Clear plastic fluidic devices with ports for incorporating electrodes to enable electrochemiluminescence (ECL) measurements were prepared using a low-cost, desktop three-dimensional (3D) printer based on stereolithography. Electrodes consisted of 0.5 mm pencil graphite rods and 0.5 mm silver wires inserted into commercially available 1/4 in.-28 threaded fittings. A bioimaging system equipped with a CCD camera was used to measure ECL generated at electrodes and small arrays using 0.2 M phosphate buffer solutions containing tris(2,2′-bipyridyl)dichlororuthenium(II) hexahydrate ([Ru(bpy)3]2+) with 100 mM tri-n-propylamine (TPA) as the coreactant. ECL signals produced at pencil graphite working electrodes were linear with respect to [Ru(bpy)3]2+ concentration for 9-900 μM [Ru(bpy)3]2+. The detection limit was found to be 7 μM using the CCD camera with exposure time set at 10 s. Electrode-to-electrode ECL signals varied by ±7.5%. Device performance was further evaluated using pencil graphite electrodes coated with multilayer poly(diallyldimethylammonium chloride) (PDDA)/DNA films. In these experiments, ECL resulted from the reaction of [Ru(bpy)3]3+ with guanines of DNA. ECL produced at these thin-film electrodes was linear with respect to [Ru(bpy)3]2+ concentration from 180 to 800 μM. These studies provide the first demonstration of ECL measurements obtained using a 3D-printed closed-channel fluidic device platform. The affordable, high-resolution 3D printer used in these studies enables easy, fast, and adaptable prototyping of fluidic devices capable of incorporating electrodes for measuring ECL.

Alzheimer's disease (AD) is a progressive, irreversible, neurodegenerative disease. The key to understanding AD is to elucidate the pathogenesis of neuron degeneration in specific brain regions.We hypothesize that there is increased DNA oxidation in AD brain compared to age-matched control subjects, especially in mitochondrial DNA (mtDNA), and that the changes in DNA bases will affect protein expression in mitochondria and contribute to neurodegeneration in AD. To test this hypothesis:1) We quantified multiple oxidized bases in nuclear DNA (nDNA) and mtDNA of frontal, parietal, and temporal lobes and cerebellum from late-stage AD (LAD), mild cognitive impairment (MCI), and age-matched control subjects using gas chromatography/mass spectrometry with selective ion monitoring (GC/MS-SIM). Also, we quantified oxidized DNA bases in cortex of APP/PS1 transgenic mice. (a) nDNA and mtDNA were extracted from eight LAD and eight control subjects. We found levels of multiple oxidized bases were significantly higher in frontal, parietal, and temporal lobes and that mtDNA had approximately 10-fold higher levels of oxidized bases than nDNA. Eight-hydroxyguanine was approximately 10-fold higher than other oxidized base adducts in both LAD and control subjects. These results suggest that oxidative damage to mtDNA may contribute to the neurodegeneration of AD. (b) Mild Cognitive Impairment (MCI), the phase between normal aging and early dementia, is a common problem in the elderly with many subjects going on to develop AD. Results from eight amnestic MCI and six control subjects suggest oxidative damage to DNA occurs in the earliest detectable phase of AD. (c) Analysis of nDNA from the cortex of four groups (3m, 6m, 9m, 12m) of APP/PS1 and wild type mice showed elevations of 8-hydroxyguanine in 12 month old APP/PS1 mice.2) To analyze mitochondrial protein changes in LAD, 2D gels were run to separate proteins and MALDI-TOF mass spectrometry was used to identify proteins.Five mitochondrial proteins were significantly decreased in LAD. This proteomic study provides a proteome map of mitochondria in LAD brain and an insight into the pathogenesis of neuron degeneration in Alzheimer's disease.

