Biochemistry, Biophysics, and Structural Biology Commons^™

Fundamental Causes Of Racial And Ethnic Covid-19-Related Health Disparities, Hana Neutz

Student Scholar Symposium Abstracts and Posters

Underserved low-income communities of color in the U.S. have endured an unequal burden of COVID-19 morbidity and mortality. This pattern of pandemic-related health disparities has been pervasive throughout history. However, no known studies have simultaneously examined social and biological factors that contribute to these concerning health disparities. Therefore, this paper aims to bridge the gap by employing a scoping literature review of (1) the deleterious impacts of systemic racism on COVID-19-related outcomes; and (2) the cellular and molecular mechanisms connecting COVID-19 and hypertension (a comorbidity known to exacerbate COVID-19 severity). My findings indicate that systemic racism manifests in inequitable access …

Characterizing The Dormancy And Repair Of A Circumneutral Passive Remediation System Receiving Iron And Sulfate-Rich Amd, Garrett Struble

Electronic Theses and Dissertations

The Wingfield Pines remediation system is a ~20-acre circumneutral, gravity-fed system constructed in 2009 to passively remediate Fe from an ~2000 gallon/minute effluent. In 2017, a fracture to the system’s underground cavern caused the AMD effluent to bypass the system, flowing directly into Chartiers Creek and leaving the system decommissioned between 2017-2019. Soil slurry and water samples were collected in the weeks prior to the system’s reinstalment in September 2019 through January 2020 in order to determine the effect of the repair on remediation efficiency and microbial community composition. This study acted as the first to describe the temporary decommissioning …

Proton Pump Inhibitors Promote Apoptosis In Jurkat T Lymphocytes, Asher Utz

Departmental Honors & Graduate Capstone Projects

Cancer cells are known to rely on the anaerobic energy pathway of glycolysis even under normoxic conditions, resulting in measurable intracellular acidification that may trigger cell death by apoptosis. In normal cells, the pH is restored by activation of voltage-gated proton pumps, preventing apoptosis. Proton pump inhibitors (PPIs), such as omeprazole, inhibit the action of these voltage-gated proton pumps. Research has shown that omeprazole is also capable of inducing caspase-dependent apoptosis in Jurkat T-lymphocytes, but this area of study remains largely unexplored. The goal of this research was to determine the temporal dynamics of caspase activity in Jurkat cells treated …

Safety Of Silver Oxide Coated Biomaterials In Mice, Michael Klug, Darien L. Seidman, Rahyan Mahmoud, Destiny Morot, Lei Yu, Jeffrey D Hettinger, Renee M Demarest

Rowan-Virtua Research Day

It has been demonstrated that silver oxide coatings designed by our collaborators are able to prevent E. coli and P. aeruginosa attachment to biomaterials in vivo. These findings demonstrate that such coatings show promise in preventing the development of biofilm on biodevices. However, it is unknown if the use of silver oxide in this fashion is toxic in vivo. The goal of this project was to determine whether our silver oxide coatings are safe to use in vivo. To assess the toxicity of our silver oxide formula, mice were implanted with either silver oxide coated titanium discs or uncoated titanium …

Replication Protein A (Rpa) Targeting Of Uracil Dna Glycosylase (Ung2), Derek Chen, Brian P Weiser

Rowan-Virtua Research Day

Replication Protein A (RPA) is a single stranded DNA binding protein which stabilizes ssDNA for replication and repair. One function of RPA is to bind the DNA repair enzyme uracil DNA glycosylase (UNG2) and direct its activity towards ssDNA dsDNA junctions.

UNG2 removes uracil bases from DNA which can appear through dUMP misincorporation or through cytosine deamination. If uracil is present instead of a cytosine, then the original GC pair becomes a GU pair. The uracil will then base pair to adenine in the replicated daughter strand. This results in a GC → AT mutation that could contribute to cancer …

Substrate-Dependent Modulation Of Sirt2 By A Fluorescent Probe, 1-Aminoanthracene, David Bi, Prashit Parikh, Jie Yang, Brian P Weiser

