Biochemistry Commons^™

Characterization Of Ghrelin O-Acyltransferase Active Site, Leslie Patton

Renée Crown University Honors Thesis Projects - All

Ghrelin, first discovered in 1999, is a 28-amino acid peptide hormone involved in the regulation of appetite, insulin secretion and sensitivity, and many neurological effects such as learning, memory, and depression.^1-6 Ghrelin has been identified to have a unique posttranslational octanoylation carried out by the enzyme ghrelin O-acyltransferase (GOAT). This distinctive modification is a point of interest in studying GOAT whereby blocking the acylation of the ghrelin could potentially halt the activity of the peptide hormone and provide a means of treating obesity, diabetes, and other diseases affected by ghrelin levels. The duration of my project involved working …

The Development Of Skeletal Muscle In Young Horses: An Ultrasonography And Satellite Cell Approach, Emma K. Lavigne

Honors Scholar Theses

Muscle growth in young horses is characterized by an increase in muscle cross-sectional area, which can be accomplished through the activation and differentiation of satellite cells. Satellite cells can be stimulated or inhibited in response to different cytokines and growth factors and are key mediators of muscle hypertrophy and regeneration. The aim of this study was to investigate the growth of the longissimus dorsi (LD) muscle in horses under 5 years of age and to obtain preliminary data on satellite cell behavior in foals. The area, width, height, and subcutaneous fat were measured using ultrasonography at 6-month increments over the …

Assessment Of Variation In Susceptibility Of The Fall Armyworm, Spodoptera Frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), To Bacillus Thuringiensis Toxins, Karen Ferreira Da Silva

Department of Entomology: Dissertations, Theses, and Student Research

The fall armyworm, Spodoptera frugiperda, is a polyphagous insect pest affecting multiple crops. Fall armyworm is managed with insecticides and corn hybrids expressing insecticidal proteins derived from Bacillus thuringiensis. The early detection of insect resistance is important for making appropriate management decisions informs IPM and IRM recommendations.

The objective of the first study was to establish baseline susceptibility of fall armyworm populations to the Cry1F Bt insecticidal protein, emphasizing collections from locations where fall armyworm overwinters in the U.S. Fall armyworm neonates were exposed to artificial diet treated with increasing Cry1F concentrations, and mortality and growth inhibition were …

Investigations Into The Molecular Mechanisms Of Bacterial Pathogen–Host Interactions: Construction Of A Dual Plasmid System For Incorporation Of Unnatural Amino Acids Into Pseudomonas Syringae Pv. Tomato Dc3000, Scotty D. Raber

Department of Chemistry: Dissertations, Theses, and Student Research

A dual plasmid system for the incorporation of unnatural amino acids into plant pathogen, Pseudomonas syringae pv. tomato DC3000, has been designed. This invention is expected to allow (a) mutations of proteins synthesized by the bacterium, P. syringae pv. tomato DC3000, that can capture molecular targets, especially for such modified proteins secreted by the phytopathogen into the host plant cells of A. thaliana and S. lycopersicum, (b) expression of biological probes in the bacterial species to monitor changes in redox, nutritional, and other small molecule states over pre-, post- and in situ disease stages, and secretion of such biological …

Venom Peptide Induced Inhibition Of Escherichia Coli Atp Synthase, Sofiya Azim

Undergraduate Honors Theses

ATP is the main cellular energy generated by the enzyme ATP synthase in almost all organisms from bacteria to vertebrates. While malfunction of the ATP synthase complex is responsible for several disease conditions, the enzyme itself can be used as a potent molecular drug target to combat many diseases including microbial infections, cancer, tuberculosis, and obesity. Recent widespread escalation of antibiotic resistant microbes in general and E. coli in particular demands novel alternative approaches to combat microbial infections. Inhibition of ATP synthase by inhibitors such as peptides is known to deprive microbes of required energy, resulting in microbial cell death. …

Granulins As Inflammatory Mediators In Alzheimer Disease, Randi G. Reed

Honors Theses

Alzheimer disease (AD) is a neurodegenerative disorder characterized by severe memory deficit and cognitive decline among the elderly. This degeneration is caused by the aggregation and deposition of a protein called amyloid-β (Aβ) in the brain. Aggregation of Aβ causes neuroinflammation in addition to other toxic events. However, it is unclear whether inflammation from an external source, such as from a traumatic brain injury (TBI), could trigger Aβ aggregation. In this context, several pro-inflammatory mediators such as cytokines and chemokines have been suspects. It is now hypothesized that a group of proteins called granulins (Grns) are unique inflammatory mediators that …

Efforts In Increasing Microdialysis Recovery Rates By Utilizing Bidirectional Flow Capabilites, Jacob Taylor Needham