Fenn, Dickson. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 74-81). / Abstract also in Chinese. / Title Page --- p.i / Thesis Committee --- p.ii / Acknowledgement --- p.iii / Table of Contents --- p.v / List of Tables --- p.ix / List of Figures --- p.x / List of Abbreviations and Symbols --- p.xv / Abstract --- p.xvii / Chapter 1.Chapter One: --- Introduction --- p.1 / Chapter 1.1 --- Oxidation and Hyperoxidation of Guanine --- p.1 / Chapter 1.2. --- DNA Replication --- p.2 / Chapter 1.3 --- Mutagenesis --- p.3 / Chapter 1.4 --- Literature Survey on Spiroiminodihydantoin (Sp) --- p.4 / Chapter 1.5 --- Purpose of This Work --- p.5 / Chapter 1.6 --- DNA Structure --- p.6 / Chapter 1.6.1 --- Nomenclature --- p.6 / Chapter 1.6.2 --- Torsion Angles --- p.6 / Chapter 1.6.3 --- Sugar Pucker Conformation --- p.7 / Chapter 1.6.4 --- Secondary Structures of DNA --- p.8 / Chapter 2.Chapter Two: --- Materials and Methodology --- p.10 / Chapter 2.1 --- Sample Design --- p.10 / Chapter 2.2 --- Sample Preparation --- p.11 / Chapter 2.2.1 --- DNA Synthesis and Purification --- p.11 / Chapter 2.2.2 --- HPLC Separation --- p.11 / Chapter 2.2.3 --- NMR Samples Preparation --- p.12 / Chapter 2.3 --- NMR Analysis --- p.12 / Chapter 2.3.1 --- Resonance Assignment --- p.14 / Chapter 2.3.1.1 --- Proton --- p.14 / Chapter 2.3.1.2 --- Phosphorous --- p.16 / Chapter 2.3.2 --- Sugar Pucker Conformation --- p.17 / Chapter 2.3.3 --- Backbone Conformation --- p.18 / Chapter 2.4 --- UV Melting Analysis --- p.19 / Chapter 3.Chapter Three: --- "HPLC, NMR and UV Results" --- p.21 / Chapter 3.1 --- HPLC Separation of Sp Diastereoisomers --- p.21 / Chapter 3.2 --- NMR Resonance Assignments --- p.24 / Chapter 3.2.1 --- 5'-GG Sample --- p.24 / Chapter 3.2.2 --- 5'-G(oG) Sample --- p.26 / Chapter 3.2.3 --- 5'-G(Sp) Sample --- p.29 / Chapter 3.2.4 --- 5'-T(oG) Sample --- p.31 / Chapter 3.2.5 --- 5'-T(Sp) Sample --- p.34 / Chapter 3.3 --- Sugar Pucker Conformation --- p.38 / Chapter 3.4 --- Backbone Conformation --- p.41 / Chapter 3.5 --- UV Melting --- p.43 / Chapter 4.Chapter Four: --- Effect of Spiroiminodihydantoin and 7-hydro-8-oxoguanine on Primer-Template Structures --- p.44 / Chapter 4.1 --- Overview --- p.42 / Chapter 4.2 --- NMR Investigations of the Primer-Template Models --- p.45 / Chapter 4.2.1 --- Incorporation of a dCTP Opposite a 5'-GG Template --- p.45 / Chapter 4.2.2 --- Incorporation of a dCTP Opposite a 5'-G(oG) Template --- p.46 / Chapter 4.2.3 --- Incorporation of a dCTP Opposite a 5'-G(Sp) Template --- p.48 / Chapter 4.2.4 --- Incorporation of a dATP Opposite a 5'-T(oG) Template --- p.50 / Chapter 4.2.5 --- Incorporation of a dATP Opposite a 5'-T(Sp) Template --- p.51 / Chapter 4.3 --- Effect of Sp and oG on Primer-Template Structures --- p.52 / Chapter 4.3.1 --- Misaligned Structure with a Sp-Bulge --- p.52 / Chapter 4.3.2 --- C·oG Base Pair in 5'-G(oG) --- p.54 / Chapter 4.3.3 --- Biological Implications --- p.54 / Chapter 5. --- Chapter Five: Preliminary Structural Calculations on Primer- Template Structures --- p.56 / Chapter 5.1 --- Experimental Restraints Extraction --- p.56 / Chapter 5.2 --- Experimental Restraints Distribution --- p.58 / Chapter 5.3 --- Structural Calculations --- p.60 / Chapter 5.4 --- Structural Results --- p.62 / Chapter 5.4.1 --- 5'-GG --- p.63 / Chapter 5.4.2 --- 5'-G(oG) --- p.64 / Chapter 5.4.3 --- 5'-T(oG) --- p.65 / Chapter 5.4.4 --- 5'-T(SpR) with 5'-T(Spl) Restraints --- p.66 / Chapter 5.4.5 --- 5'-T(SpR) with 5'-T(Sp2) Restraints --- p.67 / Chapter 5.4.6 --- 5'-T(SpS) with 5'-T(Spl) Restraints --- p.68 / Chapter 5.4.7 --- 5'-T(SpS) with 5'-T(Sp2) Restraints --- p.69 / Chapter 5.6 --- Structural Analysis --- p.70 / Chapter 6. --- Chapter Six: Conclusions and Future Work --- p.72 / Appendix --- p.73 / References --- p.74

