STRUCTURAL ANALYSIS OF RIBOSOME BINDING ELEMENTS OF THE 3´ UTR IN TWO POSITIVE-STRAND PLANT RNA VIRUSES

Turnip crinkle virus (TCV) and Pea enation mosaic virus (PEMV) are two positive (+)-strand RNA viruses that are used to investigate the regulation of translation and replication due to their small size and simple genomes. Both viruses contain cap-independent translation elements (CITEs) within their 3´ untranslated regions (UTRs) that fold into tRNA-shaped structures (TSS) according to nuclear magnetic resonance and small angle x-ray scattering analysis (TCV) and computational prediction (PEMV). Specifically, the TCV TSS can directly associate with ribosomes and participates in RNA-dependent RNA polymerase (RdRp) binding. The PEMV kissing-loop TSS (kl-TSS) can simultaneously bind to ribosomes and associate with the 5´ UTR of the viral genome. Mutational analysis and chemical structure probing methods provide great insight into the function and secondary structure of the two 3´ CITEs. However, lack of 3-D structural information has limited our understanding of their functional dynamics. Here, I report the folding dynamics for the TCV TSS using optical tweezers (OT), a single molecule technique. My study of the unfolding/folding pathways for the TCV TSS has provided an unexpected unfolding pathway, confirmed the presence of Ψ3 and hairpin elements, and suggested an interconnection between the hairpins and pseudoknots. In addition, this study has demonstrated the importance of the adjacent upstream adenylate-rich sequence for the formation of H4a/Ψ3 along with the contribution of magnesium to the stability of the TCV TSS. In my second project, I report on the structural analysis of the PEMV kl-TSS using NMR and SAXS. This study has re-confirmed the base-pair pattern for the PEMV kl-TSS and the proposed interaction of the PEMV kl-TSS with its interacting partner, hairpin 5H2. The molecular envelope of the kl-TSS built from SAXS analysis suggests the kl-TSS has two functional conformations, one of which has a different shape from the previously predicted tRNA-shaped form. Along with applying biophysical methods to study the structural folding dynamics of RNAs, I have also developed a technique that improves the production of large quantities of recombinant RNAs in vivo for NMR study. In this project, I report using the wild-type and mutant E.coli strains to produce cost-effective, site-specific labeled, recombinant RNAs. This technique was validated with four representative RNAs of different sizes and complexity to produce milligram amounts of RNAs. The benefit of using site-specific labeled RNAs made from E.coli was demonstrated with several NMR techniques.

THE DISTRIBUTION AND FUNCTION OF DENITRIFICATION GENES: EXPLORING AGRICULTURAL MANAGEMENT AND SOIL CHEMICAL IMPLICATIONS

Denitrification is a microbially-mediated process that converts nitrate (NO3-) to dinitrogen (N2) gas and has implications for soil fertility, climate change, and water quality. Using PCR, qPCR, and T-RFLP, the effects of environmental drivers and land management on the abundance and composition of functional genes were investigated. Environmental variables affecting gene abundance were soil type, soil depth, nitrogen concentrations, soil moisture, and pH, although each gene was unique in its spatial distribution and controlling factors. The inclusion of microbial variables, specifically genotype and gene abundance, improved denitrification models and highlights the benefit of including microbial data in modeling denitrification. Along with some evidence of niche selection, I show that nirS is a good predictor of denitrification enzyme activity (DEA) and N2O:N2 ratio, especially in alkaline and wetland soils. nirK was correlated to N2O production and became a stronger predictor of DEA in acidic soils, indicating that nirK and nirS are not ecologically redundant.

EXPERIMENTAL DEMONSTRATION OF LIGHT TRAPPING AND INTERNAL LIGHT SCATTERING IN SOLAR CELLS

Renewable energy technologies have long-term economic and environmental advantages over fossil fuels, and solar power is the most abundant renewable resource, supplying 120 PW over earth’s surface. In recent years the cost of photovoltaic modules has reached grid parity in many areas of the world, including much of the USA. A combination of economic and environmental factors has encouraged the adoption of solar technology and led to an annual growth rate in photovoltaic capacity of 76% in the US between 2010 and 2014. Despite the enormous growth of the solar energy industry, commercial unit efficiencies are still far below their theoretical limits. A push for thinner cells may reduce device cost and could potentially increase device performance. Fabricating thinner cells reduces bulk recombination, but at the cost of absorbing less light. This tradeoff generally benefits thinner devices due to reduced recombination. The effect continues up to a maximum efficiency where the benefit of reduced recombination is overwhelmed by the suppressed absorption. Light trapping allows the solar cell to circumvent this limitation and realize further performance gains (as well as continue cost reduction) from decreasing the device thickness. This thesis presents several advances in experimental characterization, theoretical modeling, and device applications for light trapping in thin-film solar cells. We begin by introducing light trapping strategies and discuss theoretical limits of light trapping in solar cells. This is followed by an overview of the equipment developed for light trapping characterization. Next we discuss our recent work measuring internal light scattering and a new model of scattering to predict the effects of dielectric nanoparticle back scatterers on thin-film device absorption. The new model is extended and generalized to arbitrary stacks of stratified media containing scattering structures. Finally, we investigate an application of these techniques using polymer dispersed liquid crystals to produce switchable solar windows. We show that these devices have the potential for self-powering.