Biochemistry, Biophysics, and Structural Biology Commons^™

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 …

Halogen Bonding: A Computational Chemistry Investigation Of The Interaction Between Thyroid Hormone And Deiodinase, William Rice

Honors Theses

Halogen bonding is a noncovalent interaction that continues to garner interest among the scientific community. Investigation of halogen bonds in biological contexts typically revolves around rational drug design for developing therapeutics. However, halogen bonding may be occurring naturally in our body every day. Thyroid hormone and its regulating enzyme, iodothyronine deiodinase, show promising results for a halogen bonding interaction that happens during catalysis. Prior work has examined the interaction between the iodine of thyroid hormone and the selenium of iodothyronine deiodinase. However, this study is the first of its kind to use computational chemistry methods to analyze the halogen bond …

The Socioeconomic & Environmental Factors Influencing Prevalence Of Zoonotic Pathogens In Rats: A Meta-Analysis, Katelyn Wing

Honors Theses

Background/Question/Methods

Global rat populations are increasing at an alarming rate across the world. In turn, this increases the risk of human-rat interactions and the potential spread of zoonotic pathogens and parasites. Rats are the second most common host of disease and can have detrimental effects in urban ecosystems. Rattus rattus and R. norvegicus are the two most abundantly distributed species of rats and are the target organism for this study. The aim of this study is to understand the connection between environmental and socioeconomic factors that influence the rate of zoonotic disease in rats. We developed two hypotheses to gain …

The Role Of Free Radicals In The Activation Of Epidermal Growth Factor Receptors In Murine Microglial Cells, Eliana John

Honors Theses

Regulation of cellular processes is important for proper functioning. Environmental factors, including stress, can interfere with cellular regulation. One of the diseases caused by cellular regulation disturbance is cancer and mutations in EGF-related genes highly correlate with worse outcomes in cancer. The Epidermal Growth Factor (EGF) pathway is involved in the regulation of cell growth and differentiation. Phosphorylation of the receptors activates this pathway, leading to cell growth and regulation. This study examines the impact of oxidative stress on EGF pathway activation. Previous studies using breast cancer lines have indirectly shown a decrease in Epidermal Growth Factor Receptor (EGFR) activation …

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.

Alzheimer's Disease: A Comprehensive Review Including Personal Experience From Retirement Home Patients, Sydney Fox

Honors Theses

Alzheimer’s Disease is a neurodegenerative illness and disease, the most common type of dementia, and the sixth leading cause of death (Sá et al., 2012). The disease was discovered in 1906 and named after Dr. Alois Alzheimer, a psychiatrist and neuropathologist. Over time, a variety of hypotheses have developed regarding the cause behind this multifactorial disease, and these will be disclosed in a later section. Nonetheless, the disease was first observed in changes of the brain tissue of a woman who was said to have die from an unusual mental illness with many abnormal bumps. These bumps are now recognized …

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 …

Fast Photochemical Oxidation And Footprinting Of Proteins Via Trifluoromethyl Radical Chemistry, Elaine Morrow

Honors Theses

Fast photochemical oxidation of proteins (FPOP) is a useful tool in proteomics because of the ability for modifications to occur on the scale of microseconds which reduces the modifications to tertiary and quaternary structure allowing for more accurate labeling of the protein. Labels for FPOP are generated from various radicals in our experiments which include hydroxyl radicals and trifluoromethyl radicals. Hydroxyl radicals are easily generated by using an excimer laser (KrF laser, 248 nm) or a UV flash lamp (as a part of the Fox™ System) by the photolysis of hydrogen peroxide. Trifluoromethyl radicals, however, need hydroxyl radicals to be …

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 …

Challenges Of Constructing Entrainment Map For Arbitrary Circadian Models, Yuxuan (Nelson) Wu

Honors Theses

The entrainment map, developed by Dr.Diekman and Dr.Bose, is claimed to be a 1-dimensional map that produces a better prediction for phase-locking than methods than the phase response curve for circadian models. In his paper, he constructs the entrainment map for the two-dimensional circadian model, the Novak-Tyson model, and the other two higher-dimensional circadian models. For this thesis, we concentrate on exploring if it is viable to construct the entrainment map for other circadian models that are not included in his paper: the Becker-Weimann model and the Relogio model. In addition, we discuss the challenges of constructing the entrainment map …

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 …

Construction And Analysis Of Three Multi-Partite Synthetic Microbial Communities, Alexander J. Lazzara, Jacob K. Fanning

