La capacité à assurer la mobilité sans couture avec une E2E QoS sera capitale pour la réussite du NGN (Next Generation Network). Pour ce faire, les verrous à lever que nous avons relevés dans cette thèse se positionnent à l'interconnexion de trois domaines, à savoir : les mobilités, l'hétérogénéité et les préférences utilisateur. Notre première proposition d'ordres organisationnel et fonctionnel, pour laquelle nous préconisons la convergence des trois plans (user, contrôle et gestion) et les fonctionnalités associées. Ainsi nous obtenons une QoS dynamique pour satisfaire l'approche orientée "User-Centric ". Afin de mettre en œuvre la E2E QoS incluant la personnalisation dans la session "User-Centric", nous avons proposé une "Signalisation dynamique d'E2E QoS", qui est d'ordre protocolaire, sur le niveau de service afin de parvenir à la fourniture des services demandés par l'user et de se conformer au SLA. Pour couvrir tout impact de mobilité, nous avons ensuite proposé un " cross layer E2E Session Binding" au sein de notre architecture à quatre niveaux de visibilité (Equipement, Réseau, Service et User). Par le binding nous assurons la cohérence des informations entre les quatre niveaux de visibilité. Au-delà du binding, notre contribution sur la dimension informationnelle a porté sur les profils impliqués dans chaque étape du cycle de vie du service incluant les critères de QoS, les quels fournissent une image générique des composants du système de l'utilisateur et de toutes les ressources ambiantes. Finalement, nous montrons la faisabilité de nos contributions à travers des expérimentations sur notre plate-forme.

La tesi è strutturata in 3 capitoli e analizza gli investimenti e la regolamentazione nel broadband market". Il primo capitolo analizza la letteratura teorica ed empirica sul rapporto tra gli investimenti e la regolamentazione nel settore delle telecomunicazioni. Il secondo capitolo fornisce un'analisi teorica sullo "stepping-stone theory". La terza parte fornisce un'analisi sull'impatto dei diversi regimi normativi per la costruzione della Next Generation Networks. / This dissertation is composed of three papers and discusses the issue of investment and regulation in broadband market. The first paper reviews the specialized but growing branch of the literature. It surveys the relevant theoretical and empirical literature on the relationship between regulation, at both retail and wholesale level, and investment in telecoms infrastructures. Theoretical analyses state that with respect to retail (incentive) regulation, the firm‘s incentive to invest is related to the level of price cap. As for access regulation, mandatory unbundling can possibly discourage firms‘ incentive to invest, but this is not the case for all circumstances because some studies have displayed an opposite (positive) effect on investment. The influence of regulators‘ limited ability to make credible commitment ex ante is not negligible either. Evidence in empirical findings exhibits a certain disunity. The majority concludes that local loop unbundling based on forward-looking cost methodology discourages both ILECs and CLECs from investing in networks, so that the stepping-stone theory is possibly not supported by the data; other findings support the non-negative effect of access regulation on investment. The second paper provides theoretical analysis on the stepping-stone theory. We dynamically model the competition between a vertically-integrated incumbent firm and a facilities-free new entrant in broadband market, where both firms are entitled with investment options: not only can the incumbent decide how much to spend in upgrading its existing network, but also the entrant can choose whether and when to invest on the construction of its own network. The analysis is conducted under three different kinds of competition: pure services-based, pure facilities-based and mixed competition. We find that the entrant's ability to provide value-added services affects the incumbent's investment choice. Our simulation results support the stepping-stone theory that access regulation provides an impetus for the entrant to invest in their own facilities after entering the market based on leased lines. It is also socially desirable because both the overall welfare and the consumer surplus are maximized in a regulated market under mixed competition. The third paper studies impacts of different regulatory regimes on the construction of Next Generation Networks (NGNs). We model the competition between a vertically-integrated incumbent firm and a facilities-free entrant firm in broadband market, where the incumbent has an investment option to upgrade its current network to the NGN. In order to analyze how policy settings affect the incumbent firm‘s investment choice, three kinds of regulatory regimes are discussed: no regulation, partial regulation (only the traditional network is regulated and the NGN is unregulated) and full regulation (both the traditional network and the NGN are regulated). We find that not only the entrant‘s ability to provide value-added services, but also the substitution factor that indexes the decrease in consumers‘ willingness to pay for the traditional service once the investment occurs, affect the incumbent‘s investment choice. Moreover, the comparison of results under different regimes shows that the incumbent invests the most under partial regulation, which sheds some light on impelling the deployment of Next Generation Networks.

