Life Sciences Commons^™

Effects Of Statin Drugs And Tocotrienol Rich Fraction Supplementation In Chronic Hemodialysis Patients And Metabolomic Profile, Eno Latifi

Wayne State University Theses

Chronic kidney disease (CKD) is known as a heterogeneous disorder which currently is on the rise and lately has been classified as a public health issues in the United State and worldwide. CKD is an irreversible and progressive disease which can lead to kidney failure, and this is depicted by the advanced stage of the disorder when it reaches the point, that is classified as end stage of renal disease (ESRD) (Stage 5 of CKD) (eGRF <15 mL/min/ 1.73 m2 working capacity), where both organs are in a total or permanent kidney failure. End-Stage renal disease patients, on hemodialysis have been associated to experience an accelerated form of atherosclerosis, which is induced by inflammation, impairment of antioxidant system and elevated oxidative stress. Since the problem effecting ESRD patients is multifactorial, the objective of this investigation is to explore and look at the effects of supplementing with vitamin E-tocotrienol rich fraction (TRF), a micronutrient which has anti-inflammatory, antioxidant, and lipid lower capabilities into tackling these comorbid conditions experienced by this population. Therefore the aims of this investigation will be to explore changes in lipid profiles, inflammatory markers, and oxidative status, as well as look at any changes in metabolomic profiles. It was hypothesized that by supplementing with TRF a vitamin E, for 16 weeks in ESRD patients undergoing hemodialysis, it may help reverse and/or improve, oxidative status, inflammatory markers, increase antioxidants status and improve lipid profiles.

The study was double-blinded, randomized, parallel, placebo-controlled design trial, of 81 adult patients undergoing chronic hemodialysis at Great Lake Dialysis Clinic, Detroit MI, where …

Structural Characterization Of The Redox-Dependent Differences In The Cytochrome P450cam-Putidaredoxin Complex Using Solution Nmr Spectroscopy, Nicholas John Lopes

Masters Theses

Complexation between proteins as part of biological electron transfer reactions is driven by precise interactions that are often characterized by short lifetimes, weak affinities and high turnover rates. These complex interactions are difficult to study structurally in physiologically relevant oxidation states due to their transient nature and/or large molecular sizes. One such protein complex in the cytochrome P450 family of enzymes that is of great interest to researchers due to its prototypical nature is the Putidaredoxin (Pdx)- cytochrome P450cam (CYP101) electron transfer complex that is involved in hydroxylation of D-camphor in the bacterium Pseudomonas putida. While the individual protein structures …

Solid-State Nuclear Magnetic Resonance Analysis Of Cytosine-Methylated Dna Dodecamer, Caitlin A. Edmunds

Scripps Senior Theses

The interaction of deoxyribonucleic acid (DNA) and cellular proteins is absolutely central to any biological understanding of DNA replication, transcription, and even gene regulation. Because an incumbent protein latches not onto the four bases but onto the backbone phosphate groups of the nucleic acid, backbone dynamics directly pertain to an understanding of basic cell processes. Studies have unambiguously proven that DNA exists in a balance of two conformations, BI and BII, defined by the difference in their backbone torsion angles. A given DNA sequence expresses a preference for either BI or BII, though both exist in most samples (and are …

Structure, Dynamics, And Evolution Of The Intrinsically Disordered P53 Transactivation Domain, Wade Michael Borcherds

USF Tampa Graduate Theses and Dissertations

in numerous disease states, including cancers and neurodegenerative diseases. All proteins are dynamic in nature, occupying a range of conformational flexibilities. This inherent flexibility is required for their function, with ordered proteins and IDPs representing the least flexible, and most flexible, respectively. As such IDPs possess little to no stable tertiary or secondary structure, they instead form broad ensembles of heterogeneous structures, which fluctuate over multiple time scales. Although IDPs often lack stable secondary structure they can assume a more stable structure in the presence of their binding partners in a coupled folding binding reaction.

