A Study Of Histone Deacetylase Inhibitors: Determination Of The Binding Energetics Of Suberoylanilide Hydroxamic Acid With Zinc And Cobalt And Preliminary Screening Of Nitric Oxide Donors, Erin Gallagher

College of Science and Health Theses and Dissertations

Inhibiting histone deacetylases (HDACs) can suppress tumor cell growth eventually leading to their death, makeing HDACs an important drug target. Therefore, understanding the mechanism behind inhibiting HDACs is imperative. To determine the thermodynamic parameters for the interaction of a known competitive HDAC inhibitor, suberoylanilide hydroxamic acid (SAHA), with zinc(II), the metal ion in the HDAC active site, and cobalt(II), isothermal titration calorimetry (ITC) was used. The results showed that SAHA binds to zinc(II) more strongly than it does to cobalt(II) as the equilibrium binding constants were 4.3 ± 0.5 x 10² M^-1 and 2.0 ± 0.5 x 10 …

Roles Of Resveratrol And Genistein In Invasion And Metastasis Of Breast Cancer, Brittany Wolfe

College of Science and Health Theses and Dissertations

Breast cancer is a cellular disease characterized by the exploitation of several cellular and molecular mechanisms involved in cell proliferation, apoptosis, motility, and invasion. Effective treatment is available for non-invasive breast cancer at diagnosis, leading to a very high survival rate compared to the low survival rate for those where the breast cancer has spread. Thus, identifying effective therapies and preventative agents is imperative to successfully treat breast cancer. Since diet compromises a large component of the risk factors for breast cancer, it would be beneficial to examine dietary compounds that could potentially play a beneficial role in inhibiting cancer …

Urinary Copper Elevation In A Mouse Model Of Wilson’S Disease Is A Regulated Process To Specifically Decrease The Hepatic Copper Load, Lawrence W. Gray, Fangyu Peng, Shannon A. Molloy, Venkata S. Pendyala, Abigael Muchenditsi, Otto Muzik, Jaekwon Lee, Jack H. Kaplan, Svetlana Lutsenko

Department of Biochemistry: Faculty Publications

Body copper homeostasis is regulated by the liver, which removes excess copper via bile. In Wilson’s disease (WD), this function is disrupted due to inactivation of the copper transporter ATP7B resulting in hepatic copper overload. High urinary copper is a diagnostic feature of WD linked to liver malfunction; the mechanism behind urinary copper elevation is not fully understood. Using Positron Emission Tomography-Computed Tomography (PET-CT) imaging of live Atp7b^‒/^‒ mice at different stages of disease, a longitudinal metal analysis, and characterization of copper-binding molecules, we show that urinary copper elevation is a specific regulatory process mediated …

Host Pathogen Interactions: Is Arabidopsis Thaliana Remembered By Its Nemesis Pseudomonas Syringae?, Daniel Z. Kreiser

Lawrence University Honors Projects

Plants contain innate immune systems that deter pathogen infection. Pattern recognition receptors bind microbe-associated molecular patterns (MAMPs), triggering immunity. MAMPs are proteins exclusive to pathogens that are typically indispensable for their survival. For this reason, MAMPs cannot be mutated or removed without causing pathogen death. However, this does not necessitate constitutive expression of MAMPs. In this study, the MAMP response of Arabidopsis thaliana was utilized to determine differential detection of MAMPs expressed by Pseudomonas syringe pv. tomato DC3000 when pretreated with A. thaliana. Results demonstrated that more MAMPs are detected when P. syringae had previously encountered A. thaliana, …

Fret-Based Identification Of Mrnas Undergoing Translation, Benjamin Stevens, Chunlai Chen, Ian Farrell, Haibo Zhang, Jaskiran Kaur, Steven L. Broitman, Zeev Smilansky, Barry S. Cooperman, Yale E. Goldman

Biology Faculty Publications

No abstract provided.

Energy-Saving Hypothermia Reduces Flight Ability In Mourning Doves, Jennie M. Carr, Steven L. Lima

Symposium 2012

Overwintering birds are frequently exposed to thermal challenges that can quickly decrease energy reserves, thus leading to an increase in the risk of starvation. During these periods of energetic hardship, many avian species use nocturnal hypothermia to conserve energy that would otherwise be lost remaining warm throughout the night (McKechnie & Lovegrove 2002). However, a cool body temperature (Tb) may limit a bird’s ability to monitor the environment and may slow their response to a potential threat. Thus, birds likely trade-off between the benefits of energy-saving hypothermia and the potential costs of reduced behavioral responsiveness to predators (Welton et al. …

