Biochemistry Commons^™

Synthesis And Immunological Evaluation Of Type I, Type Ii, And Gamma Delta Nkt Cell Antigens, Brian L. Anderson

Theses and Dissertations

The purpose of the immune system is to protect our bodies from infection. One way it accomplishes this task is through the presentation of foreign pathogens to NKT cells. After an antigen is presented to the T cell receptor, activated NKT cells quickly release soluble chemical signals, termed chemokines and cytokines, that modulate the response of the immune system. Due to the immunological relevance of NKT cell activation, we developed and synthesised non-natural analogs of immunostimulatory type I, II, and gamma delta NKT cell antigens. The immunological evaluations of these analogs resulted in identification of sulfatide as a gamma delta …

Eastern Kentucky Farmer's Willingness To Grow Biomass For Emergy Production, Austin P. Jacobs

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science and Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Austin P. Jacobs in May of 2013.

Patatin-Related Phospholipase Pplaiiiδ Increases Seed Oil Content With Long-Chain Fatty Acids In Arabidopsis, Maoyin Li, Sung Bahn, Chuchuan Fan, Jia Li, Tien Phan, Michael Ortiz, Mary Roth, Ruth Welti, Jan Jaworski, Xuemin Wang

Biology Department Faculty Works

The release of fatty acids from membrane lipids has been implicated in various metabolic and physiological processes, but in many cases, the enzymes involved and their functions in plants remain unclear. Patatin-related phospholipase As (pPLAs) constitute a major family of acyl-hydrolyzing enzymes in plants. Here, we show that pPLAIIId promotes the production of triacylglycerols with 20- and 22-carbon fatty acids in Arabidopsis (Arabidopsis thaliana). Of the four pPLAIIIs (a, b, g, d), only pPLAIIId gene knockout results in a decrease in seed oil content, and pPLAIIId is most highly expressed in developing embryos. The overexpression of pPLAIIId increases the content …

Aerobic Degradation Of Α-, Β-, Γ-Hexachlorocyclohexane By Narragansett Bay Bacterioplankton, Ian M. Rambo

Senior Honors Projects

Hexachlorocyclohexanes (HCHs) are a family of chlorinated organic compounds that were previously used as agricultural insecticides. HCHs are recognized as persistent organic pollutants due to their toxicity, recalcitrant properties, and tendency to bioaccumulate in food webs. Although HCH was first synthesized in 1825, its use was not widespread until the discovery of the insecticidal activity of the γ-HCH isomer in 1942. γ-HCH and its toxic waste isomers α-HCH and β-HCH were banned from production and use by the United Nations in 2009, yet these chemicals still present environmental problems due to their persistence in soils and surface waters. HCHs continue …

Modeling Amyloid-Ss Self-Assembly : Stability Of On-Pathway Aggregate Formation, Andrew Kevin Mauro

Theses, Dissertations and Culminating Projects

Protein misfolding and concomitant aggregation towards amyloid formation is the underlying biochemical commonality among a wide range of human pathologies. Amyloid formation involves the conversion of proteins from their native monomeric states (intrinsically disordered or globular) to well-organized, fibrillar aggregates in a nucleation-dependent manner. Understanding the mechanism of aggregation is important not only to gain better insight into amyloid pathology but also to simulate and predict molecular pathways. One of the main impediments in doing so is the highly stochastic nature of interactions that complicates the development of meaningful insights. In this study, we have utilized a well-characterized intermediate along …

The Use Of P53-Derived Stapled Peptides As Affinity Isolation Reagents, Kathryn Margaret Headley

Renée Crown University Honors Thesis Projects - All

The transcription factor p53 can induce apoptosis and cell cycle arrest in response to cellular distress. Cancer cells often display increased cell survival. In most cases, this is due to a p53-related defect, such as mutation, deletion, degradation, or sequestration. HDM2 and HDMX are homologous proteins that regulate the function of p53, and their over-expression can lead to an ineffective p53 response. Various inhibitors, including hydrocarbon stabilized alpha-helices of p53 (SAH-p53s), have been developed to target HDM2 and HDMX and restore functionality to the p53 pathway. It has been recently found that SAH-p53 factors also elicit cell death responses in …

Characterization Of Dap2 (Defense-­‐Associated Aspartic Protease-­‐2) In Arabidopsis Thaliana And Determining Its Role In Plant Defense Responses, Kemardo Kitaro Henry

Renée Crown University Honors Thesis Projects - All

Plants defend themselves from invading pathogens by coordinating activity of several plant defense-­‐associated genes. Defense-­‐Associated Aspartic Protease-­‐1 (DAP1) gene of Arabidopsis encodes for an atypical aspartic protease with a putative proteolytic activity. The DAP1 is a negative regulator of plant immunity and the transgenic plants ectopically expressing this genes support pathogen growth and pathogenicity. The Arabidopsis genome has another putative protese that has ~75% homology to DAP1 present in close proximity and therefore was named DAP2. Here, I describe the role of the DAP2 gene in plant defense responses. Two independent knockout dap2 mutants are found to be more susceptible …

