Biology

Session I

Corban Bewley, "The Role of ppGpp in Cold Recovery in E. coli"

This project examined how the stress signaling molecule ppGpp helps E. coli recover from prolonged exposure to cold temperatures. Previous research in the Anderson Lab found that bacteria unable to produce ppGpp recover less effectively after being kept at 4°C. It was unclear whether these cells were dying during cold exposure or remained alive but were unable to grow. Fluorescent staining and microscopy were used to measure cell death in normal and ppGpp-deficient bacteria after cold exposure. This showed whether reduced recovery in ppGpp-deficient bacteria was due to actual cell death.

ppGpp controls which genes are active in the cell to help bacteria recover from cold exposure. Using rifampicin, an antibiotic that stops gene activity, we determined whether ppGpp controls gene activity before cold exposure or in response to the cold itself. This indicated when ppGpp was needed to control gene activity for effective cold recovery. These experiments clarified how and when ppGpp allows bacteria to recover from prolonged cold exposure.

Student Major(s)/Minor: Biology Major

Advisor: Dr. Sarah Anderon

Amelia Dumont, "Cyp2c Knockout Mice Model Human Like Bile Acid Dysregulation and Inflammatory Signatures in  Intrahepatic Cholestasis of Pregnancy"

Intrahepatic cholestasis of pregnancy (ICP) is a disorder having to do with bile acid levels in the liver. Current mouse models are limited because mice produce a type of bile acid not present in humans that alter bile acid signaling. This study aimed to evaluate the Cyp2c knockout (Cyp2cKO) mouse (Cyp2c gene removed) as a more humanized model of ICP. Pregnant Cyp2cKO mice were evaluated for plasma and liver markers of liver injury, bile acid concentrations and composition using mass spectrometry, lipid processing, and liver RNA alterations. During pregnancy, Cyp2cKO mice developed ICP-like features, including increased liver weight, elevated liver enzyme levels, increased bile acid concentrations, and altered bile acid signaling. There was also a strong innate immune and inflammatory signature in pregnant Cyp2cKO livers. Together, these findings support the Cyp2cKO mouse as a promising model for studying the interactions between bile acid metabolism, inflammation, and immune adaptation in ICP.

Student Major(s)/Minor: Biology Major

Advisor: Dr. Srijani Basu

Benjamin Harris, "Effects of Leaf Litter on Salamander Occupancy Under Coverboards"

Streamside salamanders rely on moist shelter, but it is unclear whether natural cover changes how often they use artificial wooden coverboards. This project asks how leaf litter depth and coarse woody debris, meaning fallen branches and logs, relate to salamander occupancy under coverboards near Williamsburg streams. Researchers surveyed seven streams, recorded salamander presence, and measured habitat conditions at each board. Preliminary data from 410 board checks found only four salamanders, producing too few detections for a reliable test of the proposed relationships. Continued sampling and analysis will determine whether deeper leaf litter or greater amounts of fallen wood correspond with higher or lower board use. These findings will clarify whether low coverboard counts indicate fewer salamanders or simply greater availability of natural shelter. The results can help the ACER Lab interpret long-term monitoring data more accurately and may inform management practices that preserve moist forest-floor habitat for local salamander populations.

Student Majors: Economics and Biology Major

Advisor: Dr. Matthias Leu

Shama Hasan, "Genomic Evolution of Apicomplexan Parasites"

Apicomplexa are a large phylum made up entirely of parasitic protists. Their diverse genomic characteristics and adaptability allow them to infect a wide range of hosts and cause serious diseases in humans and animals, including malaria and toxoplasmosis. An ongoing challenge in public health is understanding how parasites adapt to infect new host species, a process that drives the emergence of new diseases as vector distributions spread. Despite their prevalence, apicomplexa as a whole are understudied in the scientific community, resulting in knowledge gaps in the evolutionary history and invasion strategies of many free-living species. This project will examine the evolutionary relationships among apicomplexan parasites. Comparative genomic analysis will be used to determine association between host shifts and patterns of genomic change across evolutionary lineages. Ultimately, this research aims to improve understanding of how parasitic traits emerge and may help inform efforts to anticipate future disease emergence.

Student Major(s)/Minor: Computational & Applied Mathematics & Statistics Major, Data Science Minor

Advisor: Dr. Xyrus Maurer-Alcalá

Julia Huband, "Timing is Everything: Effects of Predator Cues on Hatching Plasticity of Sand Dollar, Dendraster excentricus, Embryos"

Many animals, including sand dollars, alter their hatching time in response to environmental cues, a phenomenon known as hatching plasticity. A common environmental cue – the presence of predators – is believed to alter hatching time. The goal of this study is to test the hypothesis that exposure to seafloor predator cues will cause the embryos of the sand dollar Dendraster excentricus to hatch early. To explore this, three experimental groups (N = 3 replicate beakers) were generated: (1) no predator cues (negative control), (2) predator cues (experimental group), and (3) no predator cues and low salinity (positive control). Across three trials, the experimental group hatched one to two hours before the control groups, providing evidence that sand dollar embryos detect predator cues and respond by altering their hatching times. Consequently, sand dollars are ecosystem engineers.  Understanding their relationships with their community can provide insight into what drives ecosystem structure and function.

Student Major(s)/Minor: Biology Major, French & Franchophone Studies Minor

Advisor: Dr. Jonathan Allen

Anjali Krishnan, "Investigating the Regulation of Acetone Carboxylase Expression by Two-Component Systems in Helicobacter pylori"

Helicobacter pylori is a bacterium that infects over half the world’s population, persistently colonizing the human stomach. We predict that in order to survive the harshly acidic environment, the pathogen metabolizes the acetone which accumulates during host starvation. The acxABC operon codes for acetone carboxylase, an enzyme that allows H. pylori to metabolize acetone as a source of carbon and energy. Specifically, acxA encodes a catalytic subunit of the enzyme and has been shown to provide a growth advantage when acetone is present. The goal of this project is to define how the expression of AcxA is regulated and to determine whether its contribution to growth is controlled at the transcriptional or post-transcriptional level. Using gene expression analysis, mutant strain creation, and protein tagging and detection, this study will determine how the different regulatory systems affect acetone metabolism. Understanding how H. pylori adapts to the gastric environment may help develop future treatment and prevention strategies.

Student Major(s)/Minor: Biology Major

Advisor: Dr. Mark Forsyth

Devin Lichtenstein, "The Effect of pH on Larval Salamander Growth and Abundance in Freshwater Stream Ecosystems"

Larval salamanders wellbeing is reflective of the overall health of freshwater stream ecosystems. Through understanding the conditions in which they thrive, and the conditions that harm them, we are better equipped to taking care of these crucial ecosystems and preserving them. We take environmental data such as pH, as well as salamander abundance and size measurements along 9 streams in Williamsburg. Through analyzing this data, we will be able to better understand the effect of pH on the health of these salamanders. The raw data indicates that lower and higher pH values, away from a neutral pH of 7, leads to lower growth rates and abundances, a warning to the negative effects of this environmental data.

Student Major(s)/Minor: Biology Major

Advisor: Dr. Matthias Leu

Finnur Oddsson Cricco, "Digging through the Junk Heap: A Case Study in Sustainably Handling Laboratory E-waste