Rowan-Virtua Research Day

Sirtuin isoform 2 (SIRT2) is an enzyme that catalyzes the removal of acyl groups from lysine residues. SIRT2’s catalytic domain has a hydrophobic tunnel where its substrate acyl groups bind. Here, we report that the fluorescent probe 1-aminoanthracene (AMA) binds within SIRT2’s hydrophobic tunnel in a substrate-dependent manner. AMA’s interaction with SIRT2 was characterized by its enhanced fluorescence upon protein binding (>10-fold). AMA interacted weakly with SIRT2 alone in solution (Kd = 37 μM). However, when SIRT2 was equilibrated with a decanoylated peptide substrate, AMA’s affinity for SIRT2 was enhanced ∼10-fold (Kd = 4μM). The peptide’s decanoyl chain and …

Uncovering Potential Biofilm Modulators, Liliana Margent

Theses and Dissertations

Biofilms have negative and positive impacts depending on the context they develop. In this work, I optimized a biofilm assay to evaluate the effect of three different types of compounds indole derivatives, 2,5 Diketopiperazines, and 12-hydroxystearic acid on the biofilm formation of E. coli.

Evolutionary Conservation Of The Heterochronic Pathway In C. Elegans And C. Briggsae, Maria Ivanova, Eric G. Moss

Rowan-Virtua Research Day

Heterochronic genes control the sequence and timing of developmental events during four larval stages of Caenorhabitis nematodes. Mutations in these genes may cause skipping or reiteration of developmental events.

C. briggsae is a close relative of C. elegans. These species have similar morphology and share the same ecological niche. C. briggsae undergoes the same developmental pathway consisting of four larval stages before reaching adulthood. It also has the same set of heterochronic genes.

Lin-28 is one of the heterochronic genes that also exists in other animals from flies to humans. It conservatively blocks the maturation of let-7 miRNA, the process …

Identification Of The E3 Ligase That Directs The Degradation Of Proteins That Control Cell Fate Decisions In Yeast, Prasanna Tati, Stephen D Willis, Katrina F. Cooper

Rowan-Virtua Research Day

The ubiquitin–proteasome system (UPS) and autophagy pathways are distinct, highly conserved proteolytic systems that play important roles in maintaining cellular homeostasis in response to environmental cues [1]. The goal of this project is to identify the E3 ligase that mediates the degradation of cyclin C following nitrogen starvation in yeast using quantitative Western blot analysis of cyclin C-myc following nitrogen starvation in mutants of known Ubc4/5 interacting E3 ligases. No potential E3 ligases were identified as stable after 4 hours of nitrogen starvation, suggesting redundancy in function.

Abhd5 Induced Morphological Changes On Model Membrane Systems, Nasser S. Junedi

Honors College Theses

Proper regulation of neutral lipid storage (lipogenesis) and release (lipolysis) are critical molecular processes localized to an organelle called the Lipid Droplet (LD). The LD consists of a core with neutral lipids such as triacylglycerols (TAGs) and sterol esters surrounded by a phospholipid monolayer. Dysregulation of the processes localized to the LD are involved in the pathology of various diseases such as Neutral Lipid Storage Disease, diabetes, stroke and cancer. The non-enzymatic protein ABHD5 (α-β Hydrolase Domain-Containing Protein 5), is thought to play a key role in the process of lipolysis by forming homo-oligomers on the surface of the LD …

Mitochondrial Distribution Of Glycine Receptors In Motor Neuron Cell Lines, Katsiaryna Milashevich

Student Theses and Dissertations

Although non-essential, glycine plays an important role in major metabolic reactions and is most known for its anti-inflammatory effects. An accumulation of contemporary research has shown that glycine is able to stabilize membrane potential using glycine receptors at the cellular level and to protect mitochondrial function directly, whether it is from inflammation, heavy metal poisoning, or ischemia-induced neuroinflammation. In this research, the existence of a hypothetical mitochondrial glycine receptor is examined. Immunofluorescence imaging was used to examine the presence of the glycine receptor subunits alpha 1 and alpha 2 in both non- differentiated and differentiated neuroblastoma cell lines. The preliminary …

Exploring The Dynamics Of Biological Macromolecules At Angstrom Scale, Calvin Foss

Honors Thesis

This thesis studied the Guanylate Kinase (GK) enzyme, which catalyzes the reaction of ATP into ADP, using nano-rheological techniques. A unique experimental setup was created in order to observe the conformational dynamics of the biological macromolecules. An oscillatory force was applied by attaching enzymes to a gold-coated surface and gold nanoparticles. An additional gold-coated surface was placed on top of the setup in order to create a parallel plate capacitor configuration. An oscillatory voltage was then applied across the capacitor to drive the gold nanoparticles and exert a force on the enzymes. The setup detected the ensemble averaged movement of …

