mutation System (ARMS) assay used to genotype mdx mice is labor intensive and sometimes fails to yield typing results, which reduce its efficiency as a screening tool. An alternative assay based on single nucleotide polymorphism (SNP) extension technology (i.e., SNaPshot®) would be advantageous because its specificity and capability to be automated would reduce the labor involved and increase the fidelity of each assay. A SNaPshot® assay has been developed that provides a robust and potentially automatable assay that discriminates between the wt and dystrophic alleles. The assay has been optimized to use: an undiluted DNA in the PCR, a 0.1 µM PCR primer concentration, a full PCR product for the SNP extension reaction, a 50ºC annealing temperature for the SNP extension in accordance with standard SNaPshot® conditions, and a 0.4 µM concentration of the SNP extension primer. The advantages of the resultant SNaPshot® assay over the ARMS assay include higher fidelity, robustness, and more consistent performance within and among laboratories, and reduced risk of human error. Master of Science