The phenomenon of the dynamic …

Characterization Of The Interaction Between The Parkin Ubiquitin-Like Domain And Ataxin-3 Ubiquitin Interacting Domains, Jane J. Bai

Electronic Thesis and Dissertation Repository

The ubiquitin signaling pathway (USP) consists of hundreds of enzymes which are tightly regulated for proper maintenance of intracellular protein level homeostasis. The main goals of this thesis were to characterize the interaction of two proteins involved in the USP, the E3 ubiquitin ligase called parkin, and the Deubiquitinating (DUB) enzyme, ataxin-3. The effect of disease-state substitutions in the parkin ubiquitin-like domain (UbLD) on the interaction with ataxin-3 was investigated through NMR ¹H-¹⁵N HSQC titration experiments and affinity binding assays. The three UIM regions in ataxin-3bind the hydrophobic patch of parkin UbLD (K_D = 680 μM) …

31p Nmr Of Backbone Conformation And Dynamics In Dna At Cre Binding Site In Terms Of Sequence Context, Kelly A. Garton

Scripps Senior Theses

The Cre sequence (ACGT) is a site responsible for the binding of specific transcription factors that determine the activation of genes. Due to its major role in gene transcription, it has become a subject of immense research. The binding of transcription factors to the Cre binding site has been determined to be dependent on DNA conformation. In this study, the effects of flanking sequence around the Cre binding site on the conformation and the dynamics of DNA were investigated. The Cre binding site was studied in its native form with differing flanking sequences to determine the BI/BII profile (conformation) and …

Aqueous Micellar Gels Of Multiresponsive Hydrophilic Aba Linear Triblock Copolymers, Jeremiah Wallace Woodcock

Doctoral Dissertations

This dissertation presents the synthesis of a series of well-defined multiresponsive hydrophilic ABA linear triblock copolymers and the study of their aqueous micellar gels. By incorporating a small amount of stimuli-responsive groups into thermosensitive outer blocks of ABA triblock copolymers, the lower critical solution temperatures (LCST) of thermosensitive blocks can be modified by external stimuli. Consequently, the sol-gel transition temperatures (T_sol-gel) of their aqueous solutions can be altered.

Chapter 1 describes the synthesis and solution behavior of a series of thermo- and light-sensitive triblock copolymers, poly(ethoxytri(ethylene glycol) acrylate-co-o-nitrobenzyl acrylate)-b-poly(ethylene oxide)-b …

Nmr Structural Studies Of Endotoxin Receptor Cd14 In Complex With Gram-Negative And Gram-Positive Endotoxin, Seth Andrew Albright

Doctoral Dissertations

Endotoxin recognition by the innate immune receptor CD14 is a critical part of the innate immune system’s early detection and activation of the inflammatory response during microbial invasion. The differential recognition and high affinity binding of endotoxins from gram-negative and gram-positive bacteria is performed by the innate immune receptor CD14. Upon endotoxin binding, CD14 transfers the specific endotoxins to a Toll-like receptor signaling complex, which is responsible for initiating the intracellular signaling cascade. In the presence of overwhelming infection, the effects of CD14 lead to the over-activation of the inflammatory response, which results in the life threatening condition known as …

Deciphering Substrate Promiscuity By Aminoglycoside Resistance Enzymes Via A Biophysical Characterization And Dynamics Of The Aminoglycoside Acetyltransferase-(3)-Iiib And The Aminoglycoside Phosphotransferase-(3′)-Iiia, Adrianne Lee Norris

Doctoral Dissertations

Aminoglycoside antibiotics are losing their bactericidal efficacy due to the spread of enzymes that catalyze a covalent modification to them. A common property of many of these aminoglycoside modifying enzymes (AGMEs) is the capacity to modify multiple diverse aminoglycosides thus conferring resistance to these drugs among several pathogenic bacterial species. To gain a better understanding of the protein-antibiotic interactions responsible for resistance and the promiscuous nature of AGMEs, a variety of biophysical techniques including nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC), steady state kinetics, intrinsic tryptophan fluorescence, and computational modeling are employed in this work. Results and discussion presented …

Homologous And Heterologous Crystallin Protein Interactions As The Molecular Basis Of Inherited Cataract, Priya Ranjan Banerjee

Legacy Theses & Dissertations (2009 - 2024)

Age-related cataract is the most common cause of blindness worldwide. Nearly fifty percent of Americans above the age of 75 are diagnosed with this disease (http://www.nei.nih.gov/eyedata/pbd_tables.asp), and surgical intervention is the sole method of treatment at present (http://www.nei.nih.gov/healthyvision/objective/cataracts.asp). In the developing world, even this treatment is not readily available. These are compelling reasons to search for better treatments to delay, prevent or arrest cataract formation. Recent evidence suggests that age-related cataracts also have a genetic component. Therefore, determining the mechanisms underlying genetic cataracts with a known association to a protein-mutation is one important strategy towards understanding the molecular basis for …

In-Cell And In Vitro Studies Of Disease Related Protein-Protein Interactions Using Nmr-Spectroscopy, Andres Yudiel Maldonado

