Biochemistry, Biophysics, and Structural Biology Commons^™

Functionalized Gold Nanoparticles And Halogen Bond Interactions With Neonicotinoid Pesticides, Molly Mccuen “Mackey” Sherard

Honors Theses

Neonicotinoid (NN) pesticides have emerged globally as one of the most widely used agricultural tools for protecting crops from pest damage and boosting food production. Unfortunately, some NN compounds, such as extensively employed imidacloprid-based pesticides, have also been identified as likely endangering critical pollinating insects like honey bees. To this end, NN pesticides pose a potential threat to world food supplies. As more countries restrict or prohibit the use of NN pesticides, tools are needed to effectively and quickly identify the presence of NN compounds like imidacloprid on site (e.g., in storage areas on farms or pesticide distribution warehouses). This …

Cd46 Isoforms And Viral Receptor For Adenovirus Type 64d, Corina Stasiak

Honors Theses

Adenovirus Type 64 (Ad.64) belongs to the adenovirus subgroup D, which causes epidemic keratoconjunctivitis (EKC), otherwise known as viral pink eye. There is currently no known effective treatment for EKC. Membrane Cofactor Protein (CD46) is an integral membrane glycoprotein that, in previous studies, has been identified as a protein receptor for the closely related Ad.37. It has been determined that Ad.64 uses CD46 as a receptor on the cell surface in HeLa cells. CD46 is alternatively spliced when expressed to have different isoforms of interest, including the BC and C isoforms. Certain cell types, like A549 lung carcinoma cells, express …

Cd46 Is A Protein Receptor For Human Adenovirus Type 64, Alexander Michael Robertson

Honors Theses

Adenoviruses are important gene delivery vectors and causative agents for a variety of human diseases such as the common cold and gastrointestinal infections. Human adenovirus type 64 (Ad64; formerly 19c) and type 37 are associated with epidemic keratoconjunctivitis. Based upon its high homology and similar disease tropism to Ad37, we hypothesized that Ad64 would have the same protein receptor, CD46 (membrane cofactor protein), as Ad37. We show that a recombinant Ad64 containing an enhanced Green Fluorescent Protein transgene (Ad64.eGFP) enters Chinese hamster ovary cells expressing human CD46 (CHO-CD46) on the surface. Entry into human cervical carcinoma (HeLa) cells is increased …

Structural Phylogenetics Of A Family Dna Polymerases, Yagmur Bingul

Honors Theses

The transition from the RNA to the DNA world stands as an important event, demanding the emergence of enzymatic activities for DNA precursor synthesis, retro-transcription of RNA templates, and replication of single and double-stranded DNA molecules. The distribution of protein families associated with these activities across the three domains of life—Archaea, Eukarya, and Bacteria—adds layers of complexity to the narrative. While Archaea and Eukarya often share similar protein structures, structural biology shows homologous, but distinct, structures in Bacteria. On the other hand, viral polymerases emerge as a crucial part of genome replication and transcription. Their versatility, including RNA-dependent RNA polymerase, …

Heterocycles As Peptide-Based Cleavable Linkers, John Blobe

Honors Theses

As cancer cases continue to rise, the need for advancing the treatment options for cancer is ever increasing. Current cancer therapeutics, while effective at treating localized cancers and a fraction of advanced cancers, generally lack the specificity needed to target more advanced cancers. Recent advancements in cancer treatments have leveraged antibodies to target certain cancers. A class of drugs that utilize antibodies to deliver anti-cancer therapy preferentially to cancer cells, termed antibody-drug conjugates (ADCs), have been quite effective in treating certain advanced forms of certain cancers. These ADCs could be more effective if they could allow for the facile release …

Diaryl Oxazoles As Cleavable Linkers For Drug Discovery Platforms, Elizabeth Taggart

Honors Theses

Within the field of medicine and pharmacology, discovering small molecule or biologic based molecules with therapeutic potential is a difficult task. Current methods involve individually screening hundreds of compounds on a potential target biomolecule, and recent technologies have explored peptide encoded libraries (PELs) as a means of making this screening process more high-throughput. These libraries produce a large number of small molecule drug candidates each conjugated to a unique peptide fragment, functioning as a barcode. Analysis of PELs requires the capture of hit small molecules and the subsequent release of their peptide tags; however, current approaches are limited in their …

