Life Sciences Commons^™

Computational Modeling Of Rna-Small Molecule And Rna-Protein Interactions, Lu Chen

Dissertations & Theses (Open Access)

The past decade has witnessed an era of RNA biology; despite the considerable discoveries nowadays, challenges still remain when one aims to screen RNA-interacting small molecule or RNA-interacting protein. These challenges imply an immediate need for cost-efficient while predictive computational tools capable of generating insightful hypotheses to discover novel RNA-interacting small molecule or RNA-interacting protein. Thus, we implemented novel computational models in this dissertation to predict RNA-ligand interactions (Chapter 1) and RNA-protein interactions (Chapter 2).

Targeting RNA has not garnered comparable interest as protein, and is restricted by lack of computational tools for structure-based drug design. To test the potential …

Gallic Acid-Grafted Chitosan Films As Antioxidant Food Packaging, Ping Guo

Masters Theses

Chitosan is the second most abundant natural polysaccharide in the nature. Due to its biodegradability and film forming ability, chitosan has the potential to be used as an alternative to petroleum-based polymers for food packaging. The presence of a primary amine as well as primary and secondary hydroxyl groups enable chitosan to be chemically modified with various functional groups. Gallic acid (GA) is a natural occurring antioxidant (AOX), which can be grafted to chitosan using by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) and N-hydroxysuccinimide (NHS). The first project deals with the effect of ethanol (EtOH) concentration on efficiency of grafting GA onto chitosan. …

Structural Elucidation Of Aggr-Activated Regulator, Aar, In Enteroaggregative Escherichia Coli, Andrew Heindel

Senior Honors Projects, 2010-2019

Travelers’ Diarrhea is the number one cause of childhood death in the world. Enteroaggregative Escherichia coli (EAEC) is one of the main causes of this disease. EAEC adhere to the surface of the intestine and stack in a brick-like pattern. Via an unstudied quorum-sensing mechanism, these bacteria express a variety of virulence factors that lead to diarrhea. The long-term goal of this research is to elucidate the mechanism by which EAEC changes from benign to virulent. A previously-unstudied open-reading frame in EAEC, AggR activated repressor (Aar), has recently been hypothesized to act as one of the major transcription factors influencing …

Conformational Heterogeneity And Exchange Within The Junction Of The Human U2-U6 Snrna Complex Measured By 19f Nmr Spectroscopy, Caijie Zhao

Dissertations, Theses, and Capstone Projects

Pre-mRNA splicing, the process by which non-coding sequences are removed and coding sequences are ligated, plays an important role in the maturation of precursor messenger RNA molecules prior to their translation into proteins. In eukaryotes, splicing is catalyzed by the spliceosome, a large and dynamic nuclear macromolecular "machine" that comprises five small nuclear (sn)RNA molecules and more than one hundred proteins. Among the RNA components, the complex formed between the U2 and U6 snRNA molecules is implicated in catalytic activity. In this dissertation, I have used ¹⁹F NMR techniques to characterize the conformation ("fold") and dynamics of a protein-free …

Carbon Storage And Preservation In Seagrass Meadows, Mohammad Rozaimi Jamaludin

Theses: Doctorates and Masters

Seagrass meadows are important ‘Blue Carbon’ sinks but many questions remain unaddressed in regards to the organic carbon (OC) sequestration capacity and processes leading to retention and persistence of OC in seagrass sediments. The research summarised in this dissertation examined 37 sediment cores from twelve Australian seagrass meadows (Posidonia australis and Halophila ovalis) in order to improve our understanding of OC storage and preservation in seagrass sediments. The research: quantified the OC storage in seagrass meadows and the reduction in stores after ecosystem degradation; the rates of OC accumulation; the roles of species composition and the depositional nature …

Profiling Fatty Acid Composition Of Brown Adipose Tissue, White Adipose Tissue And Bone Marrow Adipose Tissue Of Healthy And Diet-Induced Obese Mice, Urszula Osinska Warncke

Browse all Theses and Dissertations

Bone marrow adipose tissue (MAT) contains a fat depot of unknown function. Characterization of this tissue in healthy and pathophysiological conditions may be an important step in order to understand MAT contribution to development of osteoporosis and perhaps to develop means to improve bone health by manipulation with a phenotype of MAT. Here we demonstrate that MAT, brown adipose tissue (BAT), and white adipose tissue (WAT) derived from healthy mice differ in fatty acid and phospholipid composition. The profile of MAT changed to resemble a less-metabolically active tissue upon metabolic impairment as seen in diet-induced obesity. Additionally, PPARγ activation alters …

Sharp Rna Recognition Motif Optimizations, Extensions, And Mutations For Use In 2d And 3d Nmr Experiments, Shaun M. Christie

Williams Honors College, Honors Research Projects

SMRT/HDAC Associated Repressor Protein interacts with the long noncoding RNA, produced by SRA, by binding at the RRMs. Three projects were done to prepare the truncated proteins for use in 2D and 3D NMR experiments. The first focuses on RRM 3 and its optimization during the purification process. The second focuses on RRM 2-4, which was found to be missing two alpha helices that may be important for protein stability. These helices can also interact with RRM 3 as well due to the tight association of RRMs 3 and 4. The two step PCR extension of RRM 2-4 was assumed …