Covalent Modification Of Genetically Engineered Polymers With Bodipy Fluorophores, Emilie Smith

Honors Theses

Osteoarthritis and other debilitating diseases cause chronic pain that is difficult to manage. Nonsteroidal Anti-inflammatory Drugs (NSAIDs) are the current standard of treatment for many long-term pain management, but there are potential systemic effects when using NSAIDs long-term. Therefore, it isnecessary to have an alternative option for NSAID delivery that doesn’t include these systemic effects. Hydrogels can be that alternative option. Hydrogels’ distinct characteristics allow them to be viable in the body, degrade under unique conditions, and be modified through many different chemistries. Additionally, hydrogels can be engineered and their properties optimized for the use as a drug depot inside …

Effects Of Crowding Agents On I-Motif Dna, Hayden Brines

Honors Theses

Deoxyribonucleic acid (DNA) is a well-known double stranded, helical, biological molecule. In addition to its more commonly known structure, DNA can also form more complicated structures like G-quadruplexes and i-motifs (iM). The iMs are formed by cytosine rich DNA and are a four stranded structure that is typically looped around itself. The iM formation is typically pH-dependent and is favored in more acidic conditions; the pKa value is approximately 6.5. This pKa value allows for potential in vivo formation, since the cells have a pH of approximately 7.3. Due to this, iMs are thought to be powerful, innovative molecules for …

Chemical And Co-Solute Effects Of Polyethylene Glycol On I-Motif Formation, Lindsey Rutherford

Honors Theses

DNA typically forms Watson and Crick double helix structures in which adenine, thymine, guanine, and cytosine pair with their complimentary DNA base. However, DNA i-motif structures can form in cytosine rich DNA, typically under slightly acidic conditions (~pH 6). DNA i-motifs are four stranded secondary structures in which cytosine pairs with cytosine to form a quadruplex. The i-motifs are typically formed in acidic conditions because of the protonation in the C•C base pair between one of the three hydrogen bases. Recent studies have suggested i-motifs can also form under neutral conditions, which is more realistic for a cell. It is …

Using Crispr-Cas9 To Characterize The Role Of Gli-Similar 3 (Glis3) In Insulin Regulation, Pancreatic Development, And Type 2 Diabetes, Lilyanne Grieve

Honors College Theses

The prevalence of type 2 diabetes continues to rise nationally and internationally, impacting millions of people worldwide. Type 2 diabetes results from insulin resistance leading to chronic hyperinsulinemia and dysfunction of the insulin producing β cells of the pancreas. While environmental factors can influence the development of type 2 diabetes, research has shown genetics are also involved. Gli-similar 3 (Glis3), a Krüppel-like zinc finger transcription factor, has been identified as a novel regulator of insulin transcription. Evidence has shown that loss-of-function Glis3 mutations decrease insulin expression, implicating Glis3 in the development of type 2 diabetes. However, the distinct role Glis3 …

Cholesterol And Cholesterol Bilayer Domains Inhibit Binding Of Alpha-Crystallin To The Membranes Made Of The Major Phospholipids Of Eye Lens Fiber Cell Plasma Membranes, Raju Timsina, Geraline Trossi-Torres, Matthew O'Dell, Nawal K. Khadka, Laxman Mainali

Physics Faculty Publications and Presentations

The concentration of α-crystallin decreases in the eye lens cytoplasm, with a corresponding increase in membrane-bound α-crystallin during cataract formation. The eye lens’s fiber cell plasma membrane consists of extremely high cholesterol (Chol) content, forming cholesterol bilayer domains (CBDs) within the membrane. The role of high Chol content in the lens membrane is unclear. Here, we applied the continuous-wave electron paramagnetic resonance spin-labeling method to probe the role of Chol and CBDs on α-crystallin binding to membranes made of four major phospholipids (PLs) of the eye lens, i.e., phosphatidylcholine (PC), sphingomyelin (SM), phosphatidylserine (PS), and phosphatidylethanolamine (PE). Small unilamellar vesicles …

Cyclin C Determines Cell Fate In Response To Oxidative Stress And Proteasome Inhibition, David C. Stieg

