STEM

My research contributed to a Virginia Institute of Marine Science (VIMS) led project that seeks to explore the effectiveness of using a Living Shoreline technique to manage coastal wetlands. Living Shorelines use native plant species and less abrasive designs to better preserve the natural marsh conditions while still controlling tides from adjacent bodies of water. Our team of researchers used large fishing nets set at various locations to examine the difference in species diversity, sizes, and demographics across three varieties of sites: living shoreline, natural marsh, and bulkheads (rock walls built to break incoming tides, typically at the expense of the wildlife behind them). My area of focus is examining crustacean populations caught in our nets,  aggregating and analyzing all of the shrimp data collected throughout July, August, and September. We anticipate gathering strong evidence to support the proposed hypothesis that living shorelines do successfully maintain the diversity and strength of the wildlife found on natural wetland shores.

Student Major(s)/Minor: Biology and ENSP double major

Advisor: Randy Chambers, Biology

Eukaryotic cells experience abiotic stressors that threaten the stability of proteins, causing misfolding and aggregation that damages cell tissues. Cells protect against this damage through increased attachment of small ubiquitin-like modifiers (SUMO) to proteins during cellular stress, a process called the SUMO stress response (SSR). The SSR is mediated by the dimerization and inactivation of Ulp1, a protease that removes SUMO from proteins. Ulp1 dimerization can be visualized by splitting green fluorescent protein (GFP) into two substituents and attaching those to Ulp1 proteins. Once Ulp1 dimerizes, GFP substituents colocalize and fluoresce, illuminating the interaction. This is the split-GFP approach. Funding from this grant will be used to procure restriction enzymes, ligation reaction reagents, electrocompetent cells, and plasmid sequencing. The continuation of my research in the Kerscher lab through this grant could result in publication of a peer-reviewed journal article, which would greatly aid me in my post-graduate and career studies.

Student Major(s)/Minor: Biology

Advisor: Oliver Kerscher, Biology

Tourism is a major aspect of economies around the world, and many developing countries rely on tourism as a primary source of income. However, whether coastal tourist activity has a significant positive or negative impact on coral reefs and the surrounding environment is unclear. This project explores previous research as well as economic and environmental data to determine if there is a significant link between an area’s economic dependence on tourism and the environmental impact that an area causes, more specifically taking a look at coral reefs. If a significant linkage is found, this project will also explore public policy measures that can be taken to balance an area’s economic and environmental health. Given the results, further research recommendations will be given to help bolster sustainable ecotourism.

Student Major(s)/Minor: CAMS Applied Statistics

Advisor: Sarah Stafford, Economics

In the sperm-producing gonad of C. elegans, cells are cytoplasmically connected by a rachis. Such connections are highly conserved across animal species, including humans. In C. elegans, the rachis of oocyte and sperm producing gonads are similar during mitosis, but diverge during meiotic prophase. ANI-2, a shortened version of the annillin protein ANI-1, maintains the cytoplasmic connections in the rachis. Here, we examine the male rachis structure and the role of sperm-specific proteins in its formation. ANI-2 immunofluorescence and actin staining showed 1) sperm specific features occur during meiotic prophase, coinciding with sperm specific production 2) rachis structure is independent of sperm size 3) ANI-2 is required for rachis structure in both oocyte and sperm producing gonads whereas the kinase SPE-6 is sperm-specific and 4) differences in rachis structure reflect the gamete and not the somatic sex. Further research should explore spermatogenic specific features of the rachis and its regulators.

Students Major(s)/Minor: Quilla: Biology, Rosemary: Biology major, Chemistry minor 

Advisor: Diane Shakes, Biology

This research examines trust in large language models (LLMs) for software engineering tasks, addressing three key questions: the definition of trust, the antecedents of trust, and the trust measurement. Utilizing a combination of literature review and survey study, we explored existing literature to find that trust needs to be better contextualized in this domain. Our survey, conducted with developers having varying levels of software engineering and LLM experience, revealed a general reluctance to trust LLMs over human input. Preliminary findings indicate a high demand for LLMs to exhibit clear trustworthiness cues to assist users in evaluating their reliability. The implications of this research suggest that enhancing LLMs' ability to demonstrate trustworthiness can significantly improve their acceptance and utility in software engineering. This study provides insights for developers and researchers aiming to enhance trust in AI-driven tools within the software development process.

Student Major(s)/Minor: Computer Science

Advisor: Yixuan Zhang, Computer Science

Taro (Colocasia esculenta L.) is a plant that originates from Southeast Asia and is now prevalent throughout the Pacific Islands. Poi is a food product with strong cultural connections and is made from macerating and fermenting steamed taro. This study aimed to observe changes in fresh to aged commercially purchased poi using comprehensive two-dimensional gas chromatography-quadrupole mass spectrometry with flame ionization detection (GC×GC-qMS/FID). Samples were prepared according to package instructions, extracted via headspace SPME Arrow, and analyzed in replicates of 10. All brands showed a clear distinction between fresh and aged samples. While Hanalei and Taro brand poi had similar profiles, He Mea Ono brand poi differed substantially. Visual distinctions in chromatographic plots were supplemented by principal component analysis (PCA) and volcano plots, identifying distinguishing compounds. Investigating the profile of poi via GC×GC-qMS/FID can enhance understanding of its unique qualities, historical context, and contemporary uses. 

Student Major(s)/Minor: Biology and Chemistry

Advisor: Katelynn Perrault, Chemistry

This study provides a comprehensive review of the use of sensors in the passive detection and prediction of social anxiety, anxiety, and stress. By systematically searching the ACM Digital Library, IEEE Xplore, JMIR, and Frontiers using keywords such as "sensor," "passive detection," "prediction," "social anxiety," "anxiety," and "stress," 1590 relevant studies were initially identified. After applying further filtering criteria, including relevance, source credibility, and publication date, 27 papers were selected for detailed analysis. The selected studies were examined based on sensor types, physiological features, AI algorithms, experimental protocols, and anxiety references. Performance metrics across these studies ranged from 72% to 99.47%, with a pooled mean accuracy of 86.96% for 21 studies (77.78%). Subgroup analysis revealed that the effectiveness of using sensors to detect social anxiety, anxiety, and stress is influenced not only by the chosen features and algorithms but also by the experimental protocols, anxiety references, and sample size.

Student Major(s)/Minor: Computer Science

Advisor: Janice Zhang, Computer Science

The Virginia Piedmont is comprised of terranes accreted onto Laurentia during Paleozoic Appalachian orogenesis, but key aspects of these terranes’ metamorphic history remain poorly understood (Bailey & Owens, 2012). The Chopawamsic terrane, an Ordovician volcanic island-arc metamorphosed to amphibolite facies (~600ºC, ~6 kbar), contains kyanite quartzites with an unusual assemblage of quartz and kyanite (Owens & Pasek, 2007). In this study, I document kyanite textures using cathodoluminescence (CL) imaging and constrain pressure-temperature (P-T) metamorphic conditions recorded across the terrane using Ti-in-quartz and Zr-in-rutile geothermometry. CL imaging of kyanite reveals (1) core-rim zoning patterns with CL-dark cores and CL-bright oscillatory rims, and (2) kyanite with no core-rim structure. Preliminary geothermometric data support amphibolite facies P-T conditions. Next steps include application of U-Pb petrochronology to constrain the timing of (1) igneous/hydrothermal protolith crystallization using small, <50µm zircons with core-rim structure, and (2) timing of kyanite quartzite metamorphism using monazite and rutile petrochronology.  

Student Major(s)/Minor: Geology

Advisor: Clem Hamelin, Geology

Patterns in Hillslope Asymmetry are used to identify the primary force driving erosion in Virginia’s Coastal Plain region. Remote sensing observations at a broad scale quantify the trends in Slope-Aspect across this landscape, determining to what degree the steepness of a slope is influenced by the aspect, or cardinal direction it faces. Slope-Aspect relationships are further investigated with a series of soil samples from undeveloped public lands in the Virginia Coastal Plain. Assessments of characteristics such as sediment composition, carbon content, and degree of chemical weathering provide insight into how asymmetric hillslopes impact soil production. By combining sample analysis and mapping, this study will determine if latitude, underlying geology, or other factors influencing microclimate have the most significant impact on erosional processes. Results will display how the Coastal Plain changes over time, which can assist public and private land management sectors with decision making for conservation and infrastructure. 

Student Major(s)/Minor: Geology and Environment & Sustainability, Public Policy Concentration

Advisor: Joanmarie Del Vecchio, Geology

Synucleinopathy dementias (Syn-dementias) are a group of neurodegenerative diseases characterized by the neuronal accumulation of alpha-synuclein (aSyn)-rich inclusions termed Lewy bodies (LBs). Although LBs are best associated with Parkinson’s disease (characterized by nigrostriatal dopamine neuron degeneration), they are far more common in Syn-dementias, which includes Dementia with Lewy Bodies (DLB), and ~40-50% of Alzheimer’s disease cases. Research has shown that microglia-mediated neuroinflammation is prominent in Alzheimer’s disease, DLB, and other Syn-dementias. Recent findings have provided insights into microglia-mediated neuroprotective/immunopathological signaling in Alzheimer’s disease, but the mechanisms linking microglial responses to DLB-related aSyn aggregation are less understood. The hyperactivation of The Stimulator of Interferon Genes (STING) pathway, an innate immune signaling complex initially known for initiating inflammatory antiviral program via type-I interferon (IFN) signaling, has been shown to contribute to neurodegeneration in PD and DLB models, but the mechanisms and consequences of STING assembly contribute in DLB-associated neurodegeneration remain uncharacterized. Our preliminary data utilizing cultured murine and human iPSC-derived microglia, the aSyn pre-formed fibril (PFF) model and postmortem DLB brain tissue indicate crosstalks between Nod-like Receptor Protein-3 (NLRP3) Inflammasome activation and cGAS/STING activation in microglia. This project also focused on the role of the protein Gasdermin D (GSDMD), which when cleaved by activated caspases in the inflammasome, forms pores in the mitochondrial membrane, leading to the release of pro-inflammatory cytokines such as Interleukin-1β (IL-1β) and cell death. Understanding these mechanisms may lead to new therapeutic strategies for Syn-dementias.

Student Major(s)/Minor: Neuroscience and Data Science

Advisor: Paul Kieffaber, Psychological Sciences

Helicobacter pylori is a bacterium that affects more than half of the world’s population and persistently colonizes the human stomach, an acidic environment inhospitable to most bacteria. Infection with this bacterium is a risk factor for the development of gastric ulcers, gastritis, and gastric cancer. The hypothesis that this project investigates through computational and wet lab methods is that DNA methylation, the addition of a bulky molecule to bases of an organism’s DNA, contributes to its infectious ability. Using data analysis tools, we found changes in methylation patterns in H. pylori grown in different acidities and when the ability for the bacterium to sense acid is removed. We also hope to confirm that one methylation site in the gene encoding nikS, a small RNA regulating genes involved in the infection process, is critical for this gene to be expressed. This is done by converting an experimental mutant back to its original wild type DNA sequence.

Student Major(s)/Minor: Biology and CAMS Mathematical Biology

Advisor: Mark Forsyth, Biology

A preordered set P, or proset, is a set with binary relation ⪯ that is reflexive and transitive. Corresponding to each proset is a matrix Lie algebra whose entries are determined by the relations of the proset. This project focuses on calculating the index– an important, but generally difficult to compute, Lie-algebraic invariant– of Lie proset algebras using combinatorial methods. By comparing index values to certain directed graphs and permutations associated with Lie proset algebras, we were able to develop methods to predict the index of certain families as well as construct index-realizing functionals.

Student Major(s)/Minor: Math

Advisor: Nicholas Russoniello, Math

Mild traumatic brain injury (mTBI), or concussion, is usually caused by head impact or violent shaking. While symptoms like headaches and confusion often resolve quickly, longer-term issues such as mood disorders and cognitive decline are major public health concerns.

Regulatory T cells (Tregs) play an neuroprotective, reparative, and analgesic role in the brain following brain injury. This study investigated how low-dose interleukin-2 (IL-2), known to increase Treg levels, affects mTBI recovery.

 A controlled cortical impact model of mTBI was made by dropping 75g weights from 15 inches onto adult mice head under general anesthesia, followed by intraperitoneal injections of low-dose IL-2 or vehicle control. Immunohistochemical analysis of spinal trigeminal nucleus revealed significantly increased Treg cell numbers in IL-2-treated mice compared to controls.

The findings suggest low-dose IL-2 therapy could be a novel approach to reduce neuroinflammation and promote mTBI recovery by modulating Treg cells in key brainstem regions.