Synthesis Of S-Ribosyl-L-Homocysteine And Analogs Modified At The Homocysteine-C3 Position, Ruoyi Liu

Master's Theses

Quorum sensing (QS) is a process of bacterial cell-to-cell communication that conveys population density information in order to coordinate gene expression to produce synchronized behaviors. QS regulates the expression of virulence genes in many species of bacteria; hence, the manipulation of QS pathways may lead to treatment options against many bacterial diseases. The LuxS enzyme converts S-ribosyl-L-homocysteine (SRH) into homocysteine (HCys) and 4(S),5-dihydroxypentane-2,3-dione (DPD), which is the precursor of autoinducer-2 (AI-2). Thus, inhibitors of LuxS could prevent QS by halting the conversion of SRH to AI-2 rendering the cell “uncommunicative”. This work shows the successful chemical synthesis …

Elevating Ascorbate Content In Tomato And Studying The Role Of Jasmonates In Modulating Ascorbate In Arabidopsis, Shashank S. Kulkarni

Student Theses and Dissertations

Vitamin C (ascorbate, AsA) is the most abundant water soluble antioxidant in plants and is essential for plant and human health. Ascorbate plays a key role in protecting plants from reactive oxygen species generated during normal metabolic processes and under stress conditions including wounding, pathogen attack, salt, heat, light, and ozone exposure. Jasmonates (JAs), a group of plants hormones involved in stress responses also protect plants from these stresses. There is evidence indicating that JAs modulate AsA content in plants. The recent discovery of the inositol pathway has opened possibilities for AsA enhancement via metabolic engineering in plants. Over-expression of …

Shoc2 Is Targeted To Late Endosomes And Required For Erk1/2 Activation In Egf-Stimulated Cells, Emilia Galperin, Lina Abdelmoti, Alexander Sorkin

Molecular and Cellular Biochemistry Faculty Publications

Shoc2 is the putative scaffold protein that interacts with RAS and RAF, and positively regulates signaling to extracellular signal-regulated protein kinases 1 and 2 (ERK1/2). To elucidate the mechanism by which Shoc2 regulates ERK1/2 activation by the epidermal growth factor (EGF) receptor (EGFR), we studied subcellular localization of Shoc2. Upon EGFR activation, endogenous Shoc2 and red fluorescent protein tagged Shoc2 were translocated from the cytosol to a subset of late endosomes containing Rab7. The endosomal recruitment of Shoc2 was blocked by overexpression of a GDP-bound H-RAS (N17S) mutant and RNAi knockdown of clathrin, suggesting the requirement of RAS activity and …

Synthesis Of Fluorogenic Substrates For The Enzymatic Characterization Of Rv0045c From M. Tuberculosis, Kelly Jo Mckenna

Undergraduate Honors Thesis Collection

Mycobacterium tuberculosis is the pathogenic bacterial agent commonly responsible for tuberculosis, or TB. Although treatment exists for the active form of tuberculosis, no method has been developed for eliminating M tuberculosis in its dormant state. One hypothesized method for the elimination of dormant TB is to develop an inhibitor specific for M tuberculosis esterases and lipases, as these esterases and lipases are essential to the survival of dormant TB infection. In this research, the substrate specificity of the Rv0045c esterase from M tuberculosis was studied due to the essential role of Rv0045c in TB metabolism and its dissimilarity to other …

Exploring The Interaction Between Human Granulin-A (Hgrn-A) And Amyloid-Β (Aβ) Peptide, Michael Samel

Honors Theses

Alzheimer’s disease (AD) is the most common form of dementia affecting people over the age of 60, yet a detailed understanding of the molecular changes involved in AD remains a significant challenge to modern medicine. The hallmarks of an AD brain include the presence of senile plaques formed by a protein called amyloid-β (Aβ), along with inflammation of the brain. Aβ self-associates to form clumps of protein called “aggregates” which are known to be the primary toxic agents in AD pathology; however, several other proteins have also been implicated in this pathology. One such protein called progranulin (PGRN), which under …

Refining Vibrationally-Resonant Sum Frequency Generation Spectroscopy For Studies Of Interfacial Interactions, Alexander D. Curtis

Theses and Dissertations

Many phenomena of interest to science and engineering occur at interfaces; however, access to, or discrimination of, interfacial interactions has been challenging, especially at buried interfaces. Vibrationally resonant sum-frequency generation (VR-SFG) spectroscopy is a powerful tool for investigating the molecular structure of free or buried interfaces, but spectral analysis has relied on many assumptions. To claim accurate new insights, practitioners must be able to make unique determinations from the data without experimental artifacts affecting the final results. For example, two independent and overlapping studies for the polystyrene/air interface were carried out, but reported different surface structures. Initially, this difference was …