Vitamin B12-Based Bioconjugate Probes For In Vitro And In Vivo Imaging, Anna Kahkoska

Renée Crown University Honors Thesis Projects - All

Cancer is the second leading cause of death in the United States. This year, an estimated 577,190 Americans will die as a result of this family of diseases. Finding cancer at its most treatable stage gives patients the greatest chance of recovery; novel imaging agents that target primary and metastasized tumors offer hope for improved prognoses in the future. Based on the hypothesis that vitamin B12 (B12) and its association with specific transport proteins could offer selective access to cancer cell lines, a series of B12-based imaging agents were synthesized, characterized, and assayed for both in vitro and in vivo …

Investigation Of Ghrelin Acylation By Ghrelin O-Acyltransferase, Edward P. Prybolsky

Renée Crown University Honors Thesis Projects - All

Ghrelin is a peptide hormone involved in hunger signaling and other physiological processes. To become active, ghrelin first must be acylated by ghrelin O-acyltransferase (GOAT). This enzyme carries out a post-translational modification that attaches an octanoyl group to the side chain of the serine 3 (S3) residue of ghrelin. With ghrelin linked to hunger signaling, memory, and other physiological processes, GOAT has been identified as a potential drug target. However, inhibitor design is difficult because not much is known regarding the active site structure and catalytic mechanism of GOAT. This study reports the design of a novel fluorescence-based assay that …

Development Of Protein Farnesyltransferase Variants With Altered Substrate Selectivity, Susan Zhang

Renée Crown University Honors Thesis Projects - All

Post-translational modifications play an essential role in regulating protein structure and function. Enzymes catalyzing these modifications must often recognize and modify multiple substrate proteins from among a plethora of non-substrates with similar structures and amino acid sequences. For example, protein farnesyltransferase (FTase) catalyzes the addition of an isoprenoid group to a cysteine near the C-terminus of a substrate protein and is proposed to modify a pool of substrates numbering more than one hundred. We seek to understand the interactions in the FTase active site that engender substrate selectivity. By mutating two residues within FTase, we have developed FTase variants with …

Design Of Metalloproteins For Catalysis And Bioimaging, Krystyna Zhezherya

Renée Crown University Honors Thesis Projects - All

Abstract

Metalloenzymes constitute a large subclass of proteins with diverse functions including metal-sensing, signal transduction pathways, and metal transport. In this report, I aim to study the intricate relationship between structure and function as it relates to metalloproteins in the fields of catalysis and bioimaging. For catalysis, I used existing platforms in addition to de novo design to study small scaffolds with varying secondary structure, and their function in catalyzing the hydrolysis of a p-nitrophenol ester. For bioimaging, I used an existing enzyme known as human carbonic anhydrase I, hCA, to develop a bioimaging agent that can be fused to …

Interaction Of Bacillus Anthracis Exosporium Protein Bcla With Complement Factor H And Spore Persistence In The Lung, Sarah A. Jenkins

Dissertations and Theses (Open Access)

Anthrax outbreaks in the United States and Europe and its potential use as a bioweapon have made Bacillus anthracis an interest of study. Anthrax infections are caused by the entry of B. anthracis spores into the host via the respiratory system, the gastrointestinal tract, cuts or wounds in the skin, and injection. Among these four forms, inhalational anthrax has the highest lethality rate and persistence of spores in the lungs of animals following pulmonary exposure has been noted for decades. However, details or mechanisms of spore persistence were not known. In this study, we investigated spore persistence in a mouse …

A Cell Simulator Platform: The Cell Collective, Tomáš Helikar, B. Kowal, J. A. Rogers

Department of Biochemistry: Faculty Publications

Diseases are often a result of multiple malfunctions in complex, nonlinear biological/biochemical networks. As such, these processes are far more complicated to understand because they tend to give rise to functions that are emergent in nature, i.e., higher-level (mal)functions that are more than the sum of their parts. Systems biology provides a new approach to understanding biological systems and diseases from a holistic perspective.

What Can Biochemistry Students Learn About Protein Translation? Using Variation Theory To Explore The Space Of Learning Created By Some Common External Representations, Thomas J. Bussey

UNLV Theses, Dissertations, Professional Papers, and Capstones

Biochemistry education relies heavily on students' ability to visualize abstract cellular and molecular processes, mechanisms, and components. As such, biochemistry educators often turn to external representations to provide tangible, working models from which students' internal representations (mental models) can be constructed, evaluated, and revised. However, prior research has shown that, while potentially beneficial, external representations can also lead to alternative student conceptions.