Myoclonus-Dystonia (MD) is an inherited, rare, autosomal dominant movement disorder characterized by quick, involuntary muscle jerking or twitching (myoclonus) and involuntary muscle contractions that cause twisting and pulling movements, resulting in abnormal postures (dystonia). The first MD locus was mapped to 7q21-q31 and called DYT11; this locus corresponds to the SGCE gene. Our group previously identified a second MD locus (DYT15) which maps to a 3.18 Mb region on 18p11. Two patients were chosen to undergo next-generation sequencing, which identified 2,292 shared novel variants within the critical region. Analysis of these variants revealed a 3 bp duplication in a transcript referred to as CD108131, which is believed to be a long non-coding RNA. Characterization of this transcript determined that it is 863 bp in size, it is ubiquitously expressed, with high expression in the cerebellum, and it accounts for ~3% of MD cases.

Recent advances in next generation sequencing have provided unprecedented opportunities for high-throughput genomic research, inexpensively producing millions of genomic sequences in a single run. Analysis of massive volumes of data results in a more accurate picture of the genome complexity and requires adequate bioinformatics support. We explore computational challenges of applying next generation sequencing to particular applications, focusing on the problem of reconstructing viral quasispecies spectrum from pyrosequencing shotgun reads and problem of inferring informative single nucleotide polymorphisms (SNPs), statistically covering genetic variation of a genome region in genome-wide association studies. The genomic diversity of viral quasispecies is a subject of a great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software cannot be used to simultaneously assemble and estimate the abundance of multiple closely related (but non-identical) quasispecies sequences. Here, we introduce a new Viral Spectrum Assembler (ViSpA) for inferring quasispecies spectrum and compare it with the state-of-the-art ShoRAH tool on both synthetic and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. While ShoRAH has an advanced error correction algorithm, ViSpA is better at quasispecies assembling, producing more accurate reconstruction of a viral population. We also foresee ViSpA application to the analysis of high-throughput sequencing data from bacterial metagenomic samples and ecological samples of eukaryote populations. Due to the large data volume in genome-wide association studies, it is desirable to find a small subset of SNPs (tags) that covers the genetic variation of the entire set. We explore the trade-off between the number of tags used per non-tagged SNP and possible overfitting and propose an efficient 2LR-Tagging heuristic.

Biosynthetic natural products are invaluable resources that have been gleaned from the environment for generations, and they play an essential role in drug development. Natural product biosynthesis also possesses the latent ability to affect biological systems adversely. This work implements recent advances in genomic, proteomic and microbiological technologies to understand further biosynthetic molecules that may influence progression of human disease. Azinomycin A and B are antitumor metabolites isolated from the terrestrial bacterium Streptomyces sahachiroi. The azinomycins possess an unusual aziridine [1,2-a] pyrrolidine ring that reacts in concert with an epoxide moiety to produce DNA interstrand cross-links. Genomic sequencing of S. sahachiroi revealed a putative azinomycin resistance protein (AziR). Overexpression of AziR in heterologous hosts demonstrated the protein increases cell viability and decreases DNA damage response in the presence of azinomycin. Fluorescence titration indicated AziR functions as an azinomycin binding protein. An understanding of azinomycin resistance is important for future engineering and drug delivery strategies. Additionally, the S. sahachiroi draft genome obtained via 454 pyrosequencing and Illumina sequencing revealed several silent secondary metabolic pathways that may provide new natural products with biomedical application. β-lactoglobulin (BLG), the most abundant whey protein in bovine milk, has been observed to promote the self-condensation of retinal and similar α,β-unsaturated aldehydes. BLG is a possible non-genetic instigator of cycloretinal and A2E accumulation in the macula, a condition associated with age-related macular degeneration. BLG-mediated terpenal condensation has been optimized for in vitro study with the retinal mimic citral. In rabbits fed retinal and BLG or skim milk, cycloretinal formation was detected in the blood by 1H-NMR, and SDS-PAGE analysis indicated BLG was present in blood serum, suggesting the protein survives ingestion and retains catalytic activity. Mass spectrometry and site-directed mutagenesis provided mechanistic insight toward this unusual moonlighting behavior. The experiments described in this dissertation serve to further natural product biosynthesis discovery and elucidation as they relate to consequences for human health. Efforts to solve azinomycin biosynthesis via enzymatic reconstitution, characterize compounds produced by orphan gene clusters within S. sahachiroi, and obtain a clear mechanism for BLG-promoted cycloterpenal formation are immediate goals within the respective projects.