Graduate School of Biomedical Sciences Theses and Dissertations

In response to various sources of cellular stress, the coordination of intracellular events is necessary to elicit the appropriate molecular response. In particular, the reprogramming of gene expression by stress-specific transcription factors drives the activation of signaling pathways, triggering either cell survival or regulated cell death pathways. The Cdk8 kinase module (CKM) is a highly conserved transcriptional regulatory complex with a role in this decision. The CKM is composed of Cdk8, its activating partner cyclin C, and two scaffold proteins, Med12 and Med13. The CKM is a detachable subunit of the Mediator complex, which interacts with RNA polymerase II to …

Sharing Raw Data From Bacterial Genomes For Collaborative Research On The Amped Server At Uri, Deborah Adenekan

Senior Honors Projects

No abstract provided.

Reaction Pathways Initiated By One-Electron Oxidation Of Guanine: Reaction Pathways Leading To Stable End Products, Zach Cutright

Undergraduate Honors Theses

8-hydroxyguanine (8-oxoG) is one of the most important products resulting from the oxidation of guanine in DNA. 8-oxoG is known as a biomarker of oxidative stress such as lung cancer. 2,5-diamino-4H-imidazol-4-one (Iz) and its hydrolysis product 2,2-diamino-4-[(2-deoxy-β-D-erythro-pentofuranosyl)-amino]-2,5-dihydrooxazol-5-one (Oz) are also important products of oxidation of guanine in DNA. Recently, novel types of dimer intermediates related to 8-oxoG and Iz have been identified in our research lab. Using high performance liquid chromatography (HPLC), LC-MS, and NMR coupled with educated hypotheses, it is possible to identify the products, X1 and X2, resulting from the oxidation of guanine and decipher the mechanisms leading …

Validation Of Anti-Oxidative Stress Genes From Genome-Wide Screening Of Escherichia Coli, Carson Ercanbrack

Chemistry & Biochemistry Undergraduate Honors Theses

The primary purpose of this project is to evaluate the genes that play a role in the oxidative stress response in Escherichia coli. In doing so, the entire genome of E. coli was subject to throughput in which individual genes were determined to have a role in the bacteria’s oxidative stress response. Moreover, this project focused on the validation of the genes that were able to pass the initial throughput stage. The genes were subject to two forms of validation. In the first validation technique, candidate genes were overexpressed and minimum inhibitory concentrations of hypochlorous acid were taken. Following, a …

Understanding The Non-Classical Secretion Mechanism Of Interleukin-1 Alpha, Clay Martin

Chemistry & Biochemistry Undergraduate Honors Theses

The Interleukin 1 family is a unique collection of cytokines in that they are primarily associated with both acute and chronic inflammation, which is associated with many diseases. In classical protein secretion, a protein, typically with an N-terminal signal peptide, is synthesized on a ribosome of a cell either in the cytoplasm or on the rough endoplasmic reticulum, transported to and merges with the Golgi apparatus, and is then sent to bind with either a lysosome or the cell membrane or is released from the cell via exocytosis. Thus, a non-classical secretion mechanism is any mechanism that differs from this. …

Rna G-Quadruplex Structures: Functions In Noncoding Rnas And Disease, Emily Benner

Electronic Theses and Dissertations

Paraspeckles are a relatively newly identified subnuclear body whose function is still largely unknown. They are membraneless organelles found within mammalian nuclei originally identified as being comprised of different paraspeckle proteins (PSPs), and later proven to also contain RNA. This study investigates the long non-coding RNA nuclear enriched abundant transcript 1 (NEAT1), which has been found to be indispensable in the formation of paraspeckles, with each containing up to 50 NEAT1 molecules. NEAT1 has two isoforms, the shorter NEAT1_1, and the longer NEAT1_2. The focus of this work will be on the NEAT1_2, which acts as a scaffold in the …

Liposomes Prevent In Vitro Hemolysis Induced By Streptolysin O And Lysenin, Marcelo Ayllon, Gamid Abatchev, Andrew Bogard, Rosey Whiting, Sarah E. Hobdey, Daniel Fologea

Physics Faculty Publications and Presentations

The need for alternatives to antibiotics in the fight against infectious diseases has inspired scientists to focus on antivirulence factors instead of the microorganisms themselves. In this respect, prior work indicates that tiny, enclosed bilayer lipid membranes (liposomes) have the potential to compete with cellular targets for toxin binding, hence preventing their biological attack and aiding with their clearance. The effectiveness of liposomes as decoy targets depends on their availability in the host and how rapidly they are cleared from the circulation. Although liposome PEGylation may improve their circulation time, little is known about how such a modification influences their …

