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Cd46 Interaction With Adenovirus Type 64, A Causative Agent For Viral Pink Eye, Hanglin (Henry) Zhu

Honors Theses

Human adenovirus type 64 (Ad64) is a causative agent of contagious viral pink eye. We do not understand why Ad64 causes eye infections. One likely reason is the presence of a receptor molecule on the exposed surface of eye cells, but not other cells. Ad64 binds to a protein called CD46 on the cell surface. We aim to visualize how CD46 binds to the surface of Ad64. I mixed the extracellular portion of CD46 with purified Ad64 virus, then visualized it using negative stain transmission electron microscopy. In order to gain insight into how the virus binds CD46, we used …

Investigation Of The Vira Linker Domain To Characterize Its Phenol Interactions, Jessica Garofalo

Honors Theses

The soil bacterium Agrobacterium tumefaciens causes tumors in plants through interkingdom gene transfer. This transfer is initiated upon a wounding event that results in the release of plant signaling factors such as phenols and sugars that are recognized by protein machinery in the periplasm and inner membrane of A. tumefaciens. The histidine kinase protein VirA, in combination with the periplasmic protein ChvE, recognizes these signals and initiates induction of virulence genes via a signaling pathway, culminating with the insertion of tumor-inducing T-DNA into the wounded plant cells. While the interaction between the Periplasmic domain of VirA and sugar-bound ChvE …

Analysis Of Wild Rodent Gut Microbiota As A Function Of Exposure To Ticks And Tick-Borne Pathogens, Joshua Pandian

Honors Theses

Due to advances in high-throughput parallel sequencing, researchers have conducted novel studies exploring relationships between microbiome compositions and different aspects of organism health. Some of these studies have shown that the gut microbiome of rodent models has effects on organism health and behavior and that infection with pathogens and the composition of the skin microbiome are linked to changes in gut microbiome composition. While previous studies have shown how vector microbiota impact vector behavior and pathogen transmission, the effect vectors have on reservoir species microbiomes has been a less prominent focus. We were interested in the relationships between tick parasitism, …

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 …

Investigation Of The Effects Of Resveratrol And Epigallocatechin Gallate On Woodsmoke-Induced Inflammation, Sarenna Naomi Enright

Honors Theses

Until a few years ago, most scientific investigations related to the health effects of air pollution focused on outdoor air pollutants. But in recent years, the concerns over indoor air pollution has increased. People can spend up to 90% of their time in indoor environments, especially their homes, even more so since the beginning of the COVID-19 pandemic. The concentrations of some air pollutants are five times higher than what is found outdoors.

Indoor air pollution exposure remains a significant cause of morbidity and mortality worldwide. Approximately half of the global population is exposed to abnormally high concentrations of household …

Research Towards Understanding Hox Regulation By Cdx, Joshua M. Fisher

Honors Theses

In this project, we aim to functionally test the contribution that individual Cdx binding sites have in hox gene regulation. We will achieve this by individually blocking Cdx binding sites using CRISPR/dCas9 in the zebrafish and then analyzing changes in the time, distribution, and levels of hox gene transcription.

We will focus our analysis in only one of the seven zebrafish hox clusters, the hoxca cluster. We are focusing on the hoxca gene cluster because it has lost the least number of genes relative to other clusters and is involved in specifying the axial identity of cells in …

Investigation Of The Effects Of Curcumin On Woodsmoke-Induced Inflammation, Melissa Lewis

Honors Theses

Inflammatory diseases caused by biomass smoke exposure and indoor air pollution affect millions of people worldwide. These diseases can be caused by the burning of biomass (plastic, wood, rubber, tobacco, etc.) for light or heat. Acrolein is a common indoor and outdoor pollutant from tobacco smoke or organic combustion. Wood smoke is hypothesized to cause inflammation since it contains high concentrations of particulate matter and gaseous compounds and are similar in size to other well-known damaging particles. Natural remedies, like curcumin, are hypothesized to be a natural remedy for combating inflammation. The goal of this research was to investigate the …

The Effect Of Color Morph On Behavior Interactions In Red-Backed Salamanders (Plethodon Cinereus), Taylor M. Aliferis

Honors Theses

Studies in behavioral ecology provide critical information regarding a species’ territoriality, predator-prey interactions, and reproduction. Red-backed salamanders (Plethodon cinereus) are a polymorphic terrestrial amphibian whose behavioral interactions have long been studied to provide insights on the processes that structure salamander populations, which are often cryptic and difficult to study. However, research regarding the effect of coloration on these interactions is more limited, but potentially extremely important for studies of population dynamics and speciation in terrestrial salamanders. In this study, aggressive and submissive behaviors of adult male red-backed salamanders in five different color morph treatment pairings were observed to …