The Department of Energy and the Idaho National Laboratory are developing a Next Generation Nuclear Plant (NGNP) to serve as a demonstration of state-of-the-art nuclear technology. The purpose of the demonstration is two fold: 1) efficient low cost energy generation and 2) hydrogen production. Although a next generation plant could be developed as a single-purpose facility, early designs are expected to be dual-purpose. While hydrogen production and advanced energy cycles are still in their early stages of development, research towards coupling a high temperature reactor, electrical generation and hydrogen production is under way. Many aspects of the NGNP must be researched and developed to make recommendations on the final design of the plant. Parameters such as working conditions, cycle components, working fluids, and power conversion unit configurations must be understood. Three configurations of the power conversion unit were modeled using the process code HYSYS; a three-shaft design with 3 turbines and 4 compressors, a combined cycle with a Brayton top cycle and a Rankine bottoming cycle, and a reheated cycle with 3 stages of reheat were investigated. A high temperature steam electrolysis hydrogen production plant was coupled to the reactor and power conversion unit by means of an intermediate heat transport loop. Helium, CO2, and an 80% nitrogen, 20% helium mixture (by weight) were studied to determine the best working fluid in terms cycle efficiency and development cost. In each of these configurations the relative heat exchanger size and turbomachinery work were estimated for the different working fluids. Parametric studies away from the baseline values of the three-shaft and combined cycles were performed to determine the effect of varying conditions in the cycle. Recommendations on the optimal working fluid for each configuration were made. The helium working fluid produced the highest overall plant efficiency for the three-shaft and reheat cycle; however, the nitrogen-helium mixture produced similar efficiency with smaller component sizes. The CO2 working fluid is recommend in the combined cycle configuration.

This thesis presents investigations on the potential negative effects of wind turbine noise on the human ear from a sound point source (i.e. wind farm). In Chapter 2, the tectorial membrane, which is a crucial gelatinous structural matrix located within the cochlea of the inner ear, is considered to have a similar constitutive stress-strain relationship to that of an elastomer (rubber) in tension. The tectorial membrane appears to stretch when subjected to constant heavy sound stimulation. The tectorial membrane is modeled as a simply-supported beam with an external load Pext applied at midspan. A virtual work approach is used to balance the external work at midspan Pextδz of the tectorial membrane with the internal strain energy from its hysteresis loops. These hysteresis loops quantify the amount of damage that the tectorial membrane undergoes due to an applied external loading. Normalized damage tables are presented at the end of the chapter to suggest safe distances away from the wind turbines to limit damage to the tectorial membrane. Chapter 3 considers a hypothetical autonomous village constructed in South Pretoria, South Africa. This village accommodates approximately 2000 people (~500 families) and receives electricity for hot water from a nearby 2.5 MW wind farm. The design process for the village is discussed from an architectural and design standpoint. The wind farm specifications, specifically the number of 2.5 MW wind turbines needed to provide electricity for hot water, are established. Results from Chapter 2 are used to suggest minimum safe distances between the wind farm and the autonomous village in the context of limiting damage to the tectorial membrane.

Understanding the factors influencing species ranges and dispersal are becoming increasingly important as climate change alters species distributions worldwide. If species are to persist, life-history strategies must rapidly evolve to accommodate shifting environments. This dissertation assesses the factors modulating dispersal in corals. First, I examined if there were any systematic differences in settlement between Indo-Pacific and Caribbean coral larvae that might explain Caribbean recruitment failures. No differences were observed, however I detected significant divergences in settlement cue preferences among coral species across both the Caribbean (Diploria strigosa, and Montastraea franksi) and the Indo-Pacific (Acropora tenuis, A. millepora, and Favia lizardensis), even for coral larvae from the same reef. Secondly, I established the extent of coral dispersal between remote reefs. I evaluated the genetic diversity and divergence across Micronesia for two coral species and investigated if these islands served as a connectivity corridor between the Indo-West-Pacific (Coral Triangle) and the Central Pacific. I found isolation-by-distance patterns whose strength depended on species, suggesting these corals are not panmictic across their ranges and that island stepping-stones facilitate gene flow to remote Pacific reefs. Next, I investigated genetic structure of symbionts in these same corals, to see if horizontally transmitted symbionts are less dispersive than their coral hosts. Symbiont genetic divergence between islands was an order of magnitude larger than host divergence and both host species and environment modulated symbiont composition. These results suggest that symbiont populations are host-specific and associating with local symbionts might be a mechanism for broadly dispersing corals to adapt locally. Lastly, I estimated heritable variation in dispersal-related traits in coral larvae. I observed strong heritable variation in gene expression, as well as parental effects on two phenotypic traits, settlement and fluorescence. I observed that patterns of differential expression in three-day-old larvae predicted variation in settlement and fluorescence two days later. Correlations between proteoglycan expression and settlement suggest that the larval extracellular matrix plays a role in settlement. Down-regulation of ribosomal proteins and differential expression of oxidative stress genes correlated with increasing fluorescence, possibly indicating reduced growth and increased stress. Overall, this dissertation contributes to our knowledge of factors affecting coral dispersal and the potential for evolution of dispersal-related traits. / text