Simulation Of The Interaction Between Striated Muscle Unc-45 And Transcription Factor Gata-4, Drake Alexander Duncan

Electronic Theses and Dissertations

Striated Muscle UNC-45, also known as UNC-45b, is an important protein that acts as a chaperone for myosin in cardiac and skeletal muscles, binding to myosin at its C-terminal UCS domain and regulating its assembly into thick filaments and sarcomeric structures. The UCS domain contains a large loop that is believed to be the first point of interaction between myosin and UNC-45b. GATA-4 is an essential transcription factor that facilitates transcription of several genes in cardiac development, particularly alpha-heavy chain myosin in heart tissue. Recently, studies have shown that there is interaction of GATA-4 with UNC-45b and that GATA-4 binds …

The Role Of Med31 And Med12 In Directing Adipogenesis Of Human Adult-Derived Mesenchymal Stem Cells, Joseph Straub

Doctoral Dissertations

Selective gene expression is crucial in maintaining the self-renewing and multipotent properties of stem cells. Mediator is a large, evolutionarily conserved, multisubunit protein complex that modulates gene expression by relaying signals from cell type-specific transcription factors to RNA polymerase II. In humans, this complex consists of 30 subunits arranged in four modules: head, middle, tail, and kinase. In our introduction, we show the state of the field of Mediator study with a focus on the critical kinase module. In the following chapters, we used siRNA knockdowns to investigate the roles of the highly-conserved core subunit MED31 and the kinase module …

Detailed Analysis Of The Role Of Mtr4 Arch Domain In Rna Binding And Helicase Activity, Keith J. Olsen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The central dogma of biology states that DNA is transcribed into RNA, which is translated into protein. However, this concept portrays RNA purely as an intermediary step from DNA to protein. RNA plays an essential and vital role in a cell, including; regulating protein and RNA levels, act as a template for protein synthesis, cell differentiation, regulatory processes, and signaling molecules. If cells do not adequately monitor and regulate RNA levels, it can lead to disease states and even cell death. The main protein complex that regulates the maturation and degradation of RNA in the nucleus is the RNA nuclear …

Characterizing Oligomeric State Changes Of Protein Arginine Methyltransferase 1 As A Mechanism For Regulating Activity, Ariana N. Ortolano

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

If you imagined a living cell as a factory, enzymes would be the workers with each individually performing a very specific and important job. If a job is not done correctly it could be detrimental to the performance of assembly lines and devastate a businesses’ existence. For enzymes, their jobs occur on a biological level by catalyzing reactions inside the cell, which can include altering another protein and the pathway it is involved in. Protein arginine methyltransferases, or PRMTs, is an example of an enzyme that modifies protein substrates. It does this by adding one or two methyl groups onto …

Investigations Of Substrate Reduction By Nitrogenase: Light Powered Substrate Reduction By A Cds:Femoco System And Understanding Dinitrogen Inhibition Of Electron Transfer, Hayden Kallas

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogen fixation is a key step of the nitrogen cycle which makes biologically inert N₂ gas available for organisms to use in the form of ammonia. Nitrogen fixing microorganisms all contain the same enzyme called nitrogenase which catalyzes the six electron transfers to N₂ required for conversion into ammonia. Nitrogenase is a two-component enzyme that contains a cofactor composed of iron and sulfur as well as heavier metals whose identity can be molybdenum, vanadium, or an additional iron atom depending on the variant. The two components of nitrogenase are the MFe protein and the Fe protein. The Fe …

Resistance Screening And Association Mapping For Resistance To The Downy Mildew Pathogen Of Spinach, Dotun Olaoye

Graduate Theses and Dissertations

Spinach is an important cool leafy vegetable cultivated around the world, with large scale production in California and Arizona in the U.S. Spinach is a highly nutritious vegetable beneficial in the human diet. Spinach is affected by a number of biotic stressors. Downy mildew, caused by the oomycete pathogen Peronospora effusa, is a major threat to spinach as it affects the leaf quality and impacts the economic value of spinach. Several efforts have led to the development of resistant genotypes/cultivars to this pathogen. However, few studies have examined the genetics of resistance to the downy mildew pathogen in detail. This …