The Influence Of Flooding On Macroinvertebrate Diversity Of The James River Rock Pools, Meghan Leber

Honors Theses

Biodiversity within an ecosystem can be greatly influenced by environmental disturbances, such as fires, flooding, or other extreme events. Studying the effects of these disturbances on species diversity can be complicated though, due to difficulties tracking species-level responses and isolating the effects of disturbances. Model systems in community ecology, such as rock pools, are a beneficial way to scale down the study of disturbances in discrete communities without losing the ability to analyze important influences or interactions. In this study, macroinvertebrates within the James River rock pools were surveyed to investigate seasonal and annual differences in species richness and diversity, …

What Lies Beneath? : Removal Sampling To Test For Biases In Surface Activity Of The Eastern Red-Backed Salamander (Plethodon Cinereus), Amelia Tedesco

Honors Theses

In light of the current global amphibian extinction crisis from threats such as climate change and disease, reliable and repeatable sampling methods carry heavy importance for assessing North American salamander species.

Bartonella And Y. Pestis Screening In Ctenophyllus Armatus Terribilis For Conservation Application For The America Pika (Ochotona Princeps) In The Rocky Mountain Front Range, Hilary Rinsland

Honors Theses

As temperatures continue to disproportionally increase in alpine regions due to climate change, parasite spillover from increased pika-rodent contact could bring new diseases to a susceptible alpine specialist, the American pika (Ochotona princeps). Fleas collected from pika at four alpine and subalpine study sites in Boulder County, Colorado from 2011-2017 were screened for Y. pestis and Bartonella using conventional PCR methods. This is the first study to detect Bartonella in the American Pika flea Ctenophyllus armatus terribilis and to propose the presence of B. grahmii in the alpine region of the Rocky Mountains.

Interactions Between Two Key Amphibian Defenses To Batrachochytrium Dendrobatidis In Panamanian Glass Frogs (Espadarana Prosoblepon), Andi Levorse

Honors Theses

Research on the amphibian pathogen Batrachochytrium dendrobatidis (Bd), the causative agent of the lethal disease chytridiomycosis, has advanced from assessments of pathogenicity and species susceptibility to more specialized questions concerning the complex interactions between the pathogen, species-specific immune responses, and the environment. Our work examines the potential for interactions between the two most important innate immune defenses of frogs against Bd: secretions of antimicrobial peptides and communities of commensal cutaneous bacteria. While both defenses have been studied individually, little data are available to examine interactions between these defenses. We conducted our study with field captured Panamanian glass frogs …

Community Structure Of The Microbiome Of Ixodes Scapularis In Relation To Sex, Stage, Lineage, And Geography, Christopher Lee Clark

Honors Theses

This study sought to fill these gaps of knowledge ticks as a model species. Based on the known information on the microbiome of vectors, and ticks more specifically, I sought to answer two prominent questions: are there relationships between the microbiome of individual ticks and do ticks from different sexes or life stages have variance in their microbiomes? In reference to my first question, I hypothesized that ticks coming from the same lineage, being the males, 7 Community Structure of the Microbiome of Ixodes scapularis females, and resulting eggs, would have a more similar microbiome to each other than to …

Understanding The Structural Basis Of Sike Interactions, Alice Catalano

Honors Theses

Tank Binding Kinase 1 (TBK1) acts as a catalytic hub in the regulation of numerous immune signaling pathways. Suppressor of IκB Kinase ε (SIKE) was recently characterized as a substrate of TBK1 whose binding properties are modulated by phosphorylation state, but very little is currently known about its function. However, because SIKE is known to form a dimer with itself, previous work generated a list of potential SIKE partners based on other proteins that contain sequences homologous to SIKE. Here, computational models of four potential SIKE partners, Heavy Chain myosin, tubulin, Beta Catenin and Ezrin, were generated and docked with …

Characterizing Borrelia Burgdorferi In Virginia : Lyme Disease Prevalence As A Matter Of Bacterial Genetic Variation, Hannah Cornman

Honors Theses

yme Disease (LD) incidence and spatial distribution has grown dramatically in the past 20 years. In Virginia, the growth has been especially drastic, primarily in the Western part of the state. This research project investigates how genetic variability of the Lyme Disease causing bacteria, Borrelia burgdorferi, might be contributing to this increase in LD incidence in western Virginia. To do this, B. burgdorferi samples were isolated from ticks found across the state and were characterized by multilocus sequence typing (MLST). Phylogenetic and minimum spanning tree analyses were also performed. It was hypothesized that the increasing number of Lyme disease infections …

