Biochemistry Commons^™

Is Vdac1 A Novel Bcl2 Family Member That Binds Bax?, Claire Pearson

Honors Theses

Apoptosis is a type of regulated cell death important for normal embryonic development and maintenance of adult tissues by removing excess or dysfunctional cells to ensure proper functioning of organs. The Bcl-2 family of proteins determines whether apoptosis remains suppressed or becomes activated through the balance of interactions among pro-survival and pro-death members. A defining feature of the Bcl-2 family is a BH3 domain that drives interactions between the family members. Isoform 1 of the voltage dependent anion channel (VDAC1) has an important role in metabolism, but was recently found to have high homology with known BH3 domains. This study …

Electrochemical Reduction Of Carbon Dioxide Using Ruthenium And Amines, Sydney Moise

Honors Theses

With an increased concern for climate change in the recent years, a significant area of research has been devoted to the reduction of greenhouse gases. Carbon dioxide (CO2) resides in the atmosphere between 300 – 1000 years, making the reduction of the molecule a substantial field of study.1 Amines have been used as CO2 scrubbing agents in literature historically, due to their ability to form bonds to carbon.2 Although studies involving metal catalysts and amines have been reported numerous times, research involving chemical reduction of CO2 using purely amines is scarce. In this paper, amines, in addition to hydride donors …

Investigating The Helicase Activity Of Methylated Vs Unmethylated Ded1, Hannah Lukow

Honors Theses

Ded1 is an RNA helicase protein of the DEAD-box subfamily in eukaryotic organisms (Sharma & Jankowsky, 2014) which can act as an activator or initiation factor, during translation (Hilliker et al., 2011). Ded1 has several functions in yeast including assembly of translational initiation factors, scanning the mRNA for the start codon, and unwinding any double stranded segments of mRNA with its helicase ability. Ded1 was discovered to be methylated at four arginine sites in vivo (Low et al., 2013), with a fifth methylation site being discovered recently (Low et al., 2020), however the purpose of such post-translational modifications is still …

The Role Of Cerium(Iii) In Bacterial Growth And The Microbial Transformation Of Aromatic Hydrocarbons, Shruti Sathish

Honors Theses

Biofilms are communities of surface-attached bacterial cells encased in an exopolymeric matrix. In this state, they are more resistant to antimicrobial treatment and can have adverse effects in medical, agricultural, and industrial settings. Whereas, as biocatalysts, biofilms from nonpathogenic bacteria enhance their performance and stability in catalysis. Unfortunately, there are several challenges when using bacteria in organic transformations due to their complex cellular chemistry. Trivalent lanthanide metals were discovered to serve regulatory roles in some bacterial catalytic processes, including those of Pseudomonas putida KT2440 (P. putida), a non-infectious Gram-negative bacterium. The main goal of our research is to use cerium(III) …

Early Life Δ9-Tetrahydrocannabinol Exposure Of F0 Zebrafish Causes Hyperactivity In F1 Offspring, Jenna Cripe

Honors Theses

As cannabis increases in its accessibility, potency, and acceptance across the United States, investigation into the multigenerational effects of Δ9-tetrahydrocannabinol (THC) exposure during key stages of development is critical. The aim of this study was to evaluate whether there would be behavioral impacts in the F1 offspring following a dose-response of THC exposure (0.08, 0.4, or 1 µM) during development in the F0 generation. Zebrafish (Danio rerio) were utilized in this study. Behaviors (locomotive activity and anxiety-like behavior) in the F1 generation were evaluated at 120 hours post-fertilization (hpf) with the larval photometer response (LPR) assay, and at 3, 11, …

Expression And Purification Of The Bacterial Protein Curli Csga And Its Cross-Interactions With Amyloid-B, Leah Grace Cantrell