Chemical And Genetic Composition Analysis Of Organic And Nonorganic Tortilla Chips, Aubrey White-Day

Honors Theses

The aim of this study was to explore the chemical and genetic differences between organic and nonorganic tortilla chips using GC-MS and PCR. Twenty chip brands were selected: 10 organic and 10 nonorganic. A survey on shopping preferences was created and distributed to compare results of public opinion to experimental data. It yielded 212 responses. All organic chip brands, and one out of ten nonorganic chip brands, tested negative for GMOs. This study concluded that there are minimal chemical differences based on Jaccard similarity indicies and stark genetic differences between organic and nonorganic tortilla chips. In comparing statistical analyses to …

Diffusion Of Ionic Liquid-Modified Polymer Nanoparticles Through Nasal Mucus, Mary Vanlandingham

Honors Theses

Mucosal barriers are a natural defense system for preventing the entry of foreign objects into the body; however, they pose as obstacles for effective drug delivery. Coated polymer nanoparticles have been proven to possess improved rates of diffusion across mucus compared to their uncoated, or bare, counterparts. When choline-based ionic liquids (ILs) are introduced to an aqueous system, their dissociation leads to an increase in solution conductivity which ultimately reduces the viscosity of mucus without significantly affecting its structure. Additionally, ILs are highly tunable, so they work well in a range of pHs and conductivities, making ILs an ideal choice …

Photocatalyzed Hydrogen Evolution Using Nickel-Bound Metallothionein Protein, Windfield Swetman

Honors Theses

The continued burning of fossil fuels is not only a cause of increasing deterioration of the environment but also a financially unsustainable source of energy. Advances in energy production must be investigated to avoid the long-term effects of this current main source of energy. One of the avenues being explored is the use of metalloenzymes to catalyze hydrogen evolution via water splitting that occurs during the reductive half of artificial photosynthesis. Metalloenzyme catalysts with a single Ni(Cys)₄ active site have been previously studied, and this study explores the possibility of increasing hydrogen production by using metalloenzyme catalysts with multiple …

Structural Integrity And Stability Of Dna In Ionic Liquid And Near-Infrared Indolizine Squaraine Dye, Ember Yeji Suh

Honors Theses

Luminol, the most common presumptive test for blood at a crime scene, has multiple issues, such as false positive results with chemical agents, no luminescence due to “active oxygen” cleaning agents on bloodstains, and inability to penetrate textile materials. A combination of indolizine squaraine dye and ionic liquid (IL), or Dye Enhanced Textile Emission for Crime Tracking (DETECT), have shown potential to address these issues. The purpose of this study was to assess the binding mechanism of CG (1:1) and SO₃SQ dye to HSA and how the mechanism can explain the W214 fluorescence quenching effect and to determine …

A Synthetic Approach To The Optimization Of Silicon-Rosindolizine Swir Fluorophores, Timothy Lewis

Honors Theses

Fluorophores emitting within the near-infrared (700 – 1000 nm) or shortwave-infrared (1000 – 1700 nm) regions of the electromagnetic spectrum are of particular interest for their potential to supplement or even outright replace commonly used biological imaging techniques, such as magnetic resonance imaging and computed tomography scanning. Various characteristics make these molecules particularly appealing to researchers, such as their ease of synthetic tunability, generally low toxicity, and high solubility in biological media in comparison to other NIR- and SWIR-emissive fluorophores. Different molecular skeletons have been examined for use as the core of these imaging agents, such as squaraine, cyanine, and …

All The Rage: Assessing The Age/Rage Signaling Pathway’S Effects On Healthspan And The Physiological Processes Of Aging, Brandon Ashmore

Honors Theses

Advanced glycation end products (AGEs) are protein, lipid, or nucleotide molecules that have been combined with sugars through nonenzymatic, irreversible glycation and oxidation reactions. Their accumulation in the body has been associated with the natural aging process and a wide range of pathologies, including chronic inflammation, sustained oxidative stress, diabetes, neurodegenerative diseases, atherosclerosis, and cancer. Their interaction with the receptor for advanced glycation end products (RAGE) has been linked to several proinflammatory signaling pathways associated with neurotoxicity and vascular lesions. While some research has been done on the possible health benefits of RAGE inhibition to extend lifespan, our study hopes …