The Progression Of Lyme Disease In The State Of Virginia, Margaret Michel

Honors Theses

Lyme disease has spread in the United States from the northeast to more southern and western parts of the country. It has been shown that the tick which most often carries the Lyme disease pathogen (Borrelia burgdorferi) in North America, Ixodes scapularis, has also spread to these new areas of concern. In Virginia, the disease has progressed from the eastern shore to the western, more mountainous regions. Through obtaining historical museum specimens of mice from 11 locations in Virginia, we seek to determine whether the Lyme disease causing pathogen, B. burgdorferi, has always been present in …

Computational Studies Of Paradifluorobenzene Cations And Hydrogen Cyanide Molecule, John C. Rowe Iv

Honors Theses

Polycyclic aromatic hydrocarbons (PAHs) are hypothesized to comprise a significant portion of interstellar carbon identified from the Diffuse Interstellar Bands (DIBs). Gas phase cation-molecule reactions between compounds that previously existed as weakly bound species provides the best explanation for the emergence of PAHs in the interstellar medium (ISM). In this work, we use computational methods to characterize one of these weakly-bound systems. We discovered that intramolecular charge distribution (calculated using the Natural Population Analysis) dictate the complexes formed between a paradifluorobenzene cation and either one or two HCN molecules. Additionally, the relative stabilities of the complexes and the binding energies …

Characterization Of Catecholamine Receptors And Transporters In Murine Macrophages, Elizabeth Gonye

Honors Theses

Macrophages are a critical part of the immune response. When circulating monocytes move into tissues they differentiate int macrophages to mount the first line of defense against pathogens.

Impact Of Vector Range Expansion On Pathogen Transmission Dynamics Of Lyme Disease In Southwestern Virginia, Bishan Bhattarai

Honors Theses

Blacklegged ticks, Ixodes scapularis is the primary vector of Lyme disease in eastern United States. Borrelia Burgdorfei, the etiological agent of Lyme disease is transferred by ticks of Ixodes species. In recent years, its congener, Ixodes affinis has been expanding its range northwards from its southern population. We were interested in studying how the introduction of this new vector affected the interaction between the pathogen genotype and the host. We hypothesized that differential host use by I. affinis and I. scapularis would partly explain observed differences in B. burgdorferi infection prevalence and genotypic structure in southeastern Virginia. The result …

Host-Specialization Of Bartonella In Flea Vectors Collected From Black-Tailed Prairie Dogs, Mark D. Massaro

Honors Theses

At least 22 species of Bartonella bacteria have been named and many are associated with one of a list of potential mammalian reservoirs and arthropod vectors. One example of such a system is the parasitism of black-tailed prairie dogs (Cynomys ludovicianus) of the Western U.S. by Oropyslla hirsuta and Pulex simulans fleas. These vectors are thought to maintain B. washoensis infection in these mammals, but little is known about their role in the specialization of this strain to this reservoir. We found that the more specialist O. hirsuta fleas were much more likely to be infected with B. washoensis than …

Potent Mutagens Have Positive And Negative Effects On Viral Fitness Of Reovirus In Vitro, Jennie Altman

Honors Theses

Due to the inherently error-prone nature of RNA replication, mutations to genomes of RNA viruses occur frequently and accumulate. We hypothesized that RNA versions of nucleoside analogues that increase mutation rates in DNA could cause increases in the mutation rate of a model RNA virus, Reovirus, and decrease the fitness of the virus in vitro due to the accumulation of deleterious mutations. After conducting multiple passages of Reovirus in mouse L929 cells in the presence of these potential RNA mutagens in four separate trials, there were not only virus samples with the expected decreased infectivity, but surprisingly, samples with marked …

Exploring The Role Of Sonic Hedgehog In The Lymph Heart Development Of Xenopus Laevis, Laura Barry

Honors Theses

Xenopus as a Model Organism in Evolutionary Developmental Biology

Xenopus laevis, the African clawed frog, is an important model organism in the field of evolutionary developmental biology research. These tongue-less aquatic frogs are basally branching anuran amphibians that display marked sexual dimorphism and have webbed hind feet that sport several small, sharp claws. This species is a useful model organism despite its long generation time and genomic complexity, for historical and practical reasons. The animal adapts well to housing in a laboratory setting, and its reproduction can be …

Characterizing The Role Of Pax And Six In An Emerging Model System, The Freshwater Sponge, E. Muelleri, Ian P. Winters

Honors Theses

Sponges can be viewed as a remnant branch of the earliest successful experiments in metazoan multi-cellularity. As such, these organisms hold many clues into the genetic elements fundamental to the formation of complex animalian life. Two of these elements are the transcription factor encoding genes PaxB and Six1/2. Homologs of these genes in animals more complex than sponges have been shown to be members of a gene regulatory network involved in organ development. This is of particular intrigue since sponges do not possess such organ systems. Here, I discuss the putative function of PaxB and Six1/2 in sponges, and whether …