Structural analyses of DNA oligonucleotides indicate the presence of bound water molecules in the major and minor grooves of DNA. These water molecules participate in DNA charge transfer by their reaction with guanosine radical cation to form 7,8-dihydro-8-oxo-guanine (8-oxoG), which when treated with a base leads to DNA strand cleavage. We probed the reaction of guanosine radical cation with water with series of alkyl substituted cytidines and thymidines by incorporating the modified nucleosides into anthraquinone linked DNA duplexes and irradiating them with UV light at 350 nm. The incorporation of these hydrophobic substituents disrupt the DNA spine of hydration, and we have observed that these modifications in the major and minor groove do not effect the trapping or long distance hopping of radical cations in DNA. The second part of the work reported herein examines the role of charged nucleosides in long range charge transfer in duplex DNA. DNA methylation is a naturally occurring process mediated by enzymes responsible for such functions in biological systems. Hypermethylation of DNA can also occur as a result of environmental alkylating agents leading to mutation of the affected cells. Methylation of the ring nitrogen of a purine base can introduce a positive charge in the ring resulting in the cleavage of the glycosidic bond of the nucleoside. To understand the role of a charged nucleoside on charge transfer in DNA, we designed and synthesized cationic nucleoside mimics, which were incorporated into anthraquinone-linked DNA strands and irradiated at 350 nm. The presence of the cationic bases on the duplexes inhibits the migrating hole from hopping along the DNA strand, and induces a prominent local structural distortion of the DNA as a result of the charged nucleobase.

Previous studies from our laboratory and others show a significant increase in levels of both nuclear and mitochondrial DNA and RNA oxidation in vulnerable brain regions in the progression of Alzheimer’s disease (AD). Although total DNA oxidation is increased in AD it remains unclear whether oxidative damage is widespread throughout the genome or is concentrated to specific genes. To test the hypothesis that specific genes are more highly oxidized in the progression of AD, we propose to quantify the percent oxidative damage in genes coding for proteins shown to be altered in the progression of AD using quantitative/real-time polymerase chain reaction (qPCR/ RT-PCR). To further test the hypothesis that diminished DNA repair capacity in the progression of AD contributes to increased DNA oxidation we will use custom PCR arrays and qPCR, Western blot analysis and activity assays to quantify changes in enzymes involved in base excision repair (BER). In order to carry out these studies tissue specimens from superior and middle temporal gyri (SMTG) and inferior parietal lobe (IP), as well as, a non-vulnerable region, the cerebellum (CER) will be analyzed from normal control (NC) subjects and subjects throughout the progression of AD including those with preclinical AD (PCAD), mild cognitive impairment (MCI), and late stage AD (LAD). We will also analyze specimens from diseased control subjects (DC; Frontotemporal dementia (FTD) and dementia with Lewy bodies (DLB)) to determine if the changes we observe in AD are specific.

No description available.

No description available.