Student Major(s)/Minor: Undecided

Advisor: Yu-Qing Cao and Tingting Guo, Anesthesiology

The study of polarized Helium-3 targets for use in nuclear physics experiments often employs topics in atomic physics. An example is the Voigt effect, which occurs when light is moving perpendicular to a magnetic field in a material. This project seeks to determine if the polarization of a dense alkali gas can be calculated using the Voigt on a weak probe beam, as a method of measurement. To do this, principles in quantum mechanics were used to find how the atoms responded to the laser, which is dependent on their polarization. Then, these results were used to discover the effect on the probe beam’s polarization angle as it passes through the gas. These relationships demonstrated that the Voigt rotation angle has an approximately quadratic dependence on the polarization of the alkali. Further experimentation is needed to determine the feasibility of this method as a tool for measurement. 

Student Major(s)/Minor: Physics and Math

Advisor: Todd Averett, Physics

Rake marks and scars on the surface of a dolphin's skin can be indicative of behavioral patterns and disease risk; however, analysis of such marks is inefficient using purely manual means. The aim of this project was to create machine learning models that can detect patterns of rake marks or scarring on dolphins found in the Potomac River and Chesapeake Bay. Models were trained using the website Roboflow, and tested on a set of 366 images of 220 dolphins sighted between 2015 and 2017. Present models can detect rake marks with reasonable accuracy, and more work can be done to distinguish between fresh rake marks, healing rake marks, and other scars. This work has produced a tool that can be used to improve the efficiency of analyzing rake marks in dolphins and allows other researchers to make more rapid assessments of dolphin behavior and health.

Student Major(s)/Minor: Biology and Marine Science

Advisor: Mei Zhang, Computer Science

Nuclear magnetic resonance (NMR) relaxometry is a powerful tool in material analysis and kinetics. Its data can be described as an exponential decay that depends on the “spin-spin relaxation time constant” T2, a parameter that characterizes a material’s NMR behavior. Two methods, the inverse Laplace transform and the matrix pencil, have been developed to quantify the number of unique T2s. However, both of these methods require human intervention, such as the assignment of smoothing constants, which does not allow for confident and reproducible results. This project utilizes two machine learning methods to determine the number and character of contributing T2s from relaxometry data. These methods include a Markov Chain Monte Carlo algorithm and a sparsity matrix approach. By showing that these methods converge onto a single answer, this project offers a reproducible and systematic way of analyzing T2s from NMR relaxometry data.

Student Major(s)/Minor: Chemistry Major and Data Science Minor

Advisor: Tyler Meldrum, Chemistry

In vascular physiology, the molecule that causes arteries to constrict is called norepinephrine (or noradrenaline), with an analogous molecule, phenylephrine, often being used in models to study vasoconstriction. In opposition, acetylcholine is the molecule that induces dilation of the blood vessels both in the human body and in studies. This research focuses on finding the concentration at which each of these molecules adequately induces constriction or dilation, respectively, in the arteries of two different strains of mouse models (HET3 and C57). This was done by treating these arteries with a series of increasing doses of phenylephrine and a subsequent series of increasing acetylcholine doses, monitoring changes in the vessel's diameter with each new dose. This process was repeated in male and female mice of the two different species strains. Analysis of the collected data suggested no significant difference in the effective concentration for vasoconstriction but a significant difference (p&lt;0.05) in the effective concentration for vasodilation between the two strains of mice. These findings are important for guiding further vascular research in terms of experimental design and animal modeling. 

Student Major(s)/Minor: Kinesdiology Major and Psychology Minor

Advisor: Robin Looft-Wilson, Kinesiology

As organizations increasingly move their data to cloud object storage, they must also contend with a growing number of threats to the confidentiality of that storage. While cloud service providers (CSPs) offer their customers many options for encrypting their data, these options all encrypt the data cloud-side, providing customers little protection from an insider attacker, legal injunctions on the CSP to disclose data, or an attacker exploiting a bug in the CSP’s storage stack.

We present the design and implementation of AKESO, a cloud storage system that achieves post-compromise security of a customer’s data, and thus regains data confidentiality after an encryption key compromise. AKESO adapts the Asynchronous Ratcheting Tree protocol from messaging applications to establish and rotate a group storage key for client-side encryption. On a key rotation, AKESO leverages cloud tools to autoscale the re-encryption of a cloud bucket. We evaluate the performance and cost of AKESO under a set of diverse workloads that reflect real-world bucket usage. Our results show that AKESO’s performance is comparable to existing cloud storage encryption offerings with weaker security, and that customers can choose an AKESO configuration that meets their performance and budget goals.

Student Major(s)/Minor: Computer Science Major and Japanese Minor

Advisor: Stephen Herwig, Computer Science

This presentation describes the production process, application, and characterization of Didymosphenia geminata (Didymo) based biomaterials. Our project outlines a chemical molding process to create samples that exhibit low thermal conductivity, high porosity, and low density. These properties allow the samples to absorb oil and deflect heat, which are use cases typically absent from carbon-negative materials. We achieve a more sustainable approach when compared to conventional material production, which requires excessive amounts of CO2 and energy to produce. Along with material sample production, characterization of the extracellular matrix through spectroscopic methods and high resolution imaging provides insight into the chemical background of the novel material properties. 

Student Major(s)/Minor: Brian: Physics and Computer Science Major, Jonah: Biology Major and Applied Science: Bioengineering

Advisor: Hannes Schniepp, Applied Science

Prompt engineering is the process of curating inputs to Large Language Models (LLM) so as to guide or study its responses. This paper will examine the religious biases for Atheists, Buddhists, Christians, Jews, Muslims, and Sikhs, in ChatGPT-3.5 and its ability to identify such biases through the use of statistical analysis of prompt responses. Prompt engineering is required because biases are not intentionally programmed into an LLM such that it would be an inherent property. Instead, biases emerge as the model is trained on vast datasets of language requiring more circumspect methods to statistically measure the bias for or against particular religious groups. After providing broad prefix prompts, the first phrase(s) of narrative action performed by a religious person, the model’s completion of the prompt is classified using a strict definition of bias. This paper additionally asks ChatGPT to self-classify responses to more precisely study its ability to identify bias present in its own responses, and allow comparison between human and LLM classification of bias.

Student Major(s)/Minor: Computer Science

Advisor: Yanfu Zhang, Computer Science

The C57Bl/6J mice have been the premier model for Vascular Physiology research, especially myoendothelial feedback studies. A new model, Het-3, is more genetically diverse and robust. This research aims to compare the myoendothelial feedback response between Het-3 and C57Bl/6J mice to determine if Het-3 can serve as a new model. Both male and female Het-3 and C57Bl/6J mice were tested. Mesentery arteries were extracted and preserved in a buffer solution. These arteries underwent Western Blot procedures to quantify protein expression, focusing on eNOS (nitric oxide), essential for artery relaxation after phenylephrine-induced constriction. eNOS levels were compared to total protein and GAPDH, a housekeeping gene. The anticipated outcome is that Het-3 mice will show similar eNOS levels as C57Bl/6J, suggesting Het-3's suitability as a new model due to their similar response. This model may also better represent human myoendothelial feedback because of its genetic diversity and similar vascular system.

Student Major(s)/Minor: Kinesiology Major and Chemistry Minor

Advisor: Robin Looft-Wilson, Kinesiology

This project explored the incorporation of photocrosslinking amino acids into human proteins that are key to cancer metastasis. While the body can only naturally incorporate 20 different amino acids, this project will explore the synthesis and genetic engineering of custom amino acids that are tailored to introduce new functionality into the protein. In this case, we synthesized two amino acids called pBETpF and pBPrpF that have both site-specific handles to attach fluorophores and photocrosslinking properties, allowing for these proteins to bind to target proteins in the presence of ultraviolet light. This allows investigators to further study the interactions between human receptors such as MEMO and their roles in cancer metastasis. By synthesizing these amino acids and attaching fluorophores onto them and further photocrosslinking them to cancer cell lysates, we can better identify the mechanism that allows cancer to attach to healthy tissue.

Student Major(s)/Minor: Chemistry Major

Advisor: Douglas Young, Chemistry

Over the summer, I planned and constructed a new type of amplifier for a laser that rapidly turns off and on. Through computational simulation and experimental construction, I created a working design for the amplifier, allowing the output signal high voltage to be controlled and the output signal low voltage to be .2 millivolts. Because I built this amplifier, my lab will have a faster method to turning off the laser--a shutter gate may take 10 milliseconds, while my amplifier does it in 2--and they will be able to easily regulate the voltage of the input laser. My lab uses a laser to cool atoms down to under 1 Kelvin, and my amplifier will aid in their research. 

Student Major(s)/Minor: Physics major, Creative Writing minor

Advisor: Seth Aubin, Physics

This study addresses which mouse model better represents human cardiovascular function: the genetically diverse Het-3 or the commonly used, genetically uniform C57Bl/6J. We compare vasomotor responses in mesenteric arteries from both models using L-NAME, a nitric oxide synthase (NOS) inhibitor. We hypothesize that L-NAME will significantly reduce endothelial nitric oxide synthase (eNOS) activity by inhibiting the communication between endothelial cells and smooth muscle cells, leading to decreased vasodilation. However, slight residual vasodilation is expected due to alternative mechanisms, such as hyperpolarization of the arterial walls. By evaluating the variability in responses between the two models, we aim to determine whether Het-3 mice, with their greater genetic diversity, offer a more accurate model for human cardiovascular research. Our findings could have significant implications for the development of cardiovascular treatments that are more representative of diverse human populations.

Student Major(s)/Minor: Kinesiology Major with Concentration in Public Health and Biochemistry Minor

Advisor: Robin Looft-Wilson, Kinesiology 

The thyroid hormone receptor (TR) regulates the expression of genes important for development and metabolism in response to thyroid hormone. Chemical modification of TR by the addition of acetyl groups provides another level of regulation of this cell signaling pathway. the receptor. This project will explore the impact of Histone Deacetylases (HDACs), enzymes that remove acetyl groups, on localization patterns of TR. The results will help add to the growing body of research explaining the biological significance of deacetylation and acetylation of TR on its shuttling patterns and function.

Student Major(s)/Minor: Biology

Advisor: Lizabeth Allison, Biology

Ghost forests are areas of standing dead forest along coastlines that emerge when soil is inundated with salt water from sea level rise and increased storm surges. Traditional strategies of identifying ghost forests rely on remotely sensed data, most often in the form of NDVI (a commonly used vegetation health index). Here, we test similar traditional methods of classifying ghost forests in the Virginia coastline using satellite data products such as NDVI and additionally include predictions of sea level rise and data products from ECOSTRESS, a satellite that produces data related to land surface temperature and evapotranspiration. We are able to validate known locations of ghost forests with both the traditional NDVI method and our developing methodology using additional indicators. We also identified areas at risk for ghost forest transformation in several study areas, which is critical for future coastal mitigation and conservation efforts.

Student Major(s)/Minor: Data Science & ENSP 

Advisor: Dom Ciruzzi, Geology

This study explores the effects of dispersal on population dynamics in a fragmented, density-dependent environment. We analyze how migration between habitat patches influences total population abundance using a coupled differential equation model with Allee effect growth rate. By varying the dispersal rate, we identify three distinct outcomes based on different growth rate scenarios. Our analysis, using differential equations and bifurcation diagrams, reveals that low dispersal rates may decrease population size, while higher rates can either increase or stabilize it depending on specific thresholds. These findings provide insights into when habitat fragmentation and dispersal are beneficial or detrimental, with potential implications for conservation strategies in fragmented ecosystems.

Student Major(s)/Minor: Mathematics & Computer Science

Advisor: Junping Shi, Mathematics

This project investigated the effectiveness of certain conjugated diynes (two triple bonds connected by a single bond) as antibiotics. Over time, bacteria are becoming more and more resistant to current antibiotics. Medicine must evolve quickly to keep up with this ever-increasing rate of resistance, otherwise mortality rates due to infections will dramatically rise. However, pharmaceutical companies are not yet financially motivated to develop antibiotics with new mechanisms of action. Conjugated diynes have promising chemical properties that have been shown to be biologically active, potentially presenting new pathways for antibiotic development. This project explores how these chemicals are cytotoxic to bacteria by making minor alterations to the structure of bioactive diynes, with the goal of increasing drug potency. A selection of diynes was synthesized with a similar basic structure, with alterations to the length of the molecule and the presence of various functional groups. Other diynes were also tested for efficacy as part of an ongoing collaboration. 