De Novo Design Of Artificial Cu Peptide For Substrate Oxidation And An Electrochemical Approach To Determine Reorganization Energy, Morgan Murphy

Honors Theses

Copper enzymes are found in nature. Their mechanisms and properties are unknown, as spectroscopy is limited. By creating artificially designed copper peptides through de novo design, the behavior, characteristics, and spectroscopy of copper enzymes can be studied to enhance understanding of the mechanisms involved with enzyme catalysis. Design, synthesis, purification, and characterization are completed to create a quality peptide mutant that can be studied to learn about natural enzymes. This plays an important role in pharmaceutical research, renewable energy sourcing, and studies of biological processes in the body. In this study, 3SCC de novo peptide is mutated at different positions, …

Effects Of Group Ii Metal Binding On The Stability Of Dna I-Motif Structures, Charlotte Powers

Honors Theses

B-form DNA can adopt alternative structures while in superhelical duress. Alternative DNA structures are favored when there is an asymmetric distribution on complementary DNA strands. Cytosine rich strands may utilize cytosine-cytosine base pairing to form a four-stranded structure known as the i-motif (iM). The stability of iMs is affected by several factors such as DNA sequence, temperature, pH, ionic strength of the solution, and crowded conditions. While the effects of temperature, pH, and crowding conditions on iM stability have been well documented, the effects of ion presence in a solution has been less studied. Hence, those studies are the basis …

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 …

Role Of Cdx4 And Sp5l In Zebrafish Development, Wesley Tsai

Honors Theses

The Caudal Type Homeobox transcription factors cdx are a family of genes found in vertebrates that regulates body regionalization and anterior-posterior patterning. They are also responsible for regulating axial elongation, but the mechanisms behind this behavior are not known. Previous studies in mouse embryonic stem cells have shown that the cdx genes are necessary for upregulating the gene sp5 which may be linked to axial elongation. Sp5 is a zinc-finger transcription factor belonging to the specificity protein (sp) family. Our group has used in-situ hybridization experiments on zebrafish embryos to show that sp5-like (sp5l) is transcribed within tailbud tissues that …

Bryophytes Of Goochland County, Virginia, Mikayla Quinn

Honors Theses

Bryophytes are non-vascular land plants that include mosses, liverworts, and hornworts. Although easier to overlook because of their smaller size, bryophytes are a fundamental part of the ecosystem. As such, maintaining record of their biodiversity is important. Yet, records of bryophyte species in Goochland County, VA were low compared to more thoroughly documented counties such as Prince Edward County. This study expands the documentation of bryophyte flora and presents a checklist of bryophyte species found Virginia’s Goochland County from 2020-2023. Fieldwork conducted at public and privately-owned properties throughout the county between January 2020 and March 2023 yielded 702 specimens that …

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, …

Arabidopsis Shoot Gravitropism Requires The Mediator Coactivator Complex, Gabriella Newton

Honors Theses

Gravitropism is a plant response to gravity in directing the growth of its organs, such as the root and the stem. Gravity is sensed by statocytes, unique cells that contain starch-filled amyloplasts, which trigger gravitropic growth response by modulating the distribution of growth hormone auxin in the elongation zone of the stem and root. Despite the fact that multiple factors have been identified as key regulators of shoot negative gravitropism, how these factors are regulated at the transcriptional level is largely unknown. In this study, we explore the role of transcriptional machinery in regulating shoot gravity sensing and responses by …

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 …

Lectin-Glycan Complexes: A Comprehensive Analysis Of Docking Calculations, Ashton Custer

Honors Theses

Lectins are a type of glycan-binding protein that noncovalently bind glycans. Carbohydrates are molecules consisting of sugar units joined together. Glycans are carbohydrates. Hence, glycans are also sugars. Lectins and lectin-glycan complexes have a range of biological roles and can be found in animals (including humans), plants, bacteria, viruses, and yeasts and fungi.¹ Many scientists focus on the computational study of these complexes due to their intricate roles in many living organisms. Computational study is important in furthering our knowledge of lectin-glycan complexes and other such protein complexes. However, computational study is not perfect. There are many challenges in …

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.