Transcriptional regulation is a complicated process controlled by numerous factors such as transcription factors (TFs), chromatin remodeling enzymes, nucleosomes, post-transcriptional machineries, and cis-acting DNA sequence. I explored the complex transcriptional regulation in eukaryotes through three distinct studies to comprehensively understand the functional genomics at various steps. Although a variety of high throughput approaches have been developed to understand this complex system on a genome wide scale with high resolution, a lack of accurate and comprehensive annotation transcription start sites (TSS) and polyadenylation sites (PAS) has hindered precise analyses even in Saccharomyces cerevisiae, one of the simplest eukaryotes. We developed Simultaneous Mapping Of RNA Ends by sequencing (SMORE-seq) and identified the strongest TSS and PAS of over 90% of yeast genes with single nucleotide resolution. Owing to the high accuracy of TSS identified by SMORE-seq, we detected possibly mis-annotated 150 genes that have a TSS downstream of the annotated start codon. Furthermore, SMORE-seq showed that 5’-capped non-coding RNAs were highly transcribed divergently from TATA-less promoters in wild-type cells under normal conditions. Mapping of DNA-protein interactions is essential to understanding the role of TFs in transcriptional regulation. ChIP-seq is the most widely used method for this purpose. However, careful attention has not been given to technical bias reflected in final target calling due to many experimental steps of ChIP-seq including fixation and shearing of chromatin, immunoprecipitation, sequencing library construction, and computational analysis. While analyzing large-scale ChIP-seq data, we observed that unrelated proteins appeared to bind to the gene bodies of highly transcribed genes across datasets. Control experiments including input, IgG ChIP in untagged cells, and the Golgi factor Mnn10 ChIP also showed the strong binding at the same loci, indicating that the signals were obviously derived from bias that is devoid of biological meaning. In addition, the appearance of nucleosomal periodicity in ChIP-seq data for proteins localizing to gene bodies is another bias that can be mistaken for false interactions with nucleosomes. We alleviated these biases by correcting data with proper negative controls, but the biases could not be completely removed. Therefore, caution is warranted in interpreting the results from ChIP-seq. Nucleosome positioning is another critical mechanism of transcriptional regulation. Global mapping of nucleosome occupancy in S. cerevisiae strains deleted for chromatin remodeling complexes has elucidated the role of these complexes on a genome wide scale. In this study, loss of chromodomain helicase DNA binding protein 1 (Chd1) resulted in severe disorganization of nucleosome positioning. Despite the difficulties of performing ChIP-seq for chromatin remodeling complexes due to their transient and dynamic localization on chromatin, we successfully mapped the genome-wide occupancy of Chd1 and quantitatively showed that Chd1 co-localizes with early transcription elongation factors, but not late transcription elongation factors. Interestingly, Chd1 occupancy was independent of the methylation levels at H3K36, indicating the necessity of a new working model describing Chd1 localization.

Mitochondrial diseases involving dysfunction of the respiratory chain are the most common inborn errors of metabolism. Mitochondria are found in all cell types besides red blood cells; consequently, patients can present with any symptom in any organ at any age. These diseases are genetically heterogeneous, and exhibit maternal, autosomal dominant, autosomal recessive and X-linked modes of inheritance. Historically, clinical genetic evaluation of mitochondrial disease has been limited to sequencing of the mitochondrial DNA (mtDNA) or several candidate genes. As human genome sequencing transformed from a research grade effort costing $250,000 to a clinical test orderable by doctors for under $10,000, it has become practical for researchers to sequence individual patients. This thesis describes our experiences in applying "MitoExome" sequencing of the mtDNA and exons of >1000 nuclear genes encoding mitochondrial proteins in ~200 patients with suspected mitochondrial disease. In 42 infants, we found that 55% harbored pathogenic mtDNA variants or compound heterozygous mutations in candidate genes. The pathogenicity of two nuclear genes not previously linked to disease, NDUFB3 and AGK, was supported by complementation studies and evidence from multiple patients, respectively. In an additional two unrelated children presenting with Leigh syndrome and combined OXPHOS deficiency, we identified compound heterozygous mutations in MTFMT. Patient fibroblasts exhibit severe defects in mitochondrial translation that can be rescued by exogenous expression of MTFMT. Furthermore, patient fibroblasts have dramatically reduced fMet-\(tRNA^{Met}\) levels and an abnormal formylation profile of mitochondrially translated \(COX_1\). These results demonstrate that MTFMT is critical for human mitochondrial translation. Lastly, to facilitate evaluation of copy number variants (CNVs), we developed a web-interface that integrates CNV calling with genetic and phenotypic information. Additional diagnoses are suggested and in a male with ataxia, neuropathy, azoospermia, and hearing loss we found a deletion compounded with a missense variant in D-bifunctional protein, \(HSD_{17}B_4\), a peroxisomal enzyme that catalyzes beta-oxidation of very long chain fatty acids. Retrospective review of metabolic testing from this patient revealed alterations of long- and very-long chain fatty acid metabolism consistent with a peroxisomal disorder. This work expands the molecular basis of mitochondrial disease and has implications for clinical genomics.