Student Major(s)/Minor: Chemistry & Data Science

Advisor: Douglas Young, Chemistry

Phosphatases are important enzymes that dephosphorylate phosphorylated proteins and have important roles in many cellular signaling pathways linked to various diseases such as cancers. Phosphatases with genetic mutations within their active signature motif and/or essential motifs that determine their catalytic activity are termed pseudophosphatases. The protein tyrosine pseudophosphatase, serine/threonine/tyrosine-interacting-like protein 2 (STYXL2), has a mutation of H224S and C225S in its catalytic active motif. STYXL2 has been suggested to play a role in paralysis despite these mutations, which result in lack of catalytic activity. To compare STYXL2 to its active counterparts, bioinformatic analysis was used to visualize 3-D images and analyze the amino acid interactional differences that influence each respective protein structure. STYXL2’s active signature motif was “restored” by mutating S224H and/or S225C. PyMol showed no change in STYXL2’s AlphaFold and I-TASSER predicted protein structure and POCASA binding pocket, despite these mutations simulating its catalytic activity being “restored.” However, p-nitrophenol phosphate (pNPP) activity assays of wildtype STYXL2 and mutated STYXL2 suggested that mutations in the active motif comparable to active counterparts did not restore catalytic activity. Future studies will include understanding the wild-type STYXL2 and the mutant in cellular mechanisms. For example, investigating this lack of catalytic restorage in STYXL2 and its cellular impact and mechanisms may elucidate its roles in sarcomere assembly and myofibril formation. 

Biology major, sociology minor

Student Major(s)/Minor: Biology major, Sociology minor

Advisor: Shantá Hinton, Biology

Rationale/Purpose: This study will assess the effect of a one-time 24 hour fast on sleep indices, fatigue, heart rate, and physical activity.

Study Aim: To compare sleep, energy levels, and heart rate before, during, and 1 day after a 24-hour fasting period.

Methodology: Participants will wear the Polar biosensor watch 24/7 and answer questionnaires about fatigue at baseline, during a 24 hour fast, and for 24 hours following the fast.

Analysis: Multi-functional assessment of fatigue scale will be utilized to assess energy levels. Sleep architecture will be analyzed through the POLAR Flow application. Subgroup analyses will be conducted by gender, age, and fatigue level.

Implications:

Fasting has become a popular lifestyle trend and this study hopes to elucidate the impact fasting may have on energy and sleep dynamics.

Student Major(s)/Minor: Psychology & Music

Advisor: Stephanie Caligiuri, Kinesiology

Previous research indicates that higher resting hypoxemia at altitude increases the risk of acute mountain sickness (AMS). This study investigates whether short-term heart rate variability (HRV) measures can predict oxygen saturation during acute normobaric hypoxia equivalent to 4572 meters. We assessed 59 healthy young adults (20.67 ± 0.99 years; 31 female, 28 male). HRV was recorded for five minutes directly before hypoxia exposure. Subjects were exposed to hypoxic air (11.8% oxygen) for 10 minutes after a 10-minute baseline in room air, followed by a 10-minute recovery in room air. Significant correlations were found between changes in oxygen saturation during hypoxia and several HRV measures: LF/HF ratio (r = 0.411), LnLF (r = 0.378), and LnLF/HF (r = 0.573). No other HRV measures showed significant correlations. These results suggest that HRV metrics related to sympathovagal balance may predict oxygen desaturation and susceptibility to AMS.

Student Major(s)/Minor: Kinesiology & Biochemistry

Advisor: Brennan Harris, Kinesiology

This project outlines the synthesis of a polypyridyl phosphonic acid-functionalized iron complex for electrocatalytic proton and carbon dioxide reduction. The long-term goal of research in this field is to find and optimize catalysts that can use electricity to convert water and carbon dioxide into fuels and other more useful substances. This particular complex is a new version of pre-existing catalysts, with a donor ligand (the organic portion that connects to the metal) modified to feature a phosphonic acid group. Previous variants have only one oxyanion, but this one has two. Ideally, the presence of a second oxyanion will increase the rate at which the ligand binds and releases the metal, which correlates to more efficient production. This new catalyst will be subject to electrochemistry, which will test its abilities compared to older examples, once more of it is produced using the synthetic methods developed in this project.

Student Major(s)/Minor: Kinesiology Major & Data Science Minor

Advisor: William McNamara, Chemistry

Myoendothelial feedback is the process of vasodilation following sympathetic nerve-induced vasoconstriction of resistance arteries. By inducing vasoconstriction with phenylephrine in extracted mesenteric arteries, we observed and analyzed differences between strains and sexes in vitro. For this project, we compared the genetically diverse UMHET3 mouse strain to the inbred C57Bl/6J strain with the intention to evaluate which strain will serve as a more robust model for resistance artery studies. We found that UMHET3 male and female mice both showed a similar vasomotor response to C57Bl/6J mice while male UMHET3 mice showed a stronger response. This research contributes vascular response data and suggests that the UMHET3 strain is a valid model for future research. 

Student Major(s)/Minor: Connor: Kinesiology, Ethan: Kinesiology

Advisor: Robin Looft-Wilson, Kinesiology

The Baker's yeast Saccharomyces cerevisiae is used as a biomedical model organism to study pathogenic fungi. Aggregative traits in which yeast cells adhere to each other and surfaces are associated with virulence. In order to understand the genetic basis of virulence in fungi, we investigated 1000 S. cerervisiae strains for five aggregative traits. Each trait was quantified through an image analysis pipeline we developed. Using these results, we identified genetic variants underlying the five traits using genome-wide association studies (GWAS). The analysis uncovered a large number of significant single nucleotide variations, supporting a complex genetic basis to most aggregative traits. Our results show there exists broad phenotypic and genetic variation in aggregative traits across this large natural set of strains.

Student Major(s)/Minor: Biology & CAMS

Advisor: Helen Murphy, Biology

Lead is a common environmental pollutant with widespread effects across ecosystems; even sub-lethal exposure is detrimental to animal health and behavior.

The mating behaviors of songbirds—the intersection of countless physiological and cognitive processes—are a mark of population health. When lead interferes, male attractiveness is decreased through stunted song-learning and dulled physical features. There remains a lack of focus, however, on a female's choice of her mate, and how it is affected by lead exposure—we aim to fill this gap in understanding through a multi-part behavioral study.

Half of our zebra finch subjects are being exposed to sub-lethal lead levels longer than in any comparable laboratory study. Subsequently, mate choice behaviors of females will be observed to determine to what degree lead exposure impacts it.

We predict that lead exposure lowers females’ ability to select high-quality partners, which would imply a weakened sexual selectivity and decreased competitiveness of exposed populations.

Student Major(s)/Minor: Cara: Biology, Computational & Applied Mathematics & Statistics, Alexandra: Biology & Classics

Advisor: John Swaddle, Biology

This project explores a specific mutated region of the pseudophosphatase MK-STYX, and will take a closer look at how its structure correlates to its function[SH1] . An unmutated version (wild-type) of this protein [SH2] can carry out critical biological processes; however, a mutation in one of the regions of MK-STYX, called the KIM domain, makes MK-STYX unable to dock to the traditional protein complex to complete these processes. Western Blots and immunoprecipitations are the methodologies used to see how different mutations of the KIM domain react when introduced to the intended binding protein complex. It is hypothesized that there is a missing repeating sequence in MK-STYX’s KIM domain that results in a conformational change, causing the inability to dock traditional proteins. Having a deeper understanding of these pseudophosphatases is important because these proteins have shown to play key roles in disease formation when dysregulated, including various cancers, obesity, and diabetes.

Student Major(s)/Minor: Biology Major & Psychology Minor

Advisor: Shantá Hinton, Biology

Maternal bonding during prepubescence is influenced by the transmission and positive perception of chemosensory signals. Maternal preference of neonatal odor facilitates a bond that enables newborns to elicit affection and attention from their mother, whose odor provides a comforting effect that is similarly preferred by infants. Preference of body odor is a tool of kin recognition, which influences social and capital investment in support of its subject. The importance of olfaction extends to newborn social development, as maternal breast odor and body odor promote multisensory behavior and reduced separation distress respectively. Considering its importance, the implications of altered chemosensory communication in maternal bonding presents adversity to a mother’s investment into her child, and a neonate’s developmental health. A literature review will be conducted on the role and mechanism of olfaction and chemosensory communication with the goal of identifying a need for future research on its influence on adverse maternal bonding.

Student Major(s)/Minor: Neuroscience

Advisor: Catherine Forestell, Neuroscience

Tropical cyclones are one of the most deadly natural disasters among all the natural hazards in the US. In 2017, hurricane Maria swept through Puerto Rico and caused at least $90 billion in damage. Inspired by our disaster relief volunteering experience in Puerto Rico, we wanted to contribute to disaster relief strategies that are specific to Puerto Rico. To do so, we decided to build a building damage detection algorithm using data in San Juan, Puerto Rico, which accurately captures the architecture type in Puerto Rico and damage characteristics. We built our model on the existing machine learning model published by ESRI: Building Footprint Extraction, USA, and fine-tuned the model using high resolution satellite imagery in Puerto Rico. Our detection model achieved a much better accuracy compared to the original unmodified model, and our classification model also had a decent performance. We hope by making our models public, both first responders and researchers will be able to utilize the information to accomplish their disaster relief tasks.

Student Major(s)/Minor: Cathy: Computer Science & Psychology, Joshua: Economics & Computer Science, Alisa: Data Science & Business Analytics

Advisor: Karinna Nunez, VIMS(Virginia Institute of Marine Science

Sepsis is defined as “life-threatening organ dysfunction caused by a dysregulated host response to infection” (“What is Sepsis?”). Common symptoms include low blood pressure, fast heart rate, fever or low body temperature, and confusion (“What is Sepsis?”).  As of 2016, Sep-3, or Sepsis-3, is the most current set of diagnostic criteria being used to identify and measure sepsis symptoms in patients undergoing critical care (Singer, Mervin et al. 2016) . However, Sep-3 definitions have not been uniformly adopted by healthcare systems in the United States due to patient- and pathogen-specific symptomatic presentations. This makes standardization of diagnostic criteria difficult to apply across populations. The aim of this research is to identify key criticisms of Sep-3 and analyze how patient outcomes have changed since Sep-3’s implementation through literature review and data analysis. By approaching this topic from two angles, the positive and negative impacts of Sep-3 on patient outcomes can be used to provide a better understanding of the usefulness of standardized sepsis criteria in healthcare. 

Student Major(s)/Minor: Public Health

Advisor: Ashleigh Queen, Kinesiology

While the body gets a large part of the focus in perfecting athlete performance, the brain is truly one of, if not the biggest, success marker. This study aims to connect the connection between physical action and brain region recruitment during success and failure in sports. Using the Functional Near-Infrared Spectrometry(FNIRS) device, athlete brain recruitment will be tracked during 10-30 minutes of a filmed practice/game scenario alongside the use of a biosensor watch. Both of these sensors will record the physical and mental changes within the athlete during their performance for further analysis. After the participant has completed 10-30 minutes of their activity, they will be asked to watch their recorded performance, comment on what occurred, and fill out a survey on their performance. Certain regions of the prefrontal cortex are associated with reward like the orbitofrontal cortex, and planning, like the dorsolateral prefrontal cortex. These brain regions are expected to have higher recruitment when successful tasks are enacted and completed, while the orbit-lateral prefrontal cortex will see inhibition when failure occurs. Participants also have the ability to perform their practice with a teammate, where the Ventral tegmental region is expected to react in relation to social acceptance. Knowledge of what brain recruitment leads to success allows a new look at understanding performance in athletes and improving it. The brain and the body work together successfully apart, but harnessing them both can allow athletes to reach higher achievements than ever before. 

Student Major(s)/Minor: Neuroscience, Kinesiology

Advisor: Stephanie Caligiuri, Kinesiology

Millions of birds are killed each year due to collisions with windows. The company, BirdShades, seeks to fix that problem by producing ultraviolet-reflective window films that, when applied to the exterior of a window, can deter incoming birds. In a previous study, the BirdShades film was shown to be effective at reducing overall collision risk when applied to clear, regular window surfaces. In this experiment, the BirdShades treatment is combined with a highly reflective solar film intended to reduce heat and light absorbance and reduce overall insulation costs.

The experiment was conducted in a flight tunnel, where someone can release a bird from one end of the tunnel with a loud sound that propels the bird towards the opposite end. There, the bird is met with two windows side by side. It can change direction and avoid the windows. However, due to the limited space of the tunnel and the bird's frantic speed, it often fails to notice that the window is not open space and it flies directly at it. The bird then collides with a mist-net directly in front of the window so it is not harmed. There were two trials of the experiment. In the first trial, the two windows were some combination of the solar-reflective window and a clear glass control group. There were runs done with all possible combinations of those two (both control, both treatment, one of both). In the second trial, one of the windows remained a clear glass control. The other window added a BirdShades ultraviolet-reflective film on top of the solar-reflective treatment.