Conservation Of Oxidative Protein Stabilization In An Insect Homologue Of The Parkinsonism-Associated Protein Dj-1, Jiusheng Lin, Janani Prahlad, Mark A. Wilson

Department of Biochemistry: Faculty Publications

DJ-1 is a conserved, disease-associated protein that protects against oxidative stress and mitochondrial damage in multiple organisms. Human DJ-1 contains a functionally essential cysteine residue (Cys106) whose oxidation is important for regulating protein function by an unknown mechanism. This residue is well conserved in other DJ-1 homologues, including two (DJ-1α and DJ-1β) in Drosophila melanogaster. Because D. melanogaster is a powerful model system for studying DJ-1 function, we have determined the crystal structure and impact of cysteine oxidation on Drosophila DJ-1β. The structure of D. melanogaster DJ-1β is similar to that of human DJ-1, although two important residues in …

Szilard Engine Reversibility As Quantum Gate Function, F. Matthew Mihelic

Faculty Publications

A quantum gate is a logically and thermodynamically reversible situation that effects a unitary transformation of qubits of superimposed information, and essentially constitutes a situation for a reversible quantum decision. A quantum decision is a symmetry break, and the effect of the function of a Szilard engine is a symmetry break. A quantum gate is a situation in which a reversible quantum decision can be made, and so if a logically and thermodynamically reversible Szilard engine can be theoretically constructed then it would function as a quantum gate. While the traditionally theorized Szilard engine is not thermodynamically reversible, if one …

Proteome-Wide Analysis Of Single-Nucleotide Variations In The N-Glycosylation Sequon Of Human Genes, Raja Mazumder, Krishna Sudeep Morampudi, Mona Motwani, Sona Vasudevan, Radoslav Goldman

Biochemistry and Molecular Medicine Faculty Publications

N-linked glycosylation is one of the most frequent post-translational modifications of proteins with a profound impact on their biological function. Besides other functions, N-linked glycosylation assists in protein folding, determines protein orientation at the cell surface, or protects proteins from proteases. The N-linked glycans attach to asparagines in the sequence context Asn-X-Ser/Thr, where X is any amino acid except proline. Any variation (e.g. non-synonymous single nucleotide polymorphism or mutation) that abolishes the N-glycosylation sequence motif will lead to the loss of a glycosylation site. On the other hand, variations causing a substitution that creates a new N-glycosylation sequence motif can …

Elucidating The Mechanism Of Antimigratory Activity Of Cardiac Glycosides, Joshua H. Johnson

Honors Scholar Theses

The focus of this research is on cell migration and how it can be better understood through the use of small molecules that modulate cell migratory activity. The results have particular relevance in the realm of cancer pharmacology. Cardiac glycosides, which are known inhibitors of the eukaryotic Na⁺/K⁺-ATPase, have been determined to have antimigratory activities through the screening of several small molecule libraries. Here we investigate the antimigratory activities of the cardiac glycoside digitoxin as well as its analogs that we synthesized. Antimigratory activity was determined by conducting a wound closure assay with MDA-MB-231 human breast …

Improvements To The Forensic Analysis Of Mitochondrial Dna Typing, Elizabeth Montano

Honors Scholar Theses

Sequence analysis of human mitochondrial DNA (mtDNA) is an effective and reliable tool for the genetic characterization of forensic samples. The nature of the mitochondrial genome (mtgenome), its high copy number and small size (~17kb) makes it more resistant to degradation and more stable than nuclear DNA. For this reason mitochondrial DNA is often the only feasible option for the forensic analysis of environmentally compromised samples. Currently the forensic analysis of the mtgenome is restricted to the hypervariable regions, also known as the Displacement loop (d-loop). Previous studies, confirmed in the Strausbaugh lab, have demonstrated an increased variability in the …

Metallothionein Gene Dose And The Immune Response, Meaghan Roy-O-Reilly

Honors Scholar Theses

Metallothionein (MT) is a small, cysteine-rich protein with significant immunomodulatory activity. It has been shown to play a critical role in important cellular mechanisms including heavy metal detoxification, essential metal management and the inflammatory response. MT production can be induced by a number of cellular stressors and acts to lessen the harmful effects of oxidizing agents and heavy metal exposure. Previous studies have shown that the dose of the metallothionein gene present in an individual may have significant effects on the adaptive immune response, yet the mechanism behind this phenomenon remains unknown. We hypothesize that the gene dose of metallothionein …