Honors Theses

One of the main causes of neurodegenerative diseases is aggregation of amyloid proteins that are toxic to the neurons. Proteins like amyloid-β (Aβ) and α-syneuclein (α-syn) form hallmark aggregate lesions that contribute to pathological processes in the brain in Alzheimer and Parkinson’s patients, respectively. Recent ground-breaking studies have suggested a link between the microbiota of the gut and neurodegenerative diseases, called the “gut-brain axis.” It has been long known that the protein, CsgA found in many enteric bacteria, forms amyloid fibers of its own called Curli. Curli fibrils are a structural component of bacterial colonies and maintain the integrity of …

Oligomerization Of Amyloid-Β Peptide In The Presence Of Gangliosides–Implications For Alzheimer Disease, Sydney Boyd

Honors Theses

Alzheimer disease (AD) is a neurodegenerative disorder that leads to memory impairment and cognitive dysfunction in elderly populations worldwide. A key characteristic of AD is the formation of neuritic plaques composed of extracellularly deposited aggregates of amyloid-β (Aβ), an intrinsically disordered protein. Although Aβ fibrils were once thought to be the prime initiators of the disease, research has since been shifted to consider soluble, low molecular weight Aβ oligomers as the driving force behind AD toxicity. Due to its origin as a cleavage product of amyloid precursor protein (APP), an integral membrane protein, Aβ is known to perpetually interact with …

Isolation Of Sphingolipids From Sphingomonas Echinoides B-3126 And Their Characterization By Ms/Ms Analysis, Edgar David Uribe Sanchez

Honors Theses

EDGAR DAVID URIBE SANCHEZ: Isolation of Sphingolipids from Sphingomonas echinoides B-3126 and their Characterization by MS/MS Analysis

Sphingolipids are important components in human cellular lipid membranes and are differentiated by the incorporation of serine with an amide bond between the amino acid and a lipid tail. Sphingolipids produced by bacteria differ in both headgroups attached to the serine alcohol and the architecture of the lipid backbone. While the synthesis of sphingolipids in mammalian cells is well studied, only a handful of steps in the pathway are described in bacteria.¹ The observations that although sphingolipid synthesis is rare in bacteria, …

Retro-Structural Analysis Of The Four Helix Bundle Motif In Binuclear Proteins, Walker Pedigo, Maggie Smith

Honors Theses

Protein structure is directly related to protein function. There are four levels of protein structure: primary, secondary, tertiary, and quaternary. The interactions amongst the structural components of a protein give rise to its unique characteristics. The four helix bundle motif is a common structural trait in a variety of binuclear proteins. In this study, PyMOL, a molecular visualization system, was used to analyze binuclear proteins that possess a four helix bundle. Images of proteins containing dicopper, diiron, and dimanganese sites were captured. The images were compiled into figures for each individual protein. After creating the figures, each protein was further …

Determining The Distribution Of Elemental Compounds And Oxidative Potential Across Fine Particulate Matter (Pm2.5) Filters, Allie Michelle Sidwell

Honors Theses

Fine particulate matter (PM_2.5) is a complex mixture of particles and sorbed chemicals that poses serious, adverse effects on human health such as increasing cardiovascular and respiratory morbidity and mortality. There is ongoing research into the impacts of PM_2.5 of differing chemical compositions, sampling location, and the mechanisms for the observed health effects. To conduct these analytical and toxicology studies of PM_2.5, researchers often split filters into sections. This process allows multiple, often destructive, assays to be performed. Our previous research showed chemical composition differences across PM_2.5 filters. The goal of our study was …

Finding The Optimal Ionic Liquid To Target White Blood Cell Subpopulations Using Nanoparticles, Meghan Gorniak

Honors Theses

Disorders and diseases of the immune system have become more prevalent in recent decades and can have life-threatening effects on those afflicted. Granulocyte disorders disproportionately affect infants and children, while chronic lymphocytic leukemia is the most common type of leukemia in adults. Unfortunately, current treatments have many drawbacks such as everyday injection, short-lived efficacy, and unknown levels of safety and effectiveness. It is imperative to find more effective treatment options that could allow for easier drug delivery to specific populations of white blood cells (WBCs). Nanoscale medicine shows promising application, but complications remain in reaching the desired target site and …