The results showed a reduction in avoidance when birds saw the solar-reflective film, indicating that this product alone could be very dangerous as it could actually attract birds. However, when the BirdShades treatment was applied there was no difference in the proportion of collisions with the treatment and control, indicating that the ultraviolet-reflective product can compensate for the solar-reflective film. 

Student Major(s)/Minor: Biology

Advisor: John Swaddle, Biology

The current project presents the results of the first half of the honors thesis, the ultimate goals of which is to: have a simulation of electron scattering off of a Graphite target; compare the output data and calculations to real data. The results presented are: the current simulation implementation; the data it outputs; and the fit of the calculated differential cross section relative to the Rutherford and Mott cross sections, which measure interaction probability.  The simulation involves electrons input at 685 MeV, and, for those with outgoing momenta of 650 MeV or above, scattered: position, momentum, deposited energy, and particle identity were obtained. These values were used to calculate scattering angle and transferred momentum, which were in turn used to calculate the differential scattering cross section. 

Student Major(s)/Minor: Physics

Advisor: Patricia Vahle, Physics

Fasting's popularity has surged in recent years, but its effects vary among individuals. We aim to determine the factors influencing fasting success.

Although clinical data on fasting exists, it lacks diversity. We seek 300 diverse participants to study the effects of intermittent fasting, focusing on brain region recruitment.

Employed are biosensor watches, blood collections, BMI measurements, and questionnaires to evaluate energy levels, stress, and eating habits. An fNIRS (functional near infrared spectroscopy) will assess brain region recruitment.                                                   

My assessment will be on the age range of 19-21, assessing their brain activity, calorie intake, and activity. Heart rate is also assessed.

Student Major(s)/Minor: Kinesiology

Advisor: Stephanie Caligiuri, Kinesiology & Health Science

Research has shown that upon exposure to microplastics and nanoplastics, bacteria can experience growth inhibition, gene mutations, and altered biofilm production. Most studies attribute these negative effects on bacterial growth to the interactions between the microbial cell walls and micro/nanoplastics (Wang et al. 2023). The exposure studies have utilized the direct application of plastic particles to test organisms but the potential influence of plastic laboratory culture containers on microbial growth has not been explored. This study investigated the cytotoxic effects of two plastic types—polycarbonate and polypropylene—on the growth of Aliivibrio fischeri. The bacteria were cultivated in Erlenmeyer flasks made of both plastic polymers and growth and luminescence were measured at regular intervals. Turbidity measurements reflected bacterial growth changes while luminescence value reflected the ability to quorum sensing activity. No significant differences in growth or maximum luminescence were observed between the two plastic types, suggesting that contact with polycarbonate or polypropylene containers does not affect A. fischeri growth. Further research should examine the potential cytotoxicity of other labware and microbial species to understand any broader impacts better. Wang R, Li X, Li J, Dai W, Luan Y. Bacterial Interactions with Nanoplastics and the Environmental Effects They Cause. Fermentation. 2023; 9(11):939. https://doi.org/10.3390/fermentation9110939 

Student Major(s)/Minor: Biology & ENSP

Advisor: Bongkeun Song, Marine Science

The electrification of heavy-duty vehicles (HDVs) holds significant promise for economic and environmental benefits. However, the transition faces considerable challenges, including limitations in battery technology, ownership costs, and the availability of supporting infrastructure.  This study intends to propose a robust methodology for the strategic deployment of fast-charging stations, taking into account the local demand from various vehicle types, transportation logistics, and grid infrastructure compatibility. We utilize the Port of Virginia as a case study to illustrate and validate our proposed approach, demonstrating the practical applications and benefits of HDV electrification in a real-world setting.

Student Major(s)/Minor: Data Science & Economics

Advisor: Yanhai Xiong, Data Science

Every mid-Atlantic coastal state except Virginia has enacted regulations involving the use of bycatch reduction devices (BRDs) on commercial-style crab pots. The Virginia Marine Resources Commission has suggested that crabbing is overregulated already, and that terrapin conservation is not a priority. Because BRDs are viewed so negatively in Virginia, we considered a crab pot modification that instead of excluding terrapins via BRDs would allow trapped terrapins to escape via a release hatch. During June and July 2024, we compared the crab catch and terrapin bycatch in unaltered crab pots, pots fitted with 2 x 6-inch BRDs, and pots modified with an elastic-covered release hatch. With captures totaling over 1000 legal-sized crabs, the average crab size was not significantly different among the three treatment groups. Relative to unaltered pots, however, the legal crab catch was almost 25% lower with BRDs, and 70% lower with the release hatch. For bycatch, unaltered pots caught 32 terrapins, BRD pots caught 12, and release hatch pots caught 4. Both terrapins and crabs were able to operate the release hatch, so the “escape” design is not a viable option for the blue crab fishery. For all recreational crabbing and for commercial crabbing in areas where terrapin conservation is promoted/desired, BRDs continue to be the best modification of commercial-style pots. 

Student Major(s)/Minor: Dylan: Biology Major, Environment & Sustainability Minor, John: Biology major, Marine Science minor

Advisor: Randolph Chambers, Environment and Sustainability

This summer research project will ask the questions (1) how do milkweed nectar microbes impact milkweed pollinia (packages of pollen) germination and (2) how do milkweed nectar microbes impact seed pod production. Nectar microbes are introduced to milkweed by pollinators and have the ability to affect nectar sugar concentrations. This impacts plant fitness because milkweed pollinia can only germinate if they are in contact with nectar of specific sugar concentrations. Previous research suggested that nectar microbes negatively impacted pollinia germination. Summer research will replicate these results and extend to study seed pod production. Nectar samples from plants exposed to microbes and those isolated from microbes will be used to study the effectiveness of pollen germination. Other plants from the microbe exposure and limitation treatments will be hand pollinated and assessed for seed pod production. This research will increase scientific understanding of how microbes impact plant-pollinator interactions.

Student Major(s)/Minor: Biology

Advisor: Harmony Dalgleish, Biology

The underlying goal of this project is to find and assemble genome sequences to create a database consisting of suspected satellite phages from metagenomic data. Paired-end shotgun metagenomic sequencing data were downloaded from the NCBI Sequence Read Archive. The reads were then trimmed using Trim Galore and assembled into contiguous sequences (contigs) using MEGAHIT. Each contig was processed through a newly developed protein clustering algorithm created by a peer utilizing BLAST and prodigal to identify satellite families. Suspected satellites within metagenomic data were cataloged into a database. This collection of new suspected satellites will serve as an important resource for researchers, allowing exploration of these phage elements which can be used in applications such as synthetic biology and may shed light on the evolutionary origins of both viruses and bacteria as well as DNA-based organisms in general.

Student Major(s)/Minor: Biology & CAMS

Advisor: Margaret Saha, Biology

Fungi are a traditionally understudied group of organisms despite being extremely diverse and ubiquitous worldwide. Fungi play important roles in material cycling, are of economic importance for food or medicine, and many form intimate associations with other organisms, especially plants. The purpose of this project is to set a baseline for macroscopic fungi that can be found throughout the College Woods for future monitoring or conservation efforts. In the face of climate change and human development, it will be important to assess how fungal communities are impacted. This project will be the first step in creating an understanding of what fungi exist in this area and how our changes to their environment impact their abundance and diversity. The study revealed a community composed of 65 families, 103 genera, and a tentative 186 species. This suggests a wealth of fungal diversity in the College Woods that should be continuously monitored and protected. 

Student Major(s)/Minor: Biology

Advisor: Joshua Puzey, Biology

This research project aims to explore the dynamics of viral trends related to makeup products on TikTok by utilizing the TikTok Research API to gather and analyze data on specific beauty items. The study focuses on three popular products: E.L.F. Halo Glow Liquid Filter, Power Grip Primer, and Suntouchable Whoa Glow Sunscreen. By collecting data on videos featuring these products, the project seeks to understand the patterns of virality, the role of influencers, and the characteristics of content that drive widespread engagement. Through temporal analysis and trend mapping, this study will provide insights into how beauty trends emerge, peak, and decline on TikTok, contributing to a broader understanding of digital culture and consumer behavior in the social media era. The findings will have implications for marketers, content creators, and researchers interested in the intersection of social media and beauty trends.

Student Major(s)/Minor: Data Science Major & Mathematics Minor

Advisor: Alexander Nwala, Data Science

This project explores the relationship between amoeba predation and the evolution of virulence in yeast. The “coincidental selection” hypothesis states that natural selection on microbes in the natural environment can favor traits that accidentally lead to increased virulence. Amoeba predation has been proposed as one such force of natural selection because the traits that help yeast escape predation could also help them escape animal immune systems. To test this, different yeast strains from a collection of isolates were co-cultured with the amoeba Dictyostelium discoideum, and rates of amoeba predation of different strains were measured. The hypothesis is that clinical strains are more resistant to predation than environmental strains. The results suggest that there is significant variation in amoeba predation among the strains, specifically between strains with larger cells compared to smaller cells. This research will further the understanding of the evolution of fungal pathogenicity, which is a growing concern in the medical field.  

Student Major(s)/Minor: Biology

Advisor: Helen Murphy, Biology

Lake Matoaka, a critical waterbody in Virginia, faces contamination from microplastics through various pathways including road runoff, wastewater effluent, and rainwater. This research aimed to assess the abundance, characteristics, and sources of microplastics in Lake Matoaka. Over a year, water samples were collected from two distinct locations in the lake, and oysters were dissected to analyze microplastic presence. A cost-effective sample preparation method was developed to accurately quantify, characterize, and evaluate the microplastics detected. Initial findings revealed a high concentration of microplastics, averaging 13 particles per liter of lake water. Microplastics originating from synthetic clothing fibers and tire wear were identified as the predominant sources of pollution in Lake Matoaka. Further analysis using Microscope FTIR will determine these microplastics' chemical composition. This research provides crucial insights into the extent and sources of microplastic pollution in Lake Matoaka, highlighting the urgent need for targeted mitigation strategies to safeguard its environmental integrity. 

Student Major(s)/Minor: Chemistry & Environmental Issues

Advisor: Randolph Chambers, ENSP

Gunshot residue (GSR) is expelled during a firearm discharge event and may be collected from surfaces within the weapon’s vicinity. GSR samples contain organic (OGSR) and inorganic (IGSR) components, which provide evidentiary information for forensic casework. Traditional GSR analyses using scanning electron microscopy with energy-dispersive x-ray spectroscopy (SEM-EDS) have lost reputability in forensic cases due to expanded use of green (heavy metal-free) ammunition. This study aimed to develop a method for the non-targeted analysis of OGSR using comprehensive two-dimensional gas chromatography – time-of-flight mass spectrometry (GC×GC-TOFMS) for use alongside traditional SEM-EDS methods. Analytical difficulties with SEM-EDS were identified when analyzing GSR from heavy metal-free ammunition. Initial testing on GC×GC demonstrated potential for positive identification of OGSR components. Future work on this project will include development of a combined protocol for sample extraction and analysis using GC×GC and SEM-EDS to provide a comprehensive profile of green GSR samples. 

Student Major(s)/Minor: Chemistry Major & Mathematics Minor

Advisor: Katelynn Perrault, Chemistry

Normal activity helps maintain muscle strength and tension. Extended periods of muscle unloading cause atrophy, degeneration, from lack of tension and muscle mass. This project will use rat soleus muscles to determine the effects of muscle unloading on juvenile muscles versus adult muscles. There will be four treatment groups, juvenile and adult muscles each of which will include a hind-limb suspension group and normal activity control group. These muscles will be treated with immunofluorescence procedures and measured for muscle size and fiber type composition. Using this data the effects of unloading can be determined and useful in recovery procedures. Juvenile muscles are at increased states of plasticity and encouraging lack of weight-bearing activity during recovery could be detrimental in development if there is a significant difference in size and fiber type composition with hind-limb suspension.

Student Major(s)/Minor: Neuroscience & Biochemistry 

Advisor: Michael Deschenes, Kinesiology

Comprehension of the dynamics of receptor interactions at the PSD is crucial for synaptic function and synaptic dysfunction. This study focuses on a kinetic model to investigate the ways in which the gene encoded SYNGAP-1 protein and AMPA eceptors interact with the PSD. We developed a detailed mathematical model to capture PSD 'slots' binded with SYNGAP versus PSD 'slots ' binded with AMPA. The model incorporates molecural interactions and reglatory mechanisms to provide an insight on the influence  of AMPA and SynGAP-1 within the post-synaptic density (PSD). This model offers a valuable framework for studying receptor dynaptics with the post-synaptic membrane which can be developed and adapted to study individuals with genetic mutations including SynGAP-1.