Sponges Of The Caribbean: Linking Sponge Morphology And Associated Bacterial Communities, Ericka Ann Poppell

Master's Theses

The ecological and evolutionary relationship between sponges and their symbiotic microflora remains poorly understood, which limits our ability to understand broad scale patterns in benthic-pelagic coupling on coral reefs. Previous research classified sponges into two different categories of sponge microbial associations: High Microbial Abundance (HMA) and Low Microbial Abundance (LMA) sponges. Choanocyte chamber morphology and density was characterized in representatives of HMA and LMA sponges using scanning electron microscopy from freeze-fractured tissue. Denaturing Gradient Gel Elextrophoresis was used to examine taxonomic differences among the bacterial communities present in a variety of tropical sponges. The results supported the hypothesis that choanocyte …

Characterization Of Microbial Community Structure In The Octocoral Leptogorgia Virgulata, Blair E. Armistead

Honors Theses

The process of spicule formation in L. virgulata results in a drop in pH, which, if left unregulated, could lead to demineralization and subsequent animal death. Carbonic anhydrase has been suggested as a possible pH regulatory mechanism in L. virgulata tissues. This study focuses on an additional hypothetical mechanism of pH regulation involving the production of urease by endosymbiotic bacteria living within L. virgulata tissue. PCR and DGGE are used as culture-independent methods to characterize facets of microbial community structure on L. virgulata in order to identify one …

Xenopus Laevis Transgenic Lines And Their Use In The Study Of Lymph Heart Musculature Development, Diana M. Filtz

Honors Theses

Lymph hearts are pulsatile organs present in lower vertebrates that propel lymph throughout the body and into the venous system, assisting in the maintenance of fluid homeostasis. In organisms such as frogs, several pairs of lymph hearts develop amidst the somites during the early tadpole stages. Due to the unique structure and function of lymph heart musculature—exhibiting characteristics of both skeletal and cardiac muscle—the origin of these cells remains highly controversial. Studies have found that in Xenopus, the engrailed gene is expressed explicitly in lymph heart muscle cells throughout development. Through designing a transgenic …

Adrenergic Receptor Expression On Raw264.7 Macrophages, Lindsay Ward

Honors Theses

In this study, AR surface expression patterns and regulation via AR-catecholamine interactions were characterized. Macrophage function was shown to be regulated by catecholamines through both Alpha- and Beta-ARs, as evidenced by corresponding alterations in cytokine production. Treatment of activated macrophages with NE, a general catecholamine, or fomoterol, a P-AR agonist, produced significant decreases in TNF and IL-6 secretion. The effecis of clonidine, an Alpha-AR agonist, produced less consistent results, but clonidine-mediated enhancement of cytokine secretion appears to be mediated by Alpha-AR signaling. LPS was shown to noticeably change the surface expression ofboth types of ARs in RAW264.7 macrophages. However, NE …

Exploring The Role Of Iscsua And Suf Operon In Shigella Flexneri Invasion And Resistance To Oxidative Stress, Benjamin R. Lloyd

Honors Theses

Shigella flexneri is a facultative intracellular pathogen capable of causing dysentery, a condition that afflicts many around the world, especially in developing countries. There are several aspects of Shigella pathogenesis that are not well understood, including a number of genetic and cellular changes that allow Shigella to adapt to stresses encountered while invading and replicating within the eukaryotic cytosol. It was the goal of this research to examine the roles of iscSUA and suf, gene systems predicted to encode for iron-sulfur cluster biosynthesis proteins, in Shigella surviving exposure to oxidative stress agents and during Shigella invasion and plaque formation …

Use Of Phylogenetic Stains To Determine The Feeding Preferences Of Microbivorous Soil Nematodes, E. Harlan Michelle

Honors Theses

Due to their numerous and diverse roles in soil ecological processes – most notably decomposition and nutrient mineralization – nematodes have long been recognized as important biotic indicators of soil health (Ekschmitt et al., 2001; Ritz and Trudgill, 1999). The predominate means of assessing the information that these organisms might contain has been through nematode community analyses, a methodology that seeks to convert the vast amount of data regarding features such as diversity, maturity and richness into a series of indices which can be used to evaluate soil health and make comparisons across samples. Performance of these analyses typically involves …

Characterization Of Sox Family Members In Sponge Stem Cells And During Development, Karen E. Leeds

Honors Theses

Sponges are considered the oldest and most basal part of the metazoan lineage and therefore possess a unique set of gene families that are highly conserved among all animals. One of these gene families is known as Sox transcription factors. Sox genes are known to play important roles in complex animals such as the specification of the primary layers of the body, determination of sex, and most recently induction of induced pluirpotent stem cells (iPS cells) from both human and mouse fibroblasts with the help of three other transcription factors. We have found that two different demosponge species Halichondria bowerbanki …