Legacy Theses & Dissertations (2009 - 2024)

The receptor for advanced glycation end products (RAGE) is a multiligand cell surface macromolecule that plays a central role in the etiology of diabetes, inflammation, and neurodegeneration. The cytoplasmic domain of RAGE, ctRAGE, is critical for RAGE-dependent signal transduction. As the most membrane proximal event, mDia1 binds to ctRAGE and is essential for RAGE ligand-stimulated phosphorylation of AKT and cell proliferation/migration. We show that ctRAGE contains an unusual alpha-turn that mediates the mDia1-ctRAGE interaction and is required for RAGE dependent signaling. The results establish a novel mechanism through which an extracellular signal initiated by RAGE ligands regulates RAGE signaling in …

Structural Interactions And Dynamics Of Disease Related Proteins By Using Nmr Spectroscopy, Shadakshara Swamy Puttamadappa

Legacy Theses & Dissertations (2009 - 2024)

Nuclear Magnetic Resonance (NMR) is a powerful spectroscopic technique to study the structure, molecular interactions, and dynamics of proteins. Modern NMR instrumentation, advancements in experimental techniques and revolutionary developments in recombinant DNA technology have made NMR a versatile and very convenient tool for biomolecule characterization.

A Synthetic Biological Engineering Approach To Secretion- Based Recovery Of Polyhydroxyalkanoates And Other Cellular Products, Elisabeth Linton

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The costs associated with cellular product recovery commonly account for as much as 80% of the total production expense. As a specific example, significant recovery costs limit commercial use of polyhydroxyalkanoates (PHA), which comprise a class of microbially-accumulated polyesters. PHAs are biodegradable compounds that are of interest as a sustainable alternative to petrochemically-derived plastics. Secretion-based recovery of PHAs was studied to decrease PHA production costs. Type I and II secretory pathways are commonly used for the translocation of recombinant proteins out of the cytoplasm of E. coli. Proteins were targeted for translocation using four signal peptides (HlyA, TorA, GeneIII, …

Dose-Dependent Effects Of Oxygen On Metabolism In Rat Cortico-Hippocampal Brain Tissue Slices, Jennifer Lynne Hollyfield

Browse all Theses and Dissertations

Studies have shown that 95% oxygen increases neuronal excitability and ROS production. We wanted to investigate the dose-dependent effects of oxygen on brain slice metabolism. We exposed rat brain cortico-hippocampal tissue slices to 0.40, 0.95, and 4.50 ATA O2 for 60 minutes, made dual-phase tissue extracts, and used multi-nuclear NMR experiments to elucidate the slice metabolism. We found that low doses of oxygen may shift metabolism toward anaerobic glycolysis. Elevated lactate suggests this shift, along with elevated ratios of NAD+/NADH which may drive the reactions toward the production of lactate. The results also suggest that high doses of oxygen may …

Nmr Analyses Show Tcdd Elicits Differences In Hepatic Metabolism In Female C57bl/6 Mice And Sprague-Dawley Rats, Meghan Katherine Makley

Browse all Theses and Dissertations

TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) elicits tissue-, sex-, and species-specific effects. This study compares the hepatic response to an oral dose of TCDD in immature ovariectomized (i.o.) C57BL/6 mice (30 µg/kg) and i.o. Sprague-Dawley rats (10 µg/kg), at 72, 120, and 168 h post-dose. Hepatic lipid extracts were analyzed by ¹³C and ³¹P NMR, and aqueous extracts by ¹H and ³¹P NMR.

Consistent with increased lipid content in mice (p≤0.05), TCDD induced increases in hepatic triacylglycerides (TAG), cholesterol, and fatty acids. Principal component analysis of ¹³C spectra show treatment groups separate in mice, but not rats. …

Structure Elucidation Of Bioactive Compounds Isolated From Endophytes Of Alstonia Scholaris And Acmena Graveolens, Nicholas James Hundley

Theses and Dissertations

Alstonia scholaris is an evergreen tree native to Southeast Asia and Australia. It is commonly used as a medicinal plant throughout these regions. In the present study, an endophyte of the genus Xylaria was isolated from a stem of Alstonia scholaris, its mycelia and exudate extracted, and the extract assayed for growth inhibition of HeLa cancer cells in vitro. Several known compounds were isolated and identified based on NMR, infrared, and mass spectral data. The compounds identified are 19,20-epoxycytochalasin C; 19,20epoxycytochalasin D; and xylobovide. Two other compounds, fusaric acid and dehydrofusaric acid, were discovered in an endophyte of the Hypocreales …