The Effects Of Crowding Agents On The Pka Of Physiologically Stable I-Motif Dna, Courtney Turner

Honors Theses

The overall goal of this thesis was to investigate the environmental conditions that induce i-Motif folding of the DNA strand DUX4L22, a cytosine-rich segment of DNA found in the human genome. Cellular conditions were simulated using sodium cacodylate buffer and multiple weights of polyethylene glycol as a crowding agent. The presence of i-motifs were confirmed by Circular Dichroism spectroscopy. I found that DUX4L22 does form i-motifs under these physiological simulations at both acidic and neutral pHs. DUX4L22 therefore shows potential for use in studies of a wide variety of biotechnological advances, such as regulatory switches in nanomachines or drug-delivery systems.

Covalent Modification Of Recombinant Protein With Reactive Thiols, Sawyer Dulaney, Bailey Taylor

Honors Theses

Many diseases cause chronic and painful inflammation in different body systems. One of the front-line drug classes to treat such inflammation is Nonsteroidal Anti-Inflammatory Drugs (NSAIDs). Despite the benefits of oral administration of NSAIDs, there are drawbacks to their long-term usage because they can cause detrimental effects on off-target systems in the body such as the liver, kidney, or the lining of the intestinal tract. An alternative to NSAIDs is the usage of hydrogels for targeted drug delivery. Hydrogels can provide drug delivery in a specific portion of the site of inflammation, thus allowing higher doses of medication to be …

Investigation Of Cotinine Concentration Found In Saliva Of Smokers And Vapers In Demographic Sectors, Seth A. Sims

Honors Theses

A simple and reproducible method for investigation of cotinine and nicotine levels in saliva was developed by utilizing gas chromatography mass spectrometry (GCMS) and simple extraction techniques. This method allowed for accurate detection of cotinine in saliva samples collected within a 50-mile radius of Searcy, AR. The observed cotinine levels proportionately depict nicotine levels, which were then compared with participants’ demographics, displaying trends among different communities. This research hopes to provide insight into vaping popularity as well as a reproducible method that future research can utilize.

Targeting Platelets Using Ionic Liquid Coated Nanoparticles, Karen Mun Wong

Honors Theses

Platelets are key players in our body’s inflammatory processes upon activation, which can create physiological problems. Researchers are actively seeking solutions by targeting platelets with therapeutics. The objective of the research in this thesis was to investigate a new and potentially less invasive drug delivery platform using nanoparticles. The topic of the project was to explore the world of ionic liquids and their abilities, when coated on nanoparticles, to bind to platelets. A library of choline carboxylic acid-based ionic liquids (ILs) was first synthesized via salt metathesis while PLGA-based nanoparticles were simultaneously being synthesized via the nanoprecipitation method. The ionic …

Synthesis Of Alpha Domain Of Metallothionein For Hydrogen Production, Aditya Surakanti

Honors Theses

The world relies on nonrenewable resources for a significant portion of its usable energy, the most common being fossil fuels. Fossil fuels release many unwanted byproducts during their extractions and conversion processes. As a result, this excessive use leads to harsh consequences upon the environment, including rapid global warming, release of numerous water and air pollutants, and it could possibly lead to an increased risk of death in those who are exposed to these toxins. In response to this scenario, the goal of my project is to design an artificial hydrogen catalyst, which can absorb sunlight and oxidize H2O into …

Attempted Synthesis & Antibacterial Properties Of Apt-6k Against Ndm-1 K. Pneumoniae, Alec Bofetiado

