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Identification And Stoichiometric Analysis Of The Monosomal Translational Complex, Xin Wang

Doctoral Dissertations

The identification of the components involved in translational complexes has relied primarily on in vitro studies. Determining which proteins associate together in these complexes, under what conditions they do so, and how the composition of the complexes change under different conditions have became the key issues of in vivo studies. After a one-step affinity purification, using a novel technique of analytical ultracentrifugation with a fluorescence detection system (AU-FDS) I have identified a 77S monosomal translational complex in the yeast Saccharomyces cerevisiae. Major components of the 77S complex include the 80S ribosome, mRNA, and components of the closed-loop structure, eIF4E, eIF4G1/eIF4G2 …

The Identification And Characterization Of The Interaction Between Upf1 And Pab1 During Nonsense-Mediated Decay & The Identification Of Novel Protein Complexes Associated With Translation Termination Factor Erf1, Roy Richardson

Doctoral Dissertations

There are still many protein interactions that occur during translation termination that are poorly understood. One of the important termination pathways still under investigation is nonsense-mediated decay (NMD), which rapidly degrades mRNAs that contain a premature stop codon (PTC). I identified that the interaction between Upfl, which is required for NMD, and PAB1 occurs via the RRM1 domain of PAB1 in the yeast Saccharomyces cerevisiae. Determining the role of this interaction during NMD was performed with pulse-chase assays using a PGKlpG mRNA. These assays revealed that the interaction between Upfl and PAB1 is required for a shift from distributive to …

I The Tandem Chain Extension-Acylation Reaction Ii Synthesis Of Papyracillic Acid A: Application Of The Tandem Homologation-Acylation Reaction Iii Synthesis Of Tetrahydrofuran-Based Peptidomimetics, Carley Meredith Spencer

Doctoral Dissertations

A zinc-mediated tandem chain extension-acylation reaction was successfully developed. This reaction was optimized with the use of beta-keto esters, amides, and imides as well as a variety of acylating agents. The tandem homologation-acylation reaction was successfully applied towards the total synthesis of papyracillic acid A.

Use of a tandem chain extension-aldol reaction, followed by a reductive cyclization, allowed for the synthesis of tetrahydrofuran-based peptidomimetics. A variety of amino acid derived beta-keto imides and aldehydes were used during the initial tandem homologation-aldol reaction. High diastereocontrol was achieved during reductive cyclization when a cis relationship was present between the substituents on the …

Regulation Of The Catalytic And Allosteric Properties Of Photoreceptor Phosphodiesterase (Pde6) By The Glutamic Acid-Rich Protein-2 (Garp2), Wei Yao

Doctoral Dissertations

The photoreceptor phosphodiesterase (PDE6) must be precisely regulated to control the sensitivity, amplitude, and kinetics of the photoresponse during excitation, termination and adaptation to light stimulation in rod and cone photoreceptors. The central hypothesis of this thesis is that one PDE6 binding partner, the glutamic acid-rich protein (GARP2), may regulate PDE6 to reduce its "dark noise", enhance its sensitivity and conserve metabolic energy during rod photoresponse saturation.

The first aim of this research is to better understand the unique biochemical and biophysical characteristics of GARP2 in order to reveal its functional attributes for regulating PDE6 during phototransduction in rod photoreceptors. …

Patterns Of Cytosine Methylation In The Genome Of Caenorhabditis Elegans, Kazufusa Okamoto

Doctoral Dissertations

Recent large-scale comparative analysis of cytosine DNA methylation across diverse eukaryotes suggest that early features of DNA methylation present in the last common ancestor of all eukaryotes some 1.6 to 1.8 billion years ago included the methylation of gene bodies and transposable elements (Zemach, McDaniel et al. 2010; Parfrey, Lahr et al. 2011). These potentially ancient patterns may reflect a primitive role of methylation in transcriptional fidelity and as a mechanism to protect the germ line from transposon, or repeat, mediated mutation. Because spurious transcription and mutation are hypothesized to be among the critical limiting factors to genome size, an …

Synthesis Of Adjacent-Bridged Benzo-Annelated Cyclam And Studies Of Mono- And Di-Benzo-Annelated Cyclam Derivatives, Amanuel B. Ghidey

Master's Theses and Capstones

A new synthetic methodology for the preparation of a novel adjacent-bridged benzoannelated cyclam is presented. This methodology utilizes reductive ring expansion followed by deallylation to give the desired adjacent-bridged benzo-annelated cyclam. This novel ligand is designed to complex metal cations with a trans coordination geometry. Derivatives of this ligand can be prepared by attaching pendant arms on the nitrogens which can aid as coordinating arms and linkers for potential use of this ligand as bifunctional chelator (BFC).