Honors Theses

Microbial Communities are of interest to molecular biologists hoping to understand the nature of metabolic interactions between co-existing, or possibly mutualistic, organisms. These interactions are ubiquitous in nature, but understanding the molecular mechanisms involved remains challenging and not well understood. Here, we design three tri-partite microbial circuits based on possible interactions among involved microbes, which are discussed and may suggest mutualistic interactions. Carbon and nitrogen molecular pathways and the intracellular metabolism of each microbe is discussed. We present minimal growth media that will ensure that organisms utilize available resources, which may originate from metabolic processes in neighboring microbes, simulating a …

Biochemical And Computational Characterization Of Small Regulatory Rnas In The Eastern Oyster, Crassostrea Virginica, Isabelle Townsend

Honors Theses

RNA interference (RNAi) is a process by which gene expression is regulated using small non-coding RNAs (ncRNAs). Three classes of ncRNAs, including micro-RNA (miRNA), short-interfering RNA (siRNA), and Piwi-interacting RNA (piRNA), are readily distinguishable in eukaryotic systems based on unique characteristics such as read sizes, overlap signatures, and mode of biogenesis. In this study, a method for purification of small RNAs was explored in the eastern oyster, Crassostrea virginica. This method involved the use of Sepharose beads for anion exchange chromatography to enhance purification of Argonaute associated small RNAs. Following RNA extraction and purification, small RNA libraries were created …

Molecular Characterization Of Galectin From Amblyomma Americanum In Context Of Α-Gal Syndrome, Sumar Beauti

Honors Theses

The lone star tick Amblyomma americanum is a vector of various disease-causing pathogens and tick-borne alpha-gal syndrome (AGS) with rapidly expanding populations in the south- and northeast regions of the United States. This study aimed to molecularly characterize galectin and determine its involvement in galactose-α-1,3-galactose (α-gal) synthesis, transport, reproductive fitness, and microbial homeostasis in this tick. The lone star tick galectin possesses two conserved carbohydrate recognition domains and shares homology with other Ixodid tick galectins. Time and tissue-dependent expression data shows that galectin is constantly expressed in salivary glands, midgut, and ovary tissues. An RNA interference approach was used to …

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 …

Analyzing The Effects Of E-Hook Peptides On Kinesin-1, Ashton Ward Murrah, Baylee Hope Howard

Honors Theses

Cancer is the second leading cause of death in the United States. Cancerous growth is a result of oncogenes, or mutated genes that increase the rate of cell division in an uncontrolled manner. Cell division, which consists of mitosis and cytokinesis phases, is dependent upon the active movement of kinesin motor proteins along microtubules to rearrange the cytoskeleton for equitable distribution of genetic material to daughter cells. As kinesins are vital to this process, if we could prevent kinesin from binding to the microtubules, cell division would cease.

The goal of this study is to develop a method to prevent …

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 …

The Role Of Inflammasome In Vascular Remodeling Following Injury, Ted Amadi

Honors Theses

The purpose of the project presented in this thesis is to assess the contribution of inflammasome activation in mediating vascular wall remodeling that occurs following carotid artery injury due to decreased blood flow. To examine this, we used a mouse model of carotid artery ligation in mice lacking the expression of a key mediator of the inflammasome signaling pathway. Following ligation, we completed a histological assessment to compare the degree of the neointima formation and expression of inflammasome related proteins in both injured and the non-injured contralateral carotid artery in both wild-type (WT) and Caspase 1 knockout mice (Cas1 -/-).

Characterization Of Bpa Sensitive Strains In C. Elegans, Giulianna I. Escobar

Honors Theses

Bisphenol A (BPA) has been present in our environment since 1891 when it was first synthesized by Aleksandr Dianin. BPA has since been a topic of interest due to the possibility of diseases associated in human consumption of the chemical. Interestingly, Caenorhabditiselegans, commonly known as C.eleganshave shown to be able to tolerate the chemical. Thisorganism is an advantageous model organism for research since they are simple organisms to study, cheap, produce a large brood size, and have a short life cycle. Previously a forward genetic screen was done to isolate 2000 healthy strains in order to determine which strains showed …

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 …

Investigatin Actin-Myosin Mechanics To Model Heart Disease Using Fluorescence Microscopy And Optical Trapping, Justin Edward Reynolds

Honors Theses

Hypertrophic cardiomyopathy (HCM) is a hereditary disease in which the myocardium becomes hypertrophied, making it more difficult for the heart to pump blood. HCM is commonly caused by a mutation in the β-cardiac myosin II heavy chain. Myosin is a motor protein that facilitates muscle contraction by converting chemical energy from ATP hydrolysis into mechanical work and concomitantly moving along actin filaments. Optical tweezers have been used previously to analyze single myosin biophysical properties; however, myosin does not work as a single unit within the heart. Multiple myosin interacts to displace actin filaments and do not have the same properties …