Honors Theses

NDM-1 K. pneumoniae is a highly resistant bacterial organism that is capable of causing debilitating nosocomial infections in immunocompromised patients. Only "last-resort" antibiotics--such as colistin--work against this organism. Therefore, new antibiotics are needed to help fight against these types of infections. APT-6K is a novel compound that was demonstrated to be effective against MRSA with nanomolar concentrations in a prior study. Novel methods of APT-6K synthesis and its testing for antibiotic effects against NDM-1 K. pneumoniae were attempted in this research. APT-6K synthesis was unsuccessful. Commercially-prepared APT-6K also did not demonstrate growth inhibition against NDM-1 K. pneumoniae nor against a …

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 …

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 …

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 …

The Effect Of The Apolipoprotein A1 (Apoa1): The Stability And Folding In Potassium Chloride Environment, Alexandra Paladian

Honors Theses

Healthy levels of potassium chloride (KCl) can significantly affect the workings of the cholesterol level of the human body and how they pertain to an individual person. The search for a better salt additive for the human diet can provide a better option for people who experience high cholesterol levels and heart disease. The study focuses on the experimental design of the Molecular Dynamic (MD) simulation of the Apolipoprotein A1 (APOA1) in the potassium ion solution environment to determine the stability and folding of the protein. The study also compares its data to the previous experimental design of chloride ions …

Molecular Dynamic Simulation Of The Complex Folding Patterns Of Apolipoprotein A1 In Various Concentrations Of Potassium Chloride, Hannah Holmberg

Honors Theses

Apopliprotein or ApoA-1 is a complex lipoprotein that functions in the removal of cholesterol from the blood, removing cholesterol from the area around white blood cells and promoting the excretion of lipids through the lymphatic system. Previous research has found that ApoA-1 shows both folded and unfolded conformations depending on the concentration of NaCl in solution in the water around it. The protein was studied using molecular dynamics simulations. Once this state of equilibrium was reached, various structural properties of the protein were measured including the radius of gyration and the radial distribution function. The goal of the project was …

Thermodynamic Analysis Of Pamam Dendrimer Synthesis, Ryutaro Einar Jacobson

Honors Theses

The objective of this research was to determine kinetic and thermodynamic data about the reaction between ethylene diamine and methyl acrylate which is used in the production of PAMAM dendrimers. Establishing a rate law and finding values such as rate constant, activation energy, and Arrhenius coefficient will help in determining the best possible conditions for the reaction. A rate law was established through the method of initial rates, comparing the rates of reactions with different initial concentrations to one another. Additional reactions were run with active cooling to observe the effects on rate and reaction progress, and finally reactions were …

Finding Optimal Opa-Iblc Derivatized Amino Acid Analysis Parameters With Three-Dimensional Fluorometric Scans For Hplc Method Validation, Aaron Jacobs

Honors Theses

Three-dimensional fluorometric scans of OPA-IBLC derivatized glutamic acid and histidine solutions revealed that decreasing concentration maintained maximum λem but produced different maximum λex. In pH 0.4 M sodium borate buffer (pH 10.4), 50 μM derivatized amino acid solutions had maxima around 350- to 450-nm λex-λem where 12.5 μM solutions had maxima around 230- to 450-nm λex- λem. In the lower concentration, the λex peak at 230 nm was about 80% higher than 350 nm. Thus, collecting spectra with 230 nm λex would provide better LOD and LOQ. Results inform HPLC standard concentrations since differential quenching effects may produce non-linear calibration …

Indolizine Donor-Based Dyes For Applications In Fluorescence Biological Imaging, William Meador

Honors Theses

NIR emissive fluorophores are intensely researched due to their potential to replace modern imaging procedures. Many molecular strategies have been employed in the literature to optimize fluorophores for deeper NIR absorption and emission, biocompatibility, and higher fluorescence quantum yields. Amongst the fluorophores studied to date, proaromatic indolizine donors are attractive alternatives to traditional alkyl amine and indoline based donors due to their 1) lower energy absorption and emission facilitated by proaromaticity, 2) large Stokes shifts due to increased dihedral angles about the π-system, 3) ease of functionalization and capacity for bioconjugation at the phenyl ring, and 4) potential for further …