Student Major(s)/Minor: Neuroscience & Psychology

Advisor: Greg Conradi Smith, Applied Sciences

Reactive oxygen species (ROS) are created as a natural byproduct in the body, but they are also formed during unnatural oxidative stress (cigarette smoke, pollution). While most ROS are neutralized by cellular mechanisms, as we age, the effects of oxidative stress accumulate and has been linked to diseases such as Alzheimer’s and Parkinson’s. Diet composition is integral to neutralizing ROS in the body. However, the role of dietary chlorophyll as an antioxidant is not well studied. The Landino lab studies red-light dependent redox reactions using chlorophyll to mimic the role it has when we consume it. This project explores the reactions of different biochemically relevant molecules in our novel photochemical system. Each of these experiments warranted further scrutiny because light-activated reactions generate byproducts that were previously uncharacterized. Through the understanding of specific reactions, this project broadly aims to understand how dietary chlorophyll can prevent disease and delay aging.

Student Major(s)/Minor: Chemistry & Mathematics

Advisor: Lisa Landino, Chemistry

The tweety gene family is highly conserved and implicated in human neurological disorders and cancers. This project investigates the expression and regulation of tweety 1 (ttyh1) and tweety 3 (ttyh3) during neural development in Xenopus laevis. While the role of ttyh1 in neural progenitor cell regulation and the Notch signaling pathway is established, the function of ttyh3 is largely unexplored. X. laevis embryos at the two-cell stage were injected with mRNA vectors to assess tweety expression and regulation: ICD mRNA to hyperactivate the Notch signaling pathway and ttyh1 or ttyh3 mRNA to induce overexpression. Embryos were fixed at a variety of developmental stages, and in situ hybridization was used to evaluate changes in spatiotemporal gene expression. Thus far, neither ttyh1 nor ttyh3 overexpression has induced significant changes in expression of Neural Beta Tubulin (NBT), a marker for postmitotic neurons, or SRY-box 2 (Sox2), a marker for neural progenitor cells.

Student Major(s)/Minor: Neuroscience & English

Advisor: Margaret Saha, Biology & Neuroscience

Proteins are crucial to life as they are responsible for virtually all functions necessary for cellular survival. Thus, the ability to both image and study proteins is an important scientific tool. Profluorophores are a class of molecules that become fluorescent only after a reaction occurs. This research aims to synthesize and react a profluorophore directly with a protein. This facilitates protein imaging as the molecule would not exhibit fluorescence when unreacted, eliminating background noise. Moreover, due to the reactivity at a single site in the desired protein of interest, it is extremely specific and diagnostic. To accomplish this, a profluorophore compound, EBTZ, was synthesized, and a commercially available profluorophore compound, 7-ethynylcoumarin was purchased. A unique handle was introduced into model proteins via the site specific incorporation of a non-canonical amino acid during protein translation.These compounds were conjugated to proteins and monitored for fluorescence. The fluorescence was measured between the conjugated and unreacted compounds, and a significant change was observed. This implies that they could function as useful diagnostic tools for biological imaging for proteins.

Student Major(s)/Minor: Chemistry & Mathematics

Advisor: Doug Young, Chemistry

The main goal of my research this summer was to create an optical set-up that could be used for future research on metastable helium. This goal can be broken into three distinct tasks that I completed this summer. First, I found the laser conditions needed to see the transitions for the first excited state of metastable helium. Figuring out these conditions is important as we can use the transitions found with the experiment to check against the expected transitions to make sure they match up. The second task was helping to make the components needed to complete the box containing the glass helium cell. This included making a tesla coil to go around the helium cell and 3d printing pieces that stabilized the components in the box. The last task was to add a saturation spectroscopy to the optical set-up. This addition caused more light to go through the helium cell than the gas could absorb and led to more accurate frequency readings of the gas. The research I conducted this summer is just the beginning of a new experiment that is hoping to study plasma. As helium is found in plasma, being able to use a laser to measure helium would mean that we would also be able to use a laser to measure plasma, something that is currently hard to do. Although it is still far from achieving this currently, this experiment could possibly help figure out how plasma could be used as a renewable energy source in the future.

Student Major(s)/Minor: Physics

Advisor: Irinia Novikova, Physics

Stem cells are essential for organ development and tissue maintenance, particularly in the reproductive system. This study investigates the novel gene CG11180 (Chingo) in Drosophila ovaries and embryos. Using transgenic Chigno::EGFP flies, we identified the cell types expressing Chigno in adult and developing ovaries. Chigno is widely expressed in adult reproductive systems and various developing tissues, including gonads, gut, and epithelial cells, and is localized to subnuclear punctae. In both adult and developing gonads, Chigno is present in germline and somatic cells. Loss-of-function experiments show that Chigno is crucial for viability, with adult flies lacking Chigno unable to develop and death occurring during late embryonic or early larval stages. Chingo's vital role in development and its broad expression in gonadal tissues highlights the importance of understanding this gene. Further research on Chigno and its human homolog, PINX1, may provide significant insights into reproductive health and stem cell biology.

Student Major(s)/Minor: Biology & Data Science

Advisor: Matthew Wawersik, Biology

Xenopus Laevis embryos exhibit a remarkable ability to maintain a consistent appearance throughout development despite any mechanical alterations made to their central nervous system. This project will explore the ability of Xenopus Laevis embryos to recover after undergoing mechanical tissue rotation of their Anterior-Posterior Neural Axis (central nervous system) during the gastrula stages of development. Previous work from the lab has shown that X. Laevis embryos are able to recover from a rotation of the anterior-posterior axis during gastrula stages and this window of plasticity disappears several hours later in development. To determine the molecular basis of this window of plasticity, the project will employ RNA-Sequencing to reveal the array of genes that mediate the ability of the nervous system to recover following physical perturbations.  The research will hopefully shed light on how to enhance regeneration of neural tissues in humans.

Student Major(s)/Minor: Computational and Applied Mathematical Biology & Data Science

Advisor: Margaret Saha, Biology

A fluorescein-based fluorescent probe was synthesized and found to sense iron (III), palladium (II), aluminum (III), and molybdenum (V) in water, utilizing a fluorescence quenching mechanism. The selective metals can be detected with a limit of detection of 8.75 μg/L for iron (III), 21.0 μg/L for palladium (II), 14.9 μg/L for aluminum (III), and 36.6 μg/L for molybdenum (V), below regulations set by the EPA. Chelation of the metals to the fluorescent probe appears to play a role in fluorescence quenching, and a reversal of quenching for the fluorescent probe is observed in the presence of phosphate or carbonate ions. Additionally, multiple new fluorescent probes are being synthesized with varying functional groups to optimize the ligand for detection of other metals. 

Student Major(s)/Minor: Chemistry

Advisor: William McNamara, Chemistry

This project will center on synthesizing and characterizing products formed between copper iodide (CuI) and organic nitrogen or sulfur containing molecules. This will continue previous research which included the discovery of several novel responsive and highly fluorescent complexes. What is new in this research is that these CuI-organic compounds display a tendency to form patterns of hydrogen bonding within them. Hydrogen bonding is a powerful type of force between atoms that allows for them to form long-range networks. Interestingly, the four products (which differ due to variations in hydrogen bonding) exhibit different colors of light emission under ultraviolet irradiation. These properties, including the ease at which hydrogen bonding may be disrupted, suggest applications to detector materials and light-emitting diodes (LEDs) - a light emitting diode is a device which gives off light under presence of an electric current. Consequentially, the observed differences in emission under varying environmental conditions suggest a range of potential sensory applications. 

Student Major(s)/Minor: Chemistry

Advisor: Robert Pike, Chemistry

Ascent to high altitudes with lower concentrations of oxygen can cause variable physical impairments, sometimes ensuing in Acute Mountain Sickness (AMS). This study aimed to use heart rate variability (HRV) metrics during normoxia (sea level) to predict arterial oxygen saturation (SpO2) decline during hypoxia (altitude). HRV data was measured across a trial period where subjects underwent hypoxic exposure (30 min. total, 10 min. at 11.8% FiO2 - equivalent to 4572m of elevation, sea level air for control) from a normobaric (sea level pressure) chamber. Subjects with a lower lnLF/HF ratio during normoxia experienced greater O2 desaturation than subjects with higher lnLF/HF ratios during normoxia. Other normalized frequency domain (lnHF) and time domain values (RMSSD, SDNN) did not have significant correlations with O2 desaturation. These results imply that subjects with suppressed sympathetic activity evidenced by their HRV are more susceptible to arterial desaturation during hypoxia. 

Student Major(s)/Minor: Kinesiology & Health Sciences

Advisor: M. Brennan Harris, Kinesiology & Health Science

Simulation of computer architecture is essential for the development of modern chips and systems, allowing designers to explore various configurations and evaluate performance without needing physical hardware. However, developers of these simulators often struggle to balance usability, accuracy, and performance. To address these challenges, we present Akita, a novel computer architecture simulator engine designed to streamline the development process while maintaining high performance and robust functionality. Akita stands out as an accessible and efficient simulation tool, featuring innovative elements such as Smart Ticking and Availability Backpropagation, which provide the ease of cycle-based simulators alongside the high performance of event-driven simulators—resulting in an average speedup of 4.2X. Additionally, Akita enables parallel simulation without requiring changes to existing simulator code, achieving a 2.5X speedup when utilizing 4 cores. Akita also enhances performance analysis, allowing users to effectively examine systems under simulation both during and after execution.

Student Major(s)/Minor: Computer Science & Mathematics

Advisor: Yifan Sun, Computer Science

Over the past 70 years, theoretical physics research has sought a singular theory to encompass all fundamental forces, objects, and interactions in our universe. Many different unification theories have been developed, and while they have yet to comprehensively describe our universe, many require more dimensions than our familiar four. For these theories to be consistent, these extra dimensions must be hidden to reduce the theory back to 4 dimensions. In specific we consider a framework called the “braneworld.” Within this ontology, our 4-dimensional universe would be described as a 4-dimensional membrane or “brane” moving through a higher dimensional space called a “bulk.” Past research has shown that when a brane moves through a higher dimensional bulk such as a circle, the laws of physics are not necessarily the same for all inertial observers, allowing for extensions of our physical laws. This project intends to study the implications of a 4-dimensional brane moving through varied higher-dimensional bulks. Specifically, we extend dynamic braneworld models to a toroidal compactification model, as well as Kasner cosmological models. Within these models, we consider the possibility of superluminal signal propagation, Lorentz violation, and paths towards extensions of our known physical law.

Student Major(s)/Minor: Physics

Advisor: Joshua Erlich, Physics

Our heart's rhythm is controlled by a series of electrical signals.  When these signals misfire, they can form patterns in the shape of spiral waves that are associated with critical cardiac conditions that require early detection.  This research utilized an applet simulation to generate images with three different types of possible electrical patterns (still, spiral and chaotic) by adjusting specific parameters.  Images at various ranges of parameters were then taken and measured using different texture and topological analysis techniques. Metrics such as range and standard deviation of pixel intensities, as well as numbers of connected components were all analyzed.  The goal of this project was to use these metrics to detect an early warning signal for the onset of these spiral wave patterns that could potentially be applied in a clinical setting.

Student Major(s)/Minor: CAMS Mathematical Biology

Advisor: Sarah Day, Mathematics

A notable characteristic of oscillatory systems is their tendency to demonstrate resonance; that is, they oscillate with greater amplitude at a particular resonance frequency. There is evidence that there are individual differences in neural resonance and that identifying those resonance frequencies can be used to tailor and subsequently boost the effects of auditory entrainment on cognitive functions. Research also suggests that some clinical populations, like those on the autism spectrum, may demonstrate resonance at different frequencies than those who are low on the autism spectrum

Binaural beats, an auditory phenomenon that occurs when two pure tones of slightly different frequencies are presented separately to the left and right ears, were used to drive neural entrainment at frequencies between 1Hz and 50Hz, in 1Hz increments, while EEG was recorded from 32 sensors. Participants also completed the BAPQ, a measure of autism spectrum personality traits, and The BFI-2-S personality questionnaire.

Preliminary results indicate that individuals whose neural resonance profile includes higher peak entrainment frequencies in the gamma range and lower peak entrainment frequencies in the alpha and theta ranges scored significantly higher on the Aloof subscale of the BAPQ and significantly lower on the Extroversion subscale of the BFI-2-S.