Identifying Progenitor Cells Of Heterotopic Ossification, Eileen E. Semancik

Honors Scholar Theses

Heterotopic Ossification (HO) is the abnormal formation of bone within extraskeletal soft tissues. The condition can occur through both genetic and acquired means. Acquired cases of HO result from invasive surgery or traumatic injuries, with increasing prevalence of ectopic skeletogenesis as a result of combat-related blast injuries. HO has been characterized to some extent, including the histological features and the mutation underlying the genetic form, but the cells resident in skeletal muscle that represent the progenitors of heterotopic bone have yet to be determined. Only a few publications have attempted to definitively determine the progenitor cells in this disorder. Findings …

Fundamentals Of Protein Structure Alignment, Allen Holder, Mark Brandt, Yosi Shibberu

Mathematical Sciences Technical Reports (MSTR)

The central dogma of molecular biology asserts a one way transfer of information from a cell’s genetic code to the expression of proteins. Proteins are the functional workhorses of a cell, and studying these molecules is at the foundation of much of computational biology. Our goal here is to present a succinct introduction to the biological, mathematical, and computational aspects of making pairwise comparisons between protein structures. The presentation is intended to be useful for those who are entering this research area. The chapter begins with a brief introduction to the biology of protein comparison, which is followed by a …

Cholesterol Lowering Effects Of Milk With Added Phytosterols, Laura Kells Cusack

Master's Theses

Foods incorporating plant sterols (PS) reduce Low-density lipoprotein (LDL) on average approximately 10%. PS with a higher lipid solubility may promote greater reductions. We examined the cholesterol lowering effect of a novel triglyceride recrystallized phystosterol (TRP). Twenty subjects (mean ± SD; age, 56 ± 10 years; BMI, 27 ± 5) with elevated LDL (>100 mg/dL) participated in three 4-week phases; Phase I, 2% milk; Phase II, milk with 2.0 grams (g) free PS; Phase III, milk with 2.0 g TRP. Before and after each phase two fasting blood draws were obtained for determination of serum cholesterol. Between the 2% …

Locking Down The N-Terminus Of Prmt1 In Order To Assess The Role Of Motion In Activity, Taylor James Rasmussen

Undergraduate Honors Capstone Projects

Protein arginine methyltransferases (PRMTs) are involved In many major biological pathways in the human body. Processes that demonstrate arginine methylation by PRMTs include, but are not limited to, histone modification, DNA transcription, and post-translational protein modifications. Although recent research has allowed the identification of several PRMT isoforms and exposed their involvement in these processes, relatively little is known about the details of how these enzymes perform their biochemical duties. It is currently hypothesized that the N-terminus of PRMT variant I is involved in recognizing substrates and aiding in catalysis by virtue of a change in its conformation. To understand how …

Mutation And Complementation Of A Cellulose Synthase (Cesa) Gene, Ahmed Y. El-Araby

Senior Honors Projects

Cellulose is a carbohydrate polymer that is composed of repeating glucose subunits. Being the most abundant organic compound in the biosphere and comprising a large percentage of all plant biomass, cellulose is extremely plentiful and has a significant role in nature. Cellulose is present in plant cell walls, in commercial products such as those made from wood or cotton, and is of interest to the biofuel industry as a potential alternative fuel source. Although indigestible by humans, cellulose is nutritionally valuable, serving as a dietary fiber. Because of its ubiquity and importance in many areas, studying cellulose will prove to …

Transport And Spectroscopic Studies Of The Effects Of Fullerene Structure On The Efficiency And Lifetime Of Polythiophene-Based Solar Cells, Emilee L. Sena, Justin H. Peel, Devin Wesenberg, Shreya Nathan, Marianne Wallis, Maxwell J. Giammona, Thorsteinn Adalsteinsson, Brian J. Mcnelis, Richard P. Barber Jr.

Physics

Time-dependent measurements of both power conversion efficiency and ultraviolet-visible absorption spectroscopy have been observed for solar cell blends containing the polymer poly(3-hexylthiophene-2,5-diyl) (P3HT) with two different functionalized C60 electron acceptor molecules: commercially available [6,6]-phenyl C61 butyric acid methyl ester (PCBM) or [6,6]-phenyl C61 butyric acid octadecyl ester (PCBOD) produced in this laboratory. Efficiency was found to decay with an exponential time dependence, while spectroscopic features show saturating exponential behavior. Time constants extracted from both types of measurements showed reasonable agreement for samples produced from the same blend. In comparison to the PCBM samples, the stability of the PCBOD blends was …

The Time-Course Of The Effects Of Growth Hormone During Zebrafish (Danio Rerio) Auditory Hair Cell Regeneration, Yajie Wang