Coupling chemistry studies have been carried out in an attempt to increase the lipophilicity of a dibenzo-annelated tetracyclic bisaminal and to functionalize at …

Theoretical Analysis Of The Reaction Of Peroxymethyl Radical With Atomic Hydrogen And Of Dibenzofuran With Atomic Chlorine, Mikhail Zhukovskiy

Master's Theses and Capstones

Experimental determination of rate constants for gas phase radical reactions is challenging. When rate constants necessary for modeling complex processes in atmospheric and combustion science are unknown, theoretical predictions are useful. We used Variational Transition State Theory with Multidimensional Tunneling (VTST/MT) with Density Functional Theory (DFT) to calculate the rate constant and isotope effects for reaction between the peroxymethyl radical and the hydrogen atom.

Polychlorinated dibenzofurans (PCDFs) are a group of extremely toxic compounds formed during waste incineration. Currently, their chemical degradation in the atmosphere is poorly understood. While some experimental and theoretical results regarding the reaction of PCDFs with …

Spectroscopic Investigations Of The Photochemical Properties Of I. Spiropyran On Y Zeolite For Photochromic Applications Ii. Rhenium(I) Bipyridyl Tricarbonyl On Mesoporous Zsm-5 Zeolite And Silica For Photocatalytic Reduction Of Carbon Dioxide, Kevin Dubois

Master's Theses and Capstones

Immobilization of photoactive molecules on porous and nano-sized solid supports provides unique interactions which affect photophysical properties. In situ diffuse reflectance FTIR and UV-vis spectroscopies were primarily used to investigate the properties of surface functionalized materials. Spectroscopic characterization of photochromic spiropyran molecules physically adsorbed on Y zeolite revealed the importance of surface water in controlling kinetics and reversibility of photoswitching by stabilizing the merocyanine isomer. Re(bpy)(CO)3C1 was both physically adsorbed on a mesoporous ZSM-5 zeolite and covalently bound via the bipyridyl ligand on fumed silica to generate photocatalytic CO2 reduction materials. Upon light irradiation of the solids in the presence …

Novel Synthesis Of Sulfur Based Ligands Used In Modeling Biological Hydrogen Bonding Interactions, Tyler Jesse Jacinto

Master's Theses and Capstones

Heme-thiolate proteins are known to have hydrogen bond donors proximal to the axial thiolate ligand. The specific roles of these conserved H-bond donors have not yet been elucidated. However, various sources agree upon the positive influence that increased X-H···S interactions have on protein redox potentials. For example, synthetic modeling studies of the cytochromes P450 show similar positive shifts in potential in iron-porphyrin-thiolate model systems. The ligands used in modeling the H-bonding interactions in the P450 cytochromes included a series of 2,6-substituted thiophenols, -S(2,6-(CX3CONH)2C6H3), where X = H, F, CH3. The current synthetic route to these ligands is vague and employs …

Covalent Attachment Of A Diimine Tricarbonyl Re(I) Catalyst On Solid State Nano-Material Surfaces For Solar Carbon Dioxide Reduction, He He

Master's Theses and Capstones

Reduction of carbon dioxide to useful chemicals and fuels is of significant interest. Transition metal complexes, such as tricarbonyl rhenium(I) compounds, are efficient molecular catalysts for photocatalytic carbon dioxide reduction. To improve the stability and catalytic activity of homogeneous catalysts, a mesoporous silica material, SBA-15, was synthesized and applied as catalyst support for immobilizing the tricarbonyl rhenium(I) compound via both covalent bonding and physical adsorption. The covalently bonded tricarbonyl rhenium(I) catalyst in SBA-15 exhibited excellent stability and good activity during the photocatalytic reduction process, compared with its homogeneous counterpart and the physically absorbed one. Another solid-state nano-material, Kaolin, was also …