These results are interpreted to support the hypothesis that neural resonance profiling could be used in the development of biomarkers associated with both normal and pathological sensory, perceptual, and cognitive functions.

Student Major(s)/Minor: Psychology & Mathematics

Advisor: Paul Kieffaber, Psychology

Milroy Disease (MD) is an autosomal dominant disorder that causes defects in the lymphatic system, leading to lymphedema. MD is caused by mutations in vascular endothelial growth factor receptor-3 (VEGFR3, Figure 1) and mainly affects newborns and infants. Children with MD have an increased risk of developing lymphangiosarcoma, a rare cancer with a poor prognosis and a 5-year survival rate of less than 5%. The traditional imaging modalities of computed tomography (CT) and magnetic resonance imaging (MRI) are size-dependent anatomical imaging methods; they have limitations in probing functional changes of lymphatic disorders and progression. Positron emission tomography (PET) using radioactive imaging agents provides a noninvasive way to investigate the biochemical and metabolic processes in the body (Figure 1).

The active ester F-Py-Ester was synthesized by condensation of carboxylic acid 1 with phenol 2 in 79% yield over 95% purity. The VEGFR3-specific peptide AA187 was custom synthesized with high purity ( &gt; 95%) and characterized by HPLC and mass spectrometry (Figure 3). The conjugation between the active ester F-Py-Ester and peptide AA187 proceeded smoothly and provided the resulting peptide with a 55% yield. The target peptide F-Py-AA187 was characterized by HPLC and HRMS with over 95% purity (Figure 4). Stability tests show the peptide was stable for up to 90 min in water and PBS.

Based on the preliminary results, a new peptide targeting VEGFR-3 for lymphatic disorders was synthesized with high purity and stability. The next steps in this project are to determine the binding affinity of the new peptide and compare the results with the parent peptide using the VEGFR3 kinase assay kit and develop an efficient method for fluorine-18 incorporation. The imaging probe will provide a noninvasive and quantitative strategy to study MD that affects children.

Student Major(s)/Minor: Psychology 

Advisor: Joshua Burk, Psychology

This project examined the fluorescent characteristics of peri-substituted acyl pyrrolyl naphthalene derivatives and any hindered rotations they may possess. Acyl pyrrolyl naphthalenes were synthesized from commercially available chemicals, and their fluorescence in different solvents, as well as their rotational behavior, were studied using fluorescence spectroscopy and dynamic NMR, respectively. All derivatives were found to be fluorophores. The intramolecularly cyclized derivative also turned out to be a chromophore, demonstrating both polarity and proticity-related fluorescent intensity and highly H-bonding-dependent solvatochromism. Surprisingly, the ethyl ester derivative did not exhibit any hindered rotations at room temperature. The benzoyl derivative was unstable and spontaneously rearranged to form an amide-containing, highly conjugated scaffold. The conditions leading to the formation of this scaffold remain to be studied. This study will contribute to the design of more powerful chemosensors.

Student Major(s)/Minor: Computer Science & Chemistry

Advisor: Christopher Abelt, Chemistry

Pseudomonas aeruginosa is a human pathogen responsible for multidrug resistant infections. This bacteria relies on a process called quorum sensing to harm its host by forming biofilms and releasing toxins. The protein PqsE is a key player in quorum sensing. Past work has identified small molecules as potential inhibitors against PqsE’s pathogenic action. However, without crystal images, their exact binding mechanism remains unknown. Determining crystallization conditions of PqsE is essential for the drug development process. By using the hanging drop method and altering the composition of the crystal buffer solution, reliable crystallization of PqsE has been achieved. This allows for future co-crystallization of PqsE bound to small molecule inhibitors. This technique can be used to screen drug candidates and guide the synthesis of new molecules, working towards the goal of creating an antibiotic that targets quorum sensing in P. aeruginosa.

Student Major(s)/Minor: Chemistry Major & Biology Minor

Advisor: Isabelle Taylor, Chemistry

Pseudomonas aeruginosa, a bacterial pathogen notorious for hospital-borne infection and antibiotic resistance, uses quorum sensing to coordinate group behaviors. Quorum sensing is the process by which bacteria regulate gene expression in response to changes in cell population density conveyed by changes in concentration of released chemicals known as autoinducers. The quorum sensing transcription factor RhlR is activated by the autoinducer C4-homoserine lactone (C4-HSL) and its activity is modified by a protein-protein interaction with the enzyme PqsE. Under the control of RhlR, azeB is the primary gene responsible for the production of the natural product azebicyclene. Construction of an E. coli luciferase reporter assay allows for the quantification of azeB promoter activation in response to pqsE mutants with varied rhlR-interacting and catalytic abilities. In the presence of the autoinducer C4-HSL, RhlR-interacting pqsE mutants are found to produce decreased azeB promoter activation relative to non-interacting mutants. This pattern is similar to that observed in a homologous P. aeruginosa azeB reporter assay emphasizing the importance of the RhlR-pqsE interaction as a determinant of azeB promoter activation, and presumably azebicyclene synthesis.

Student Major(s)/Minor: Biology & Chemistry

Advisor: Isabelle Taylor, Chemistry

Mis-regulation of stem cells can lead to organ dysfunction, infertility, and even cancer. The Drosophila testis germline stem cell (GSC) niche provides an opportunity to discover mechanisms controlling stem cell behavior in mammalian reproductive tissues. One such regulator is the chingo[MW1]  gene which is homologous to mammalian PINX1. Our lab has shown that inhibition of chigno causes testis tumors due to over-proliferation of cyst stem cells (CySCs) that regulate sperm production. These conditions also cause expansion of epithelial cells that regulate testis stem cells. This project explores the hypotheses that chigno functions to prevent epithelial expansion by: (i) ensuring that CySCs do not convert into female follicle stem cells, or (ii) preventing conversion of CySCs into hub epithelial cells. As male-to-female cell conversion leads to mammalian infertility, and conversion to epithelial fate can reduce cancer risk, these studies have important implications for understanding human infertility and for curing cancer.

Student Major(s)/Minor: Biology 

Advisor: Matthew Wawersik, Biology

The theory of quantum gravity is described using various mathematical approaches attempting to reconcile the physical theories of quantum fields, which describe physical phenomena as particle interactions, and general relativity, a model for gravity as changes in smooth surfaces of spacetime. The aim of this project is to further develop the theory of stochastic quantum gravity which uses stochastics as a mathematical model for random quantum fluctuations, as used in other areas such as stock market analysis, to bridge the gap between the two theories as methods of describing gravity in the case of black holes. These results will then be compared with those from other mathematical frameworks, such as string theory, to give insight into black hole thermodynamics and information problems related to the eventual fate of data that is entrapped in an evaporating black hole.

Student Major(s)/Minor: Mathematics & Physics

Advisor: Joshua Erlich, Physics

Complex Human Simulation (Comp-HuSim) is an ongoing project aiming to create AI Agents that accurately emulate human behavior. These AI agents are able to have backstories, have conversations, and play strategic word games. This summer, a team of undergraduates making up the Ford AI and Society (FAIS) lab were tasked to help contribute to the model. Two goals that were focused on were creating a demographic distribution sampler that uses real census data and creating working visualizations for the agents. The purpose of these goals is to accurately represent a population using the sampler, and to properly see the actions of the agents through visualizations. By doing this, the Comp-HuSim project will have new pathways opened up to real world reflections in the future, as well as becoming more easily representable through clear visualizations.

Student Major(s)/Minor: Computer Science

Advisor: Trenton Ford, Data Science

In this project we looked at bird activity on solar panels. We did this by studying thousands of videos and recording the behavioral  data into ethograms which were then analyzed to see if any behaviors were common across all of the different solar panel sites we looked at. These sites were based in the Midwest area to see the effects of bird activity on the actual panel. Across the board the most common activity that we saw on these panels were birds perching on the panels and birds flying around or in the background of panel sites. We can speculate that this was because they were nesting nearby or under the panels. It was also observed that if there were other infrastructure such as power lines near the panel sites then the birds would perch on those as opposed to the panels. This lets us speculate further that the birds use the panels for temporary rest while migrating.

Student Major(s)/Minor: Darius: Marine Science, Megan: Biology

Advisor: John Swaddle, Conservation

The thyroid hormone receptor (TRα1) is important for controlling genes involved in development and metabolism in response to thyroid hormone. TRα1 mutations can lead to diseases such as Resistance to Thyroid Hormone (RTHα), which is characterized by symptoms such as stunted growth, constipation, and cognitive impairment. This project investigated how altered levels of Nuclear Receptor Corepressor 1 (NCoR1) impacts the nuclear retention of TRα1, and an RTHα mutant with an amino acid substitution in the hormone-binding domain (N359Y) that we showed has a more cytosolic localization than TRα1. In NCoR1-knockout human cells, nuclear retention of wild-type TRα1 was significantly decreased. In contrast, N359Y showed no change in localization, suggesting aberrant interaction with NCoR1. Additionally, we explored NCoR1’s role in recruiting histone deacetylases (HDACs) that may also deacetylate TRα1, by measuring acetylated lysine levels in TRα1 in NCoR1-knockout cells by immunoprecipitation assays. These findings can help further understanding of TRα1-related diseases. 

Student Major(s)/Minor: Biology

Advisor: Lizabeth Allison, Biology

Comprehensive two-dimensional gas chromatography (GC×GC) is a separation technique that utilizes two columns with distinct retention mechanisms to separate compounds more effectively than traditional one-dimensional gas chromatography (GC). This project strived to develop a simple workflow to develop a GC×GC method to replace more cumbersome literature approaches. A peak modeler was used to first develop an optimized GC method. Using a step-by-step workflow, six parameters were tested and optimized to make the final method, including ramp rate, initial and final oven hold times, modulation period, secondary oven offset, and hot pulse time. Method development in GC×GC is often seen as a difficult and timely task; however, this project demonstrated that a simple workflow is possible within a few days. Future research will focus on transferring this method using helium carrier gas to hydrogen carrier gas to shorten run times and decrease costs to further the use of GC×GC in labs. 

Student Major(s)/Minor: Chemistry

Advisor: Katelynn A. Perrault Uptmor, Chemistry

Chemical synthesis, including peptide synthesis, can be expensive due to waste management, equipment costs, and researcher time. Peptide synthesis specifically involves hazardous organic solvents. Recently, the Environmental Protection Agency has imposed new limitations on dichloromethane use in chemical synthesis and research, thus causing scientists to need to change the way they perform reactions.  As a greener alternative, chemistry in water is emerging but faces challenges like reagent solubility, extended reaction times, and difficult product isolation. This study investigates using cellulose-based capsules to create pre-packaged reagent "pills" for water-based peptide coupling reactions. These cellulose capsules form micelle reactors, that create a protective "bubble" for organic reagents within the aqueous environment. The study aims to address the limitations of water-based reactions and improve their efficiency and safety. The findings of this approach will be discussed in detail. 

Student Major(s)/Minor: Brianna: Undeclared, Maria: Biology & Chemistry

Advisor: Isaiah Speight, Chemistry

This project will help in the assembly and calibration of part of the apparatus for the international MOLLER experiment at Jefferson Lab. The MOLLER experiment seeks to find parity violation in the scattering of electrons from electrons, in order to find hypothesized flaws within the standard model of particle physics. The project is expected to launch in 2026 and is in collaboration with multiple universities across the world. The team at William and Mary will be in charge of constructing the tracking chamber support mechanism. Additionally the project will seek to write software in order to calibrate the tracking chambers, before any data is taken, for more precise results. This will be done by taking a simulation of ideal conditions and comparing it to the actual system, then taking those two results to calibrate the experiment to the correct system. The project will ensure that MOLLER stays on schedule and ensures that it will read precise results.

Student Major(s)/Minor: Physics

Advisor: David Armstrong, Physics

In the plant genus Mimulus, two parents with solid flower petal pigmentation can be crossed to produce spotted offspring. Previous research has indicated that Mimulus petal patterns can be recreated with a mathematical model, and this project builds on those findings to investigate connections of patterning to heterozygosity and hybridization. We examine preliminary data of petal spots across selfed generations of Mimulus and discuss the implications of our expected results. By self-pollinating these plants, we decrease heterozygosity in their offspring and expect to see a decrease in pattern variation. Additionally, we investigate the possibility of phenotype segregation in crosses of interest. These results will indicate whether pattern elements are controlled by simple single-locus systems or by more complex interactions. This research points toward larger questions, such as the rise of phenotypic novelty in plants, influences on speciation, and the genetic mechanisms by which Mimulus hybrids can form patterns.

