The translation of mRNA into functional proteins is essential for all life. In eukaryotes, aberrant RNAs containing sequence features that stall or severely slow down ribosomes are subject to translation-dependent quality control. Targets include mRNAs encoding a strong secondary structure (No-Go Decay; NGD) or stretches of positively-charged amino acids (Peptide-dependent Translation Arrest/Ribosome Quality Control; PDTA/RQC), mRNAs lacking an in-frame stop codon (Non-Stop Decay; NSD), or defective 18S rRNAs (18S Nonfunctional rRNA Decay; 18S NRD). Previous work from our lab showed that the S. cerevisiae NGD factors DOM34 and HBS1, and PDTA/RQC factor ASC1, all participate in the kinetics of 18S NRD. Upon further investigation of 18S NRD, our research revealed the critical role of ribosomal protein S3 (RPS3), thus adding to the emerging evidence that the ribosome senses its own translational status. While aberrant mRNAs mentioned above can occur endogenously, damaging agents, such as oxidative stress or UV irradiation, can negatively affect the chemical integrity of RNA. Such lesions could lead to translation errors and ribosome stalling. However, current tools to monitor the fate of damaged RNA are quite limited and only provide a low-resolution picture. Therefore, we sought to develop a deep-sequencing method to detect damaged RNA, taking advantage of reverse transcriptase's ability to insert a mutation across a damaged site. Using oxidized RNA as a model damaged RNA, our preliminary data showed increased G>T mutations in oxidized RNA. This method provides the foundation for future work aimed at understanding how cells deal with damaged RNA.

Small interfering RNAs (siRNAs) are a promising class of drugs for treating genetically-defined diseases. Therapeutic siRNAs enable specific modulation of gene expression, but require chemical architecture that facilitates efficient in vivodelivery. siRNAs are informational drugs, therefore specificity for a target gene is defined by nucleotide sequence. Thus, developing a chemical scaffold that efficiently delivers siRNA to a particular tissue provides an opportunity to target any disease-associated gene in that tissue. The goal of this project was to develop a chemical scaffold that supports efficient siRNA delivery to the brain for the treatment of neurodegenerative diseases, specifically Huntington’s disease (HD). HD is an autosomal dominant neurodegenerative disorder that affects 3 out of every 100,000 people worldwide. This disorder is caused by an expansion of CAG repeats in the huntingtin gene that results in significant atrophy in the striatum and cortex of the brain. Silencing of the huntingtin gene is considered a viable treatment option for HD. This project: 1) identified a hyper-functional sequence for siRNA targeting the huntingtin gene, 2) developed a fully chemically modified architecture for the siRNA sequence, and 3) identified a new structure for siRNA central nervous system (CNS) delivery—Divalent-siRNA (Di-siRNA). Di-siRNAs, which are composed of two fully chemically-stabilized, phosphorothioate-containing siRNAs connected by a linker, support potent and sustained gene modulation in the CNS of mice and non-human primates. In mice, Di-siRNAs induced potent silencing of huntingtin mRNA and protein throughout the brain one month after a single intracerebroventricular injection. Silencing persisted for at least six months, with the degree of gene silencing correlating to guide strand tissue accumulation levels. In Cynomolgus macaques, a bolus injection exhibited significant distribution and robust silencing throughout the brain and spinal cord without detectable toxicity. This new siRNA scaffold opens the CNS for RNAi-based gene modulation, creating a path towards developing treatments for genetically-defined neurological disorders.

<p> G93A SODI mice (G93A mice) are a transgenic model over-expressing a mutant human Cu/Zn-SOD gene, and are a model for amyotrophic lateral sclerosis (ALS), a predominantly motor neurodegenerative disease. Hippocampal neurogenesis in the subgranular zone (SGZ) of dentate gyms (DG) occurs throughout the life. It is regulated by many pathological and physiological processes. There is controversy with respect to the basal level of hippocampal neurogenesis and its response to exercise in neurodegenerative diseases and their mouse models. Little information regarding hippocampal neurogenesis is available in G93A mice. The present study was designed to study the impact of treadmill exercise and sex differences on hippocampal neurogenesis in this model. In addition, potential molecular mechanisms regulating hippocampal neurogenesis including growth factors (BDNF and IGFl) and oxidative stress (SOD2, catalase, 8-0Hdg, and 3-NT) were also addressed in the study. Bromodeoxyuridine (BrdU) was used to label newly generated cells. G93A and wild type (WT) mice were subjected to treadmill exercise (EX) or a sedentary (SEO) lifestyle. Immunohistochemistry was used to detect BrdU labeled newly proliferating cells, surviving cells, and their phenotype, as well as for determination of oxidative stress. BDNF and IGFl mRNA expression was assessed by in situ hybridization. Results showed that (1) G93A mice had an elevated basal level of hippocampal neurogenesis for both cell survival and neuronal differentiation, a growth factor (BDNF mRNA), and an oxidative stress marker (NT), as compared to wild type sedentary mice. (2) Treadmill running did not show any further effect on hippocampal neurogenesis, growth factors, oxidative stress, and antioxidant enzymes in G93A mice, while treadmill running promoted hippocampal neurogenes1s and expression of the growth factor (BDNF mRNA), and lowered oxidative stress (8-0Hdg) in WT mice. (3) There also were sex differences in hippocampal neurogenesis in G93A mice, whereby male G93A mice had a significant higher level of cell proliferation but a lower level of survival than female G93A mice. (4) The DG BDNF mRNA was associated with cell survival and neuronal differentiation in sedentary G93A mice, suggesting that BDNF is associated with a higher basal level of hippocampal neurogenesis in G93A mice. We conclude that G93A mice are more permissive in the context of hippocampal neurogenesis, which is associated with elevated DG BDNF mRNA expression. Running did not have impact on hippocampal neurogenesis and BDNF mRNA expression in G93A mice, probably due to a 'ceiling effect' of the already heightened basal levels of hippocampal neurogenesis and BDNF mRNA in this model. In addition, sex differences also affect hippocampal neurogenes1s, but the further study is needed to clarify the underlying molecular mechanisms. </p> / Thesis / Doctor of Philosophy (PhD)