Chemistry & Biochemistry Undergraduate Honors Theses

Microdialysis sampling involves the collection of biological fluids from tissues or fluid-filled cavities in vivo via diffusion through a semipermeable membrane probe. In order to increase the recovery of fluids for analysis from this process, a new regime was attempted that would allow perfusion fluids to make multiple passes through the probe in order to collect more analyte with each additional pass. This was dubbed the Bidirectional Flow Technique. Dextran-70 solution was used as the perfusion fluid while 100μM Methyl Orange solution was used as the analyte. The experiments were performed in vitro using a fully automated microdialysis ePump capable …

Devlopment Toward Fluorescence Imaging Of Microdialysis Sampling Diffusion Profiles, Nicholas Edward Baioni

Chemistry & Biochemistry Undergraduate Honors Theses

Microdialysis is a diffusion-based method used to collect analytes from specific locations in the body. Matrix Metalloproteinases (MMPs) are important enzymes located throughout the body that play a role in the breakdown of extracellular matrix. Microdialysis sampling in conjunction with appropriate analysis methods can be used to observe the reactions of MMPs in real time. This project is aimed at determining the activity of porcine pancreatic enzyme, a known substitute for MMP-12, using nanodrop spectroscopy. This is a necessary pre-requisite toward using microdialysis in an in vivo imaging setup. These experiments were performed using Succinyl(Ala)_3-p-nitroanilide (suc(Ala)3-p-NA), 4-nitroaniline, and porcine pancreatic …

Developing Graphene-Based Supercapacitors For High Temperature Applications, Lea Rachel Rogers

Chemistry & Biochemistry Undergraduate Honors Theses

Supercapacitors are ideal tools for energy storage due to their wide range of operation temperatures, long cycle-lives, high power densities of up to 13,000 W/kg, and fast rates of charge-discharge thereby having a high specific capacitance. This research reports synthesis of grapheme-based materials using a modified Hummer’s method. Graphene oxide synthesized first and then converted to reduced graphene oxide sheets and graphene-powder, which both increase the ionic conductivity due to sp2 bonding and a high surface area. These materials were then constructed into a button-cell supercapacitor for testing. For the first supercapacitors, a porous polypropylene membrane (Celgard) that acted as …

Percent Recovery Of Various Analytes Using A Wick Method, Patrick A. Naeger

Chemistry & Biochemistry Undergraduate Honors Theses

Finding alternate methods to measure and isolate interstitial fluid in vivo has become a consequence of the limited recovery of analytes when using a probe.1 These probes consist of an inlet constantly bringing perfusate into a semi-permeable membrane where the perfusate is replace with dialysate containing numerous analytes. The dialysate leaves the semi-permeable membrane via an outlet. A wick technique has been shown to be useful in analytical chemistry because it can be used to effectively isolate interstitial fluid and accurately measure the concentrations of various analytes. For long-term applications, wicks can be used to measure the concentrations of cytokines …

Molecular Mechanisms Of Tandem Cbd Of Clostridium Histolyticum, Dawn Weir

Chemistry & Biochemistry Undergraduate Honors Theses

In order to spread infections, bacterial collagenases methodically unravel collagen fibril in tissues. Collagen is the most abundant protein in the body, and can be found in the skin, bone and cartilage [1]. Two collagenases, ColG and ColH, synergistically dismantle collagen fibrils by seeking different weak links in the collagen structure. The collagen-binding domain (CBD) of these collagenases binds to most vulnerable regions in collagen [8]. Without CBDs, collagen fibril cannot be degraded. Cells express collagen receptors in order to anchor themselves, which is a critical step in cell proliferation. Binding sites for some collagen receptors, such as integrin and …

Dna Polymerase Θ (Polq) And The Cellular Defense Against Dna Damage, Matthew J. Yousefzadeh

Dissertations and Theses (Open Access)

In mammalian cells, DNA polymerase θ (POLQ) is an unusual specialized DNA polymerase whose in vivo function is under active investigation. The protein is comprised of an N-terminal helicase-like domain, a C-terminal DNA polymerase domain, and a large central domain that spans between the two. This arrangement is also found in the Drosophila Mus308 protein, which helps confer resistance to DNA interstrand crosslinking agents. Homologs of POLQ and Mus308 are found in eukaryotes, including plants, but a comparison of phenotypes suggests that not all of these genes are functional orthologs. Flies with defective Mus308 are sensitive to DNA interstrand crosslinking …

Selection Methods For Genetically-Modified T Cells: In Support Of Translational Therapy, David Rushworth

Dissertations and Theses (Open Access)

T cells are blood cells which organize the immune system of the host. These cells are necessary for the host to respond appropriately to threats from foreign organisms and cancerous growth. However, in the case of certain infections and cancer, T cells are unable to respond appropriately to a threat and establish immunity. This leads to disease when the infection or cancer is not sufficiently eliminated. On the other hand, T cells can lack tolerance for healthy tissue and perceive healthy tissue as infected. The ensuing over-reactive immune response also leads to disease. A delicate balance must exist between immunity …

Regulation Of Cell Adhesion By The Ferm Proteins, Ptpn14 And Merlin, Patty Dimarco Hewitt

Dissertations and Theses (Open Access)