Chez l’Homme, les succès de la fécondation et d’un développement embryonnaire aboutissant à la naissance d’un enfant en bonne santé résident principalement dans la qualité des cellules reproductrices. Les dommages oxydants de l’ADN spermatique sont une cause majeure d’infertilité masculine. Afin de permettre une prise en charge thérapeutique optimale et adaptée, j’ai tout d’abord mis au point et validé un test diagnostique de l’oxydation de l’ADN spermatique par immunodétection du 8-hydroxy-2'-desoxyguanosine (8-OHdG), adduit majeur de l'oxydation nucléaire. Ce travail de thèse a déterminé, pour la première fois, un seuil d’oxydation de l’ADN spermatique en relation avec les paramètres conventionnels spermatiques. Dans un second temps, je me suis focalisée sur les atteintes de la chromatine et de l’ADN spermatique les plus fréquentes en cas d’infertilité masculine, à savoir les anomalies de condensation de la chromatine, la fragmentation et l’oxydation de l’ADN spermatique. Une corrélation entre l’oxydation de l’ADN, tout particulièrement la moyenne d’intensité de fluorescence, et le pourcentage de spermatozoïde fragmenté a été mise en évidence. Pour objectiver l’impact de ces dommages nucléaires spermatiques en pratique clinique, j’ai étudié, après cryopréservation, les effets bénéfiques d’une supplémentation en hypotaurine des milieux de sélection et de congélation/décongélation des échantillons. Une baisse de la cryocapacitation et du pourcentage de spermatozoïde fragmenté et décondensé ont été retrouvées ainsi qu’une amélioration de la vitalité et de la mobilité progressive spermatique. Enfin, comme le spermatozoïde a pour but ultime de participer à la genèse d’un nouvel individu, j’ai mis en évidence que la fragmentation et l’oxydation de l’ADN spermatique avaient un impact à des moments clés de la cinétique du développement embryonnaire précoce suite à une ICSI sans pour autant modifier l’obtention de blastocystes de bonne qualité. Ce travail de thèse a permis de mieux comprendre la physiopathologie de l’infertilité masculine et de mettre en évidence de nouveaux biomarqueurs spermatiques en lien avec un développement embryonnaire normal. / In humans, the success of fertilization and embryonic development leading to the birth of ahealthy child lies mainly in the quality of reproductive cells. Oxidative damage to sperm DNAis a major cause of male infertility. In order to provide optimal and appropriate therapeuticmanagement, I first developed and validated a diagnostic test for sperm DNA oxidation byimmunodetection of 8-hydroxy-2'-deoxyguanosine (8-OHdG), a major adduct of nuclearoxidation. This thesis work determined, for the first time, a threshold for the oxidation ofsperm DNA in relation to conventional sperm parameters. In a second step, I focused on themost common chromatin and sperm DNA disorders in male infertility, namely chromatincondensation anomalies, sperm DNA fragmentation and oxidation. A correlation betweenDNA oxidation, particularly the mean fluorescence intensity, and the percentage offragmented sperm was found. To objectify the impact of this nuclear sperm damage inclinical practice, I studied, after cryopreservation, the beneficial effects of hypotaurinesupplementation to the selection and freeze/thaw media of seed samples. A decrease incryocapacitation and the percentage of fragmented and decondensed sperm has beenfound, as well as an improvement in sperm vitality and progressive mobility. Finally, sincethe ultimate goal of the sperm cells is to participate in the genesis of a new individual, I haveshown that the fragmentation and oxidation of sperm DNA has an impact at key moments inthe kinetics of early embryonic development following ICSI without modifying the obtainingof good quality blastocysts. This thesis work has led to a better understanding of thepathophysiology of male infertility and the identification of new sperm biomarkers related tonormal embryonic development.

Cognitive impairment, “Chemofog”, has been well established as a negative outcome of otherwise successful medical radiation treatments. Mitigation of this negative feature would dramatically increase quality of life for those recovering from cancer treatment. There is currently no known intervention to protect or restore cognitive function of patients undergoing radiation treatments. Development of a multiple ingredient dietary supplement (MDS) is meant to offer a non-invasive therapy to help mitigate risk and decrease damage to individuals. The MDS was originally designed to off-set 5 key mechanisms associated with aging including oxidative damage, inflammation, impaired glucose metabolism, mitochondrial dysfunction and membrane deterioration. Radiation damage shares many of the same deficiencies that develop with age and supplementation with MDS would impact many of the same pathways. Changes in cytokine profile (inflammation markers), and biomarkers of behavioural functions, sensory functions, and oxidative damage provide preliminary evidence of MDS impacts. / Thesis / Bachelor of Science (BSc) / Cognitive impairment, “Chemofog”, has been well established as a negative outcome of otherwise successful medical radiation treatments. Mitigation of this negative feature would dramatically increase quality of life for those recovering from cancer treatment. There is currently no known intervention to protect or restore cognitive function of patients undergoing radiation treatments. Development of a multiple ingredient dietary supplement (MDS) is meant to offer a non-invasive therapy to help mitigate risk and decrease damage to individuals. The MDS was originally designed to off-set 5 key mechanisms associated with aging including oxidative damage, inflammation, impaired glucose metabolism, mitochondrial dysfunction and membrane deterioration. Radiation damage shares many of the same deficiencies that develop with age and supplementation with MDS would impact many of the same pathways.