<p>Aging erodes motivation, cognition, sensory modalities and physical capacities, effectively depleting quality of life. Declining sensory, cognitive and motor function are reliable biomarkers of aging and mortality risk. These declines are associated with dysregulation of systemic and cellular processes. We developed a complex dietary supplement (DSP) designed to ameliorate five mechanisms of aging (oxidative processes, inflammation, mitochondrial function, insulin resistance and membrane integrity). Remarkably, normal mice fed the DSP retained youthful functionality into old ages, reflecting slower aging rates. Marked improvements in motor function, memory capacity, spatial learning, muscle strength, visual acuity, olfaction, fecundity and important behavioral functions were observed in aging supplemented mice. Conversely, untreated control animals showed age-related declines in all of the above. Functional improvements were associated with reduced oxidative damage, elevated mitochondrial activity, positive cellular energy balance, improved glucose tolerance, boosted neurotransmitters, greater synaptic density and higher neuronal numbers throughout the brain. A 30% reduction in cancer rates was also documented for DSP treated p53+/- mice. The vast functional benefits greatly exceed the modest longevity extension (11%) in normal supplemented mice. For aging humans, maintaining functionality and performance into later years may provide greater socioeconomic and health benefits than simply prolonging lifespan. Implications of these findings extend to common age-related pathologies including dementia and neurodegenerative diseases, diabetes, cancer, sarcopenia and age-related macular degeneration. Although identifying the role of specific ingredients remains outstanding, results provide proof of principle that complex dietary cocktails can powerfully ameliorate biomarkers of aging and modulate mechanisms considered ultimate goals for aging interventions.</p> / Doctor of Philosophy (PhD)

No description available.

Les maladies neurodégénératives, telles que la maladie d'Alzheimer (AD) et Charcot Marie Tooth (CMT), sont des maladies complexes. Leurs mécanismes pathologiques ne sont toujours pas bien compris et les progrès dans la recherche et le développement de nouvelles thérapies potentielles modifiant la maladie sont lents. Les données catégorielles, comme les échelles de notation et les données sur les études d'association génomique (GWAS), sont largement utilisées dans les maladies neurodégénératives dans le diagnostic, la prédiction et le suivi de la progression. Il est important de comprendre et d'interpréter ces données correctement si nous voulons améliorer la recherche sur les maladies neurodégénératives. Le but de cette thèse est d'utiliser la théorie psychométrique moderne: théorie de la réponse d’item pour analyser ces données catégoriques afin de mieux comprendre les maladies neurodégénératives et de faciliter la recherche de médicaments correspondante. Tout d'abord, nous avons appliqué l'analyse de Rasch afin d'évaluer la validité du score de neuropathie Charcot-Marie-Tooth (CMTNS), un critère important d'évaluation principal pour les essais cliniques de la maladie de CMT. Nous avons ensuite adapté le modèle Rasch à l'analyse des associations génétiques pour identifier les gènes associés à la maladie d'Alzheimer. Cette méthode résume les génotypes catégoriques de plusieurs marqueurs génétiques tels que les polymorphisme nucléotidique (SNPs) en un seul score génétique. Enfin, nous avons calculé l'information mutuelle basée sur la théorie de réponse d’item pour sélectionner les items sensibles dans ADAS-cog, une mesure de fonctionnement cognitif la plus utilisées dans les études de la maladie d'Alzheimer, afin de mieux évaluer le progrès de la maladie. / Neurodegenerative diseases, such as Alzheimer’s disease (AD) and Charcot Marie Tooth (CMT), are complex diseases. Their pathological mechanisms are still not well understood, and the progress in the research and development of new potential disease-modifying therapies is slow. Categorical data like rating scales and Genome-Wide Association Studies (GWAS) data are widely utilized in the neurodegenerative diseases in the diagnosis, prediction and progression monitor. It is important to understand and interpret these data correctly if we want to improve the disease research. The purpose of this thesis is to use the modern psychometric Item Response Theory to analyze these categorical data for better understanding the neurodegenerative diseases and facilitating the corresponding drug research. First, we applied the Rasch analysis in order to assess the validity of the Charcot-Marie-Tooth Neuropathy Score (CMTNS), a main endpoint for the CMT disease clinical trials. We then adapted the Rasch model to the analysis of genetic associations and used to identify genes associated with Alzheimer’s disease by summarizing the categorical genotypes of several genetic markers such as Single Nucleotide Polymorphisms (SNPs) into one genetic score. Finally, to select sensitive items in the most used psychometrical tests for Alzheimer’s disease, we calculated the mutual information based on the item response model to evaluate the sensitivity of each item on the ADAS-cog scale.

No description available.