Considering the breadth of biochemical phenomena, protein translation has been identified as an essential biochemical process and can subsequently be considered a fundamental concept for biochemistry students to learn. External representations of translation range from static diagrams to …

The Phosphoramidase Competency Of Prototypical Phosphatase Catalytic Motifs, Mark P. Haney

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Phosphorylation of proteins is ubiquitous. Phosphorylation can activate proteins, deactivate proteins, assist in signaling, or serve other roles depending upon the biochemical pathway. Attaching phosphate to proteins is accomplished by enzymes called kinases; removing phosphate from proteins is accomplished by enzymes called phosphatases. Cells must regulate their biochemical pathways, and the antipodal roles of kinases and phosphatases represent the yin-yang of phosphorylation.

Phosphorylation of proteins is known to occur on serine, threonine, and tyrosine. This creates a phosphoester bond. Phosphoester bonds have a phosphorus-oxygen (P-O) bond. The ability of phosphatases to cleave such phosphoester bonds is well studied. Phosphorylation of …

Spectroscopic Investigation Of The Interaction Of Fadh In Dna Photolyase With Uv-Damaged Dna, Kyle Luke Williams

Theses, Dissertations and Culminating Projects

Skin cancer is the most prevalent malignancy found in humans, with the diagnosis rate continuing to steadily increase. The primary cause of this disease is overexposure to harmful ultraviolet (UV) radiation from sunlight, which can induce damage to the nitrogenous bases in DNA via dimerization. The most prevalent UV-induced photoproducts in DNA are cyclobutane pyrimidine dimers (CPDs), most commonly between adjacent thymidines.

Organisms have implemented methods by which to repair these CPDs, the primary of which are nucleotide excision repair (NER) and photoreactivation by photolyases. Photolyases are blue-light activated flavoproteins that are more efficient at recognizing and repairing CPDs than …

Structure-Function Analysis Of Human Integrator Subunit-4, Anupama Sataluri

Dissertations and Theses (Open Access)

Structure-function analysis of human Integrator subunit 4

Anupama Sataluri

Advisor: Eric. J. Wagner, Ph.D.

Uridine-rich small nuclear RNAs (U snRNA) are RNA Polymerase-II (RNAPII) transcripts that are ubiquitously expressed and are known to be essential for gene expression. snRNAs play a key role in mRNA splicing and in histone mRNA expression. Inaccurate snRNA biosynthesis can lead to diseases related to defective splicing and histone mRNA expression. Although the 3′ end formation mechanism and processing machinery of other RNAPII transcripts such as mRNA has been well studied, the mechanism of snRNA 3′ end processing has remained a mystery until the recent …

Oxidation Of Thrombomodulin Methionine 388 In Cigarette Smokers, Samrat B. Thapa

Graduate Theses and Dissertations

This work tested the hypothesis that oxidation of methionine 388 in thrombomodulin is higher in cigarette smokers, and thus a likely contributor towards the hypercoagulable state in smokers. Thrombomodulin, a protein cofactor found on endothelial cell surfaces, regulates the activity of thrombin. Thrombin bound to thrombomodulin no longer converts fibrinogen to fibrin, but instead activates Protein C which, in turn, stops the coagulation cascade by inactivation of clotting factors. The oxidation of methionine 388 of thrombomodulin has been shown in vitro to dramatically decrease the anticoagulant cofactor activity of thrombomodulin. The blood of cigarette smokers is more prone to clot …

Expression, Production, And Purification Of Novel Therapeutic Proteins, Mckinzie Shea Fruchtl

Graduate Theses and Dissertations

Interest in the production of recombinant proteins consisting of collagen binding domain (CBD) fused to a bioactive material has increased due to the targeting/attachment capabilities of CBD. For example, CBD fusions can be applied to the reversing of bone density loss and the repair of the eardrum, specifically, by choosing an appropriate fusion partner (parathyroid hormone or epidermal growth factor). The production of CBD fusions was examined using batch and fed-batch culturing of Escherichia coli to express the fusion proteins, and affinity chromatography to isolate the final product.

Different medium formulations, feeding strategies, and induction methods were tested in order …

Characterization Of The Product Specificity And Kinetic Mechanism Of Protein Arginine Methyltransferase 1, Shanying Gui

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein enzymes perform a vast array of functions within living organisms, catalyzing various metabolic reactions including DNA replication, DNA repair, protein synthesis, etc. In order to maintain proper cellular functions, enzymes need to be accurately regulated under different circumstances. Specifically, enzymes can be modified after their creation to give them additional functions. These modifications can do a variety of things including activating (turning on) or inactivating (turning off) an enzyme, changing what proteins or molecules can interact with the enzyme, changing the enzyme’s location in the cell, and/or targeting the enzyme for destruction. This dissertation focuses on a single class …