Student Major(s)/Minor: Computer Science & CAMS - Mathematical Biology

Advisor: Joshua Puzey, Biology

My research explored where trees within humid forests are able to access groundwater. The influence of shallow groundwater on forests has been mapped in arid ecosystems, yet groundwater-tree interactions in humid environments are often ignored despite increasing drought variability in these environments. The study site I selected was Trout Lake watershed in Northern Wisconsin. I collected Landsat and ECOSTRESS remote sensing imagery and mapped the data using QGIS. The satellite data included surface temperature, daily evapotranspiration rates, and normalized difference vegetation index (NDVI). I then overlaid the results with a groundwater model to display correlation between tree health and groundwater. Using NDVI maps and ECOSTRESS clusters, areas of shallow groundwater were validated with the model. The methodology is able to be replicated and applied to other humid forests.

Student Major(s)/Minor: Geology

Advisor: Dominick Ciruzzi, Geology

Biofilms are a defense mechanism that specific bacteria have, forming an extracellular matrix that allows them to adhere to a surface and survive an extreme environment. Biofilms are resistant to almost all traditional antibiotics, and immune responses, and only need limited food and water, so they are hard to kill and treat. This project examines the bacteria P.Fluorescens, a model organism to characterize biofilm growth. Previously we have created novel antibiotics with polyynes, or molecules with consecutive alkynes (these are seen to have antimicrobial properties in nature); This project found that some of our polyyne antibiotics are much more effective at disrupting biofilms than traditional antibiotics. Future research will analyze the mechanism of action (how these small molecules are disrupting biofilms). These findings are incredibly valuable for the medical industry and a critical step in developing new antimicrobial compounds. 

Student Major(s)/Minor: Chemistry & Environmental Science

Advisor: Douglas Young, Chemistry

Imagine a game that is played on a board where the spaces are circles connected by lines. Each turn, you choose a space to set on fire. The next turn, the fire will spread from each burning space to its unburnt neighbors, and you can then choose another space to set on fire. The board starts with all spaces unburnt, and the game ends when every space is on fire. Your goal is to end the game in as few turns as possible. For a board with n spaces, mathematicians conjecture that, with optimal play, the board can always be burnt in the square root of n turns, rounded up. I offer progress towards that proof by reducing the number of boards that could provide counterexamples to the conjecture.

Student Major(s)/Minor: Mathematics & Philosophy

Advisor: Gexin Yu, Mathematics

Nematode sperm use a pseudopod to crawl to the site of fertilization. In mutants lacking the catalytically inactive pesudophosphatase SPE-54, sperm have abnormal pseudopods. To better understand SPE-54, we want to determine where SPE-54 resides within sperm cells. Unfortunately, attempts to generate either transgenic lines with tagged SPE-54 or antibodies against SPE-54 peptides failed.

Thus, we’ve sought to isolate bacterially expressed SPE-54 for antibody production. Initial attempts to isolate SPE-54 from bacterial supernatants using either a nickel affinity column to bind the His-tag or an ion-exchange column to bind SPE-54 by its elevated 9.1 isoelectric point were unsuccessful.  Next, we sought to isolate SPE-54 from the insoluble inclusion bodies that often form when proteins of interest are overexpressed in bacterial host. SPE-54 was extracted from isolated inclusion bodies and renatured through extended dialysis. This approach yielded 70% pure SPE-54 which is being used to generate rabbit polyclonal antibodies.

Student Major(s)/Minor: Biology

Advisor: Diane Shakes, Biology

In mathematics, it is common to study dynamical systems by looking at its asymptotic behavior. One way of doing that is by modeling the system with equations, and study the asymptotic dynamics of those equations. But, that process is inherently biased because it involves intentionally choosing equations to fit the data. So, another process would be through non parametric surrogate modeling, in which Gaussian Process Regression (GPR) had seen a lot of success in. However, there had not been a formal metric on evaluating how well it is performing. With the Ricker Map as a toy model, this project uses Wasserstein distance as a metrics to measure the distance between the asymptotic dynamics between GPR surrogate model and the Ricker Map to judge if GPR is working well.

Student Major(s)/Minor: CAMS

Advisor: Sarah Day, Mathematics

Alyssa is a newly discovered satellite phagelet that triggers the excision of the WMHerbert prophage from the bacteria, M. aichiense. Because Alyssa is one of the first satellite phages discovered in mycobacteria, little is known about its mechanisms of action. This project aims to bioengineer Alyssa in order to elucidate its mechanisms of action, starting by assembling fragments of Alyssa’s genome. Thus far, this project has shown that Gibson assembly is unable to connect a large number of DNA fragments, so this project will explore other bioengineering techniques such as Golden Gate, TXTL system, and FastCloning. Additionally, by conducting PCRs beginning in different locations, this project has shown that Alyssa’s genome is circular. Successful assembly and characterization of Alyssa would provide a bioengineering tool that is easier to manipulate due to its small genome size.

Student Major(s)/Minor: Biology & CAMS

Advisor: Margaret Saha, Biology

Nematode sperm crawl via the dynamic polymerization/depolymerization of the novel cytoskeletal protein (MSP) within their extended pseudopod.  Biochemical studies in Ascaris first identified MSP polymerization-activating kinase (MPAK) as a key regulator of MSP polymerization. Our studies of the C. elegans MPAK proteins TTBK-8.1 and TTBK- 8.2 reveal that MPAK localizes to the pseudopod. To assess MPAK function, we created single and double knockout mutants. The fertility of single knockout males is comparable to wild type, but double knockout males are infertile. ttbk-8.1/2 males inseminate females, but their sperm fails to reach the site of fertilization. When activated in vitro, both ttbk-8.1/2 and wildtype sperm initially extend filopodia-like spikes. However, ttbk-8.1/2 sperm fail to subsequently form normal pseudopods; they either arrest with spikes or form smooth, non-motile pseudopods. Our ongoing studies will characterize TTBK-8.1/2’s molecular interactors and determine how it regulates sperm motility.

Student Major(s)/Minor: Jenna: Biology, Olivia: CAMs & Statistics, Biology Track

Advisor: Diane Shakes, Biology

Parasitic dinoflagellates of the genus Hematodinium cause Bitter Crab Disease in the Chesapeake Bay blue crab population, resulting in significant economic losses for fisheries in Virginia and Maryland, even in non-epidemic years. Primary research reveals seasonal disease outbreaks, with temperature playing a crucial role in transmission and mortality.

This research is interested in developing a mathematical model of blue crab population with nonlinear incidence rate and migration. The mathematical model used is differential equations, which is to use calculus to predict the quantities of susceptible and infected blue crab populations in a disease outbreak. Overall, the research explores the effect of temperature, predation, cannibalism and fishing on the population and disease dynamics of blue crabs, empowering people with enhanced capabilities to forecast and protect the welfare of these organisms.

Student Major(s)/Minor: Math & Data Science

Advisor: Junping Shi, Mathematics

Protein vimentin is an intermediate filament involved in neurite formation. Research in Dr. Hinton’s lab has shown that MK-STYX increases neurite formation in rat’s neurons. The goal of investigating the relationship between vimentin and MK-STYX is to show the role that MK-STYX plays in neurite development,, how these two proteins interact with each other, and how this contributes to neurodegenerative diseases. This research is significant because neurodegenerative diseases such as Alzheimer’s form because of improper neurite formation involving cytoskeletal proteins such as vimentin. This research is also a continuation of the research that Priya Singh and Gwen Wagner have done. Last summer, my work on this project found results that suggested that MK-STYX was inhibiting the degradation of vimentin by certain caspases (a group of proteins involved in cell death), and one of the goals of this project is to try to replicate these results so that statistical analysis may be performed.

Student Major(s)/Minor: Biology

Advisor: Shantá D. Hinton, Biology

This research strived to produce luminescent coordination complexes of rare-earth metals (lanthanides) and copper. Making such complexes would maintain luminescence while reducing lanthanide percent composition and material costs. The main ligand (molecule which bonds to the metals) used in the complexes was thenoyltrifluoroacetonate (TTA), chosen for its strong luminescence properties. Known synthesis procedures for the complexes were further developed to be more consistent and higher yielding. Pilot syntheses of complexes of novel ligands and ligand ratios were attempted to varying degrees of success. Single crystals were produced and used in X-ray crystallography to determine the structure of the complexes. X-ray analysis confirmed the synthesis of some compounds while others are yet to be determined. Attempts to incorporate the copper by coordinating it to the thiophene sulfurs of TTA in multi-TTA complexes provided little results. Salts of a 4-TTA lanthanide anion and copper (+1) cation showed promise are still being investigated.  

Student Major(s)/Minor: Chemistry

Advisor: Robert D. Pike, Chemistry

The goal of this research is to determine function(s) of the novel PINX-1-related protein, Chigno, in Drosophila (fruit fly) testes. Our previous research shows SUMO (small ubiquitin-like modifier) may be involved in Chigno’s interactions with other proteins such as Chinmo, an essential protein in testes of male fruit flies. To identify Chigno binding proteins, a yeast two-hybrid assay was performed using a truncated form of Chigno as bait against a Drosophila cDNA library. This analysis identified ~50 clones encoding potential Chingo binding proteins, including Noc2, which functions in ribosome biogenesis, and two novel proteins, CG31687 and CG33458, with predicted functions in anaphase regulation and proteolysis respectively. Here we present the initial validation of these Chigno binding partners before exploring the in vivo significance of these interactions in adult testes.

Additionally, we also investigated PXR1, the ortholog of Chigno in budding yeast cells, by testing the interaction of PXR1 with SUMO. We constructed PXR1 bait and prey constructs and found that both constructs interacted with SUMO. Using site-directed mutagenesis, we are now identifying domains in PXR1 important for the interaction with SUMO. In summary, our analysis of Chigno in flies and yeast may be directly relevant to our understanding of PXR1’s function in human fertility and testicular cancers.

Student Major(s)/Minor: Neuroscience

Advisor: Oliver Kerscher, Biology

The search for human remains is important in forensic science and often involves water searches. There is no forensic procedure to analyze chemicals in water samples rather than relying on canine detection in the field. This study analyzed volatile organic compounds in water associated with decomposing pork tissue using comprehensive two-dimensional gas chromatography – time-of-flight mass spectrometry (GC×GC-TOFMS). Pork belly was decomposed in jars of water at different temperatures (32˚C, 22˚C, and 5˚C) for 12 days and compared to jars without pork. ChromaTOF Tile was used to identify similarities and differences between environments. Greater differentiation existed between pork and water samples over time. Warmer samples became more dissimilar from the room and cold temperatures later in the trial. Room temperature samples did not differ prominently from the coldest temperature. GC×GC-TOFMS could monitor decomposition status, providing direction for additional research into the use of water analysis by GC×GC-TOFMS for forensic investigations.

Student Major(s)/Minor: Chemistry

Advisor: Katelynn Perrault, Chemistry

This project investigates the relationship between the orexin system and schizophrenia, focusing on its impact on learning, attention, and memory. Orexin, a neuropeptide essential for regulating wakefulness and arousal, is primarily produced in the hypothalamus and widely distributed throughout the brain. Schizophrenia, characterized by hallucinations, delusions, and cognitive impairments, has been linked to overactivity in the basal forebrain cholinergic system. Blocking orexin receptors has shown promise in reducing cholinergic neuron activity projecting to the cortex, leading to decreased output from the cortical basal forebrain and diminished cholinergic neurotransmission in the prefrontal cortex. Building upon existing research, this project will explore how blocking orexin receptors, particularly with dual orexin receptor antagonists (DORAs), may mitigate excessive dopaminergic signaling, normalize psychosis-related behaviors, and potentially alleviate attentional deficits associated with schizophrenia.

Student Major(s)/Minor: Neuroscience

Advisor: Joshua Burk, Neuroscience

Exertional dyspnea and blunted exercise capacity are hallmarks of several disease states. Cardiopulmonary exercise testing (CPET) can provide unique insights through exercise testing coupled with gas exchange data. Some key variables (e.g. peak VO2) from CPET have established prognostic value. We retrospectively identified patients who underwent CPET at VCU between 2022-2023 and collected data on: demographics, laboratory results, medical comorbidities, medications, comprehensive CPET readouts, cardiovascular outcomes. We performed a stepwise multiple linear regression to identify predictors of peak VO2. There were high representations of patients with CAD, HF, and cardiac risk factors. For predicting peak VO2, the linear regression model, adjusted R2=0.401, included several independent predictors. Strongest contributions were from: age, sex, race, body size, stroke, CKD, COPD, and atrial fibrillation. With the creation of this large institutional dataset, we expect to be well poised to explore novel metrics obtained through CPET and their prognostic value.

