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.

Characterization of Copper Covetic Bulk and Films: Copper with High Carbon Content

Incorporation of carbon nanostructures in metals is desirable to combine the strongly bonded electrons in the metal and the free electrons in carbon nanostructures that give rise to high ampacity and high conductivity, respectively. Carbon in copper has the potential to impact industries such as: building construction, power generation and transmission, and microelectronics. This thesis focuses on the structure and properties of bulk and thin films of a new material, Cu covetic, that contains carbon in concentrations up to 16 at.%. X-ray photoelectron spectroscopy (XPS) shows C 1s peak with both sp2 and sp3 bonded C measuring up to 3.5 wt.% (16 at.%). High resolution transmission electron microscopy and electron diffraction of bulk covetic samples show a modulated structure of ≈ 1.6 nm along several crystallographic directions in regions that have high C content suggesting that the carbon incorporates into the copper lattice forming a network. Electron energy loss spectra (EELS) from covetics reveal that the level of graphitization from the source material, activated carbon, is maintained in the covetic structure. Bulk Cu covetics have a slight increase in the lattice constant, as well as <111> texturing, or possibly a different structure, compared to pure Cu. Density functional theory calculations predict bonding between C and Cu at the edges and defects of graphene sheets. The electrical resistivity of bulk covetics first increases and then decreases with increasing C content. Cu covetic films were deposited using e-beam and pulsed laser deposition (PLD) at different temperatures. No copper oxide or any allotropes of carbon are present in the films. The e-beam films show enhanced electrical and optical properties when compared to pure Cu films of the same thickness even though no carbon was detected by XPS or EELS. They also have slightly higher ampacity than Cu metal films. EELS analysis of the C-K-edge in the PLD films indicate that graphitic carbon is transferred from the bulk into the films with uniform carbon distribution. PLD films exhibit flatter and higher transmittance curves and sheet resistance two orders of magnitude lower than e-beam films leading to a high figure of merit as transparent conductors.

Language Outcomes of the Play and Language for Autistic Youngsters (PLAY) Project Home Consultation model—An Extended Analysis

The current study is a post-hoc analysis of data from the original randomized control trial of the Play and Language for Autistic Youngsters (PLAY) Home Consultation program, a parent-mediated, DIR/Floortime based early intervention program for children with ASD (Solomon, Van Egeren, Mahone, Huber, & Zimmerman, 2014). We examined 22 children from the original RCT who received the PLAY program. Children were split into two groups (high and lower functioning) based on the ADOS module administered prior to intervention. Fifteen-minute parent-child video sessions were coded through the use of CHILDES transcription software. Child and maternal language, communicative behaviors, and communicative functions were assessed in the natural language samples both pre- and post-intervention. Results demonstrated significant improvements in both child and maternal behaviors following intervention. There was a significant increase in child verbal and non-verbal initiations and verbal responses in whole group analysis. Total number of utterances, word production, and grammatical complexity all significantly improved when viewed across the whole group of participants; however, lexical growth did not reach significance. Changes in child communicative function were especially noteworthy, and demonstrated a significant increase in social interaction and a significant decrease in non-interactive behaviors. Further, mothers demonstrated an increase in responsiveness to the child’s conversational bids, increased ability to follow the child’s lead, and a decrease in directiveness. When separated for analyses within groups, trends emerged for child and maternal variables, suggesting greater gains in use of communicative function in both high and low groups over changes in linguistic structure. Additional analysis also revealed a significant inverse relationship between maternal responsiveness and child non-interactive behaviors; as mothers became more responsive, children’s non-engagement was decreased. Such changes further suggest that changes in learned skills following PLAY parent training may result in improvements in child social interaction and language abilities.