The Quantitative Assessment Of Pond Scum: An Examination Of The Biogeochemistry Of Phosphorus Cycling In The Belgrade Lakes, Abbey M. Sykes

Honors Theses

The internal recycling phosphorus in freshwater lake bottom sediments represents a significant source of hypolimnetic phosphorus (P) release for many of Maine’s lakes. In summer months, Maine lakes often thermally stratify and the lake hypolimnion develops anoxia, leading to a reduction in redox potential at the sediment-water interface. These reducing conditions facilitate the reductive dissolution of ferric iron, and, since phosphorus is often present in freshwater lake sediments as solid FeOOH-PO₄ complexes, results in release of soluble phosphorus into the water column. Our current study presents field and laboratory data from sediment fractionation extractions designed to quantify concentrations of …

Use Of Small Molecule Fanconi Anemia Pathway Inhibitors As Sensitizing Agents To Laromustine., Sam W. Marchant

Honors Theses

Laromustine is an experimental chemotherapeutic sulfonyl hydrazine prodrug shown in clinical trials to be effective against acute myeloid leukemia. The mechanism of action of laromustine involves interstrand crosslinking, via chloroethylation, and enzyme inhibition, caused by carbamoylation. The work described herein aims to investigate whether inhibition of the replication-dependent interstrand crosslink repair Fanconi Anemia pathway further sensitizes cells to laromustine. By measuring metabolic activity immediately after drug exposure, we find laromustine to be equally as cytotoxic towards Fanconi Anemia deficient and wild type cells. However, through clonogenic assays we show Fanconi Anemia mutations sensitize cells to laromustine’s anti-proliferative effect. Furthermore, we …

Breast Cancer Sub-Clones That Metastasize To Lung And Bone Exhibit Different Metabolic Preferences, Mollie Merrell

Honors Theses

Metastasis is responsible for the majority of cancer related deaths. In breast cancer the lungs and bones are the major sites for metastasis. Previous studies used the metastatic aggressive MDA-MB-231 breast cancer line to isolate sub-clones that preferentially invade the lungs (LM line) or bones (BoM line). While genes associated with the tissue specific metastasis have been identified, it is unknown if metabolic adaptations contribute to the growth of the LM and BoM lines in their respective organs. The goal of this study was to test the hypothesis that the LM and BoM lines exhibit differences in glucose and glutamine …

The Effects Of Insulin-Like Growth Factor-1 (Igf-1) And Insulin-Like Growth Factor Receptor (Igfr) Regulation On Cognition And Structure Of Astrocytes, Sariya Khan

Honors Theses

Insulin-like growth factor-1 (IGF-1) is a neuroendocrine signaling hormone that plays an integral role in bone and tissue growth and development. Inhibition of this hormone is known to disrupt the chemistry of the brain, resulting in cognitive impairments such as those seen in many common neurodegenerative diseases. While much research has been conducted on neurons and their relation with IGF-1, the role of astrocytes still needs to be explored. Our research investigates how astrocytes are affected as a result of IGF-1 regulation. Preliminary studies in our laboratory established a connection between IGF-1 and glial fibrillary acidic protein (GFAP), and in …

The Raphe-Hippocampal Tract And Its Age Differences: Diffusion Tensor Imaging And Probabilistic Tractography Study, Ashley Sekul

Honors Theses

The raphe-hippocampal tract links the raphe nuclei to the hippocampus and is responsible for the production of the neurotransmitter serotonin. The hippocampus is key in regulating emotional and stress responses. This study utilized diffusion tensor imaging which uses Functional Magnetic Resonance Imaging to provide scans of the brain for analyzing differences in the raphe-hippocampal tract as one ages. In this specific study, 491 samples were visually analyzed to gather data about the fractional anisotropy of the raphe nuclei in both male and female brains ranging from 6 to 85 years old. Through the ranking of images, some were discarded, and …