Student Major(s)/Minor: Neuroscience & Psychology

Advisor: Daniel Cristol, Biology

The accumulation of CO2 in Earth’s atmosphere is shifting weather patterns and threatening biodiversity. To ameliorate these negative effects, clean energy (energy that does not produce CO2) is becoming increasingly important. Certain chemical reactions can generate energy in the form of H2 without producing CO2. Hydrogen fuel cells, powered by a platinum catalyst, can react H2 with oxygen to generate electricity. However, platinum is expensive and rare, limiting the potential for Hydrogen fuel cells. My research project aims to stimulate an oxygen reduction reaction using copper catalysts, allowing greater accessibility to hydrogen fuel cells.

In order to test the efficacy of copper catalysts, light-induced reactions, known as photochemical experiments, were employed to reduce oxygen. The oxygen reduction reaction produces hydrogen peroxide. In cooperation with the Landino lab, we have developed a method of detecting hydrogen peroxide using Horse Radish Peroxidase. I hope to find a positive correlation between hydrogen peroxide concentration and amount of copper catalyst used, as this would indicate efficacy of copper catalysts in reducing oxygen. 

Student Major(s)/Minor: Chemistry

Advisor: William McNamara, Chemistry

The objective is to understand the effects bioplastics plastics in general have on the microbial life in the environment. This was conducted with a comprehensive overview of the current information through analyzing and evaluating different studies and research as well as interviews conducted on various experts. Bioplastics had been shown to have a negative effect on the microbial life within natural soil and water conditions. Nonetheless, waste management makes controlling it easier and with how bioplastics are utilized in real world applications then the positive effects outweigh the negative. Overall bioplastics represent a necessary change in the way we live today as the environment is facing rising plastics pollution. Bioplastics are an alternative to replace plastics made from fossil fuel, but similar to plastics there is more to be needed to identify the long term effects of bioplastics.

Student Major(s)/Minor: Biology

Advisor: Robert Hale, VIMS

My research this summer aimed to characterize various crystal forms of the metal cadmium and a small ligand nicknamed BPA. We varied the ratio of ligand to metal which successfully produced various different crystal forms. The reagents were dissolved in 9:1 methanol and water, and crystals formed rapidly upon the slow layering of diethyl ether. A 2:1 ligand to metal ratio creates a monomer dimer cocrystal, which means both a monomer (one BPA bound to one metal) and dimer (two monomers bound together) pack together in the same unit cell. We found a 1:1 ligand to metal ratio creates some crystals of a monomer, and some of a dimer. Lastly, a 1:2 ligand to metal ratio created a polymer. These novel crystal forms provide insight into what variables are important in creating new forms of crystals, having implications for the discovery of new materials or pharmaceuticals. 

Student Major(s)/Minor: Chemistry

Advisor: Deborah Bebout, Chemistry

Fa-arun et al. (2023) engineered a P4 cosmid, which is a plasmid containing the P4 satellite phage and the cos (or packaging) site of the P2 helper phage. Fa-arun et al. developed an E. coli cell with the P2 helper phage integrated into its genome (a lysogen). When the P4 cosmid enters this P2 lysogen, it uses the P2 helper phage to generate transducing units which allow the P4 cosmid to propagate.

My goal was to replace part of the P4 cosmid with the gene encoding RFP (red fluorescent protein) by employing PCR (polymerase chain reaction) and a Gibson Assembly to create a new P4 cosmid with the RFP gene. Sequencing results supported successful cloning, but the absence of the expected phenotype suggested the next step would be adjusting which segments of the RFP are amplified via PCR.

This would create a system with visibly detectable transducing units, which has applications in other phage/satellite systems. 

Student Major(s)/Minor: Biology Major & Chemistry Minor

Advisor: Margaret, Biology

This presentation describes the production process, application, and characterization of Didymosphenia geminata (Didymo) based biomaterials. Our project outlines a chemical molding process to create samples that exhibit low thermal conductivity, high porosity, and low density. These properties allow the samples to absorb oil and deflect heat, which are use cases typically absent from carbon-negative materials. We achieve a more sustainable approach when compared to conventional material production, which requires excessive amounts of CO2 and energy to produce. Along with material sample production, characterization of the extracellular matrix through spectroscopic methods and high resolution imaging provides insight into the chemical background of the novel material properties. 

Student Major(s)/Minor: Physics & Computer Science

Advisor: Hannes Schniepp, Applied Science

My summer research examines prevalence rates of porotic hyperostosis, which vary between populations affected by infectious diseases and non-infectious populations within New York City's African Burial Ground. The porous look of the cranial bones, a sign of porotic hyperostosis, is frequently linked to illnesses like anemia, which can be made worse by infections. 

Substantial evidence connects porotic hyperostosis to iron-deficient anemia. Malnutrition and substandard living circumstances contribute to the high occurrence of iron deficiency anemia within the New York Burial Ground (Blakey, 2003). Additional factors that contribute to porotic hyperostosis include iron loss through perspiration, diseases like sprue that cause malabsorption, prolonged breastfeeding of infants on low-iron breast milk, and weaning of infants on goat's milk, which causes folic acid deficiency and subsequently megaloblastic anemia (Zakrzewski, 2007). 

To determine how prevalence rates vary between populations affected by infectious diseases versus non-infectious causes within the New York African Burial Ground, I aim to use several comparative statistical techniques, including Chi-Square Tests, T-tests, and Logistic Regression. My comprehensive literature report intends to understand better the socioeconomic determinants of health that still exist in modern communities by revealing the intricate relationships between viral illnesses and skeletal health. 

Student Major(s)/Minor: Anthropology

Advisor: Michael Blakey, Anthropology

The Amazon River Delta is one of the one of the world’s largest and receives 10% of the annual global load of organic carbon exported from the land to the world’s oceans. Yet, it is also highly dynamic, as sand, mud, and organic matter are resuspended over thousands of kilometers as it is reworked along the Amazon Mudbanks, which stretch along the coast from Brazil to Venezuela. This project analyzed sediment cores from The Mudbanks to: 1) determine the thickness of the sediment layer deposited and resuspended in the water column (the “mixed layer”), and 2) evaluate the spatial/geographic variability of this mixed layer. In doing so, I have helped address two key biogeochemical questions: how much of the carbon exported from the Amazon River is stored in the delta’s mudbanks, and how much is converted to CO2 during this mixing process, subsequently releasing into the atmosphere?

Student Major(s)/Minor: Chemistry & Biochemistry

Advisor: Christopher Hein, Marine Science

Context: fasting has become a popular technique advertised for weight loss for the general population.

Problem: prior fasting research has only been conducted on a small, non-diverse population (primarily men and post-menopausal women).

Strategy: gather a large, diverse population of participants for the study and have them fast for 24 hours, having them complete various cognitive tasks (viewing neutral and food photos and completing a puzzle) while wearing a functional near-infrared spectroscopy device (fNIRS) to measure brain area recruitment before, during, and after a 24 hour fast.

Research significance: exploring fasting’s effects in a diverse population will help advance personalized medicine efforts because we will be better able to see which type of person may or may not respond well to a fasting period.

Student Major(s)/Minor: Neuroscience

Advisor: Stephanie Caligiuri, Kinesiology

Biofilms have widespread implications for the general public as they play a role in everything from wastewater treatment and nutrient bioavailability in soil to infectious diseases and device-related infections. These communities of microorganisms can be incredibly diverse, with more complex biofilms having cells that work cooperatively and form a community compared to simpler biofilms with cells clumped together but working individually. The cooperation found in more complex biofilms means they can provide stronger responses and are more difficult to handle.

Currently, researchers in a lab will each give an estimate on the biofilm’s visual complexity from one to five and take the average value. My works aims to create a systematic process for classifying biofilms that is robust to image noise. This analysis is centered around measurements of the biofilm's “roughness” or circularity, calculations of local binary patterns, and other image analysis techniques.

Student Major(s)/Minor: Mathematics

Advisor: Sarah Day, Mathematics

In a world where antibiotic resistance is prevalent, new antibiotic development is increasingly necessary. Previously, it was found that short-chain unsymmetric diyn-ols (two subsequent triple bonds with an alcohol (OH) group) with the alcohol placed at the end of the carbon chain exhibited antibiotic properties against e. Coli at stock and diluted concentrations. Therefore, the question became whether internally placed alcohol groups would exhibit the same antibiotic properties. Synthesis and antibiotic testing was carried out on propargylic (alcohol on carbon adjacent to diyne) and homopropargylic (alcohol on carbon adjacent to propargylic position) diyn-ols 10-13 carbons in length. To synthesize these molecules, both Glaser-Hay and Cadiot-Chodkiewicz procedures were used, depending on the state of matter of the reagents, with variable yield. Biological testing revealed that diynols with internally located alcohols function as antibiotics, however, only at stock concentrations, implicating a weaker functionality to internal alcohols compared to their terminal counterparts.

Student Major(s)/Minor: Chemistry

Advisor: Robert Hinkle, Chemistry

Mercury (Hg) is a toxic heavy metal and common waste product from industrial processes. High concentrations are detrimental to many affected animal populations in the organic form, methylmercury (MeHg). Methylmercury accumulates in biological tissue and biomagnifies throughout ecosystems. In areas surrounding the contaminated South River in Waynesboro, VA, concerning high levels of blood mercury content have been observed in songbirds with fully terrestrial diets, including wolf spiders as a primary source of mercury. As opportunistic predators, in the riverside habitat wolf spiders could be feeding on emergent aquatic prey such as dragonflies or fully terrestrial prey such as centipedes. This project will explore the diets of wolf spiders using PCR molecular gut analysis to determine the source of mercury for wolf spiders by identifying genetic sequences from prey. The result of this research will direct cleanup of the river to either the contaminated water itself, or the potentially contaminated floodplain.

Student Major(s)/Minor: Biology

Advisor: Dan Cristol, Biology

The preBötzinger Complex (preBötC) of the lower medulla generates the rhythm underlying breath. Opioid drugs – which claim the lives of tens of thousands of people each year – act upon preBötC neurons to slow the breathing rhythm down which commonly leads to death. Yet, the network- and cellular-level mechanisms by which opioid drugs modulate preBötC neuronal activity are largely unknown. Using electrophysiology, we sought to characterize opioid drug action on preBötC neurons. We expect that one mechanism of action is presynaptic inhibition: Opioid drugs suppress the release of excitatory neurotransmitters which are essential for rhythmogenesis.

Student Major(s)/Minor: Neuroscience & Mathematics

Advisor: Christopher Del Negro, Applied Science

Measurement-based quantum computing (MBQC) is considered to be a promising approach for creating practical quantum computers. This project focuses on creating a compiler framework, a software tool that translates traditional quantum circuits into a format suitable for photonic measurement-based quantum computers. These computers use clusters of entangled photons as their building blocks for quantum information used during computation. This project will begin by adapting an existing framework and then work on enhancing it to reduce computational complexity and redundancy. These improvements could make photonic quantum computers faster and more scalable, pushing the boundaries of quantum computing technology.

Student Major(s)/Minor: Computer Science Major & Mathematics Minor

Advisor: Qun Li, Computer Science

According to the CDC, approximately 1,603,844 people were diagnosed with cancer in the year 2020. The high prevalence of cancer establishes the need for novel drug treatments to be developed. Current limitations of treatments include the indiscriminate killing of all rapidly dividing cells, causing many adverse side effects. By using an antibody that can detect cancer cells and linking a therapeutic agent we can produce a highly specific antibody-drug conjugate (ADC) that delivers the drug only to cancer cells. These bioconjugates are useful, but in order to increase the utility we seek to investigate alternative coupling partners including other proteins and polyethylene glycol (PEG) units that may increase conjugate stability and function. Using Ubiquitin as a model protein, a terminal alkyne is introduced via genetic incorporation of a noncanonical amino acid (ncAA) known as p-propagyloxyphenylalanine (pPrF). This ncAA can serve as a unique handle to direct further reactivity and produce a bioconjugate.  Specifically, we are investigating employing a Glaser-Hay reaction to link another terminal alkyne to the pPrF residue. Initially we investigated the use of PEGs based on their recognized ability to stabilize ADCs via reducing degradation within the bloodstream. This facilitates visualization by SDS-PAGE as the PEG moiety should generate a notable shift in protein migration due to increased size. This research is optimizing the PEG coupling to a protein, and then strives to characterize the increased stability it affords the conjugate. Ultimately, this research may produce a novel mechanism to prepare therapeutics with increased stability, and thus higher potency.

Student Major(s)/Minor: Biochemistry

Advisor: Douglas Young, Chemistry