Masters Theses & Specialist Projects

Growth hormone (GH) was upregulated in the zebrafish inner ear following sound exposure in a previous study. To identify the specific role of GH in hair cell regeneration and the possible cellular mechanisms of this regeneration, groups of zebrafish were divided into baseline (no sound exposure, no injection), buffer-injected and GH-injected groups. Buffer- and GH-injected fish were exposed to a 150 Hz tone at a source level of 179 dB re 1 μPa root mean squared (RMS) for 36 h. Phalloidin-staining was used to assess the effects of GH on hair cell bundle density; BrdU-labeling was used to assess the …

Determination Of Selectivity And Potential For Drug Resistance Of Novel Antimalarial Compounds From Nature-Inspired Synthetic Libraries, Eric Keasler

HIM 1990-2015

As malaria, caused by Plasmodium spp., continues to afflict millions of people worldwide, there is a dire need for the discovery of novel, inexpensive antimalarial drugs. Although there are effective drugs on the market, the consistent development of drug resistant species has decreased their efficacy, further emphasizing that novel therapeutic measures are urgently needed. Natural products provide the most diverse reservoir for the discovery of unique chemical scaffolds with the potential to effectively combat malarial infections, but, due to their complex structures, they often pose extreme challenges to medicinal chemists during pharmacokinetic optimization. In our laboratory we have performed unbiased, …

Time-Dependent Density-Functional-Theory Calculation Of High-Order-Harmonic Generation Of H-2, Xi Chu, Gerrit C. Groenenboom

Chemistry and Biochemistry Faculty Publications

The observation of the isotope effect in the high-order-harmonic generation (HHG) of H-2 presents a challenge for time-dependent density-functional-theory (TDDFT) methods, since this effect is related to the dynamics of the ion created in the tunneling ionization step of HHG and it depends on the harmonic order. As an initial step toward describing this effect within current computational capacity, we benchmark a method in which the nuclear and electronic degrees of freedom are separated and both treated quantum mechanically. For the electrons two TDDFT formalisms are adopted. Although the ion-dynamics effect is not described in our method, it reproduces the …

Recombinant Expression And Purification Of Human Intrinsic Factor (If) And Mutants K159d And Q201a Designed To Interfere With Cubilin Receptor Binding, Soreen Cyphers

Renée Crown University Honors Thesis Projects - All

Although both the α- and β-domains of intrinsic factor (IF) have been previously expressed, the full crystal structure of the protein has yet to be reported. The purpose of this research is to (1) express IF in order to obtain a complete crystal structure and (2) utilize a mutant form of IF in order to orally deliver rotavirus to the ileum.The first goal of this research is to express IF in the yeast Pichia pastoris. The second goal is to express a K159D IF mutant protein. K159 of IF plays a role in salt bridge formation between IF and …

Interaction Of Environmental B. Cenocepacia Strains With Cystic Fibrosis And Non-Cystic Fibrosis Bronchial Epithelial Cells In Vitro., Annamaria Bevivino, Luisa Pirone, Ruth Pilkington, Noemi Cifani, Claudia Dalmastri, Máire Callaghan, Fiorentina Ascenzioni, Siobhan Mcclean

Articles

Burkholderia cenocepacia is an important human pathogen in patients with cystic fibrosis (CF). Non-clinical reservoirs may play a role in the acquisition of infections, so it is important to evaluate the pathogenic potential of environmental B. cenocepacia isolates. In this study, we investigated the interactions of two environmental B. cenocepacia strains (Mex1 and MCII-168) with two bronchial epithelial cell lines,16HBE14o- and CFBE41o-, which have a non-CF and a CF phenotype, respectively.

The environmental strains showed a significantly lower level of invasion into both CF- and non-CF cells in comparison with the clinical B. cenocepacia LMG16656^T strain. Exposure of polarized …

Designing An "Information-Experience" Using Creativity Science Theory And Tools, Stephanie Belhomme

Creativity and Change Leadership Graduate Student Master's Projects

An “information-experience” encapsulated by a technological/digital audio-visual tool presents data and potentially meaningful information to prompt actionable knowledge concerning: “unspoken creative process elements;” their profound impacts on both how well our “physiology of creativity” functions; but also on how well foundational creative thinking and behavioral prerequisites (energy, motivation, imagination, and ownership) are leveraged.

The product: 1) introduces the user to one component of the CPS (Creative Problem Solving) Facilitation Process - Exploring the Challenge; 2) features a content specific component which prompts exploration of the many correlations between societal, organizational / community, human physiological / behavioral data, and the direct …