Cell-cell adhesion is critical for the control of tissue organization and homeostasis. A family of proteins that regulate cell-cell adhesions is the FERM (4.1 protein, Ezrin, Radixin, Moesin) domain-containing proteins.One FERM domain protein, the non-receptor tyrosine phosphatase PTPN14, is mutated or deleted in several human cancers suggesting that it may be involved in tumor development and/or progression. Additionally, the loss of the FERM domain protein Merlin is associated with tumor development and metastasis.Both PTPN14 and Merlin have been shown to localize and possibly regulate adherens junction (AJ) functions. This work sought to determine if …

Development, Validation, And Application Of Analytical Methods For Characterizing Adsorbed Protein Orientation, Conformation, And Bioactivity, Aby Thyparambil

All Dissertations

The structure and bioactivity of adsorbed proteins are tightly interrelated and play a key role in their interaction with the surrounding environment. These factors are of critical importance in many biotechnological applications. However, because the bioactive state of an adsorbed protein is a function of the orientation, conformation, and accessibility of its bioactive site(s), the isolated determination of just one or two of these factors will typically not be sufficient to understand the structure-function relationships of the adsorbed layer. Rather a combination of methods is needed to address each of these factors in a synergistic manner to provide a complementary …

Inducing And Characterizing M2c Macrophages At A Non-Degradable Implant In Vivo, Geoffrey David Keeler

Graduate Theses and Dissertations

The implantation of biomaterials in the body leads to a reaction known as the foreign body response (FBR) which leads to the eventual encapsulation of the biomaterial. This encapsulation proves to be detrimental to certain biomaterials, such as implanted glucose sensors, which rely on interacting with the extracellular space for proper function. Altering the FBR has become of interest in an effort to increase the longevity and integration of biomaterials. One strategy for altering the FBR is by targeting the macrophage, shown to play an important role in the FBR. In this work, the microdialysis sampling technique was used to …

Chymotrypsin Digestion Analysis To Characterize Site-Specific Incorporation Of An Extrinsic Fluorescent Probe On A Ras-Related Protein., Akash D. Patel

Chemistry & Biochemistry Undergraduate Honors Theses

Ras Homolog Enriched in Brain (RHEB) is a member of Ras GTPase family and plays an important role in regulation of cell growth and cell cycle proliferation. RHEB is regulated by cycling between active (GTP-bound) and inactive (GDP-bound) state. Guanidine Nucleotide Exchange Factors (GEFs) and GTPase-activationg proteins (GAPs) are the key regulators of RHEB, and it is of interest to closely study their interactions with RHEB. Towards that end, this project was designed to label RHEB with an environmentally sensitive extrinsic fluorophore, succinimidyl 6-(N-(7-nitrobenz-2-oxa-1.3-diazol-4-yl)amino)hexanoate (sNBD), to be used to monitor RHEB-protein interactions. Due to its extreme sensitivity to the surrounding …

Design Of Antimicrobial Peptide Based On The Heparin Binding Segment Of Fgf-1, Alice Margaret Power

Chemistry & Biochemistry Undergraduate Honors Theses

Fibroblast Growth Factors (FGFs) are heparin-binding proteins known for their involvement in various biological processes such as cell differentiation and wound healing.1 The heparin binding site of FGF-1 displays a unique stretch of positive amino acid sequence and facilitates a very strong binding to negatively charged heparin due to the formation of electrostatic interaction. The aim of this study is to analyze and modify the novel antimicrobial peptide sequence (GST-HB) designed based on the heparin-binding region of FGF-1 as well as other polycationic microbial sequences. These aspects will be examined using various experimental techniques including overexpression of GST-HB, purification using …

Additional Sex Combs-Like 2 (Asxl2): A Psychological Stress-Related Gene In A Chicken Stress Model, Emily Sandra Jacobson

Chemistry & Biochemistry Undergraduate Honors Theses

Chronic stress is a problem not only in terms of its psychological effects but also due to the harmful physiological changes induced in the individual. Although chronic stress is recognized as detrimental and rampant throughout society, the stress system itself remains poorly understood in terms of comprehending which genes are involved in regulating and carrying out stress-induced signals. In a previous study, 57 candidate genes in the stress pathway had been identified based on the presence of stress-associated single nucleotide polymorphisms (SNPs) and differential expression from microarray data. The objective of this study was to investigate Additional Sex Combs-Like 2 …

Dna Methylation In Lung Tissues Of Mouse Offspring Exposed In Utero To Polycyclic Aromatic Hydrocarbons, Trevor J. Fish

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Polycyclic aromatic hydrocarbons (PAHs) comprise an important class of environmental pollutants that are known to cause lung cancer in animals and suspected lung carcinogens in humans. PAHs are also known to cause cancer in offspring when provided to a pregnant mouse. Some evidence from cell-based studies points to PAHs as modulators of the epigenome, that is modifications to DNA structure that control the expression of genes. Inappropriate changes to the epigenome and consequently expression of cancer-critical genes are often characteristic of cancer cells. The objective of this thesis research was to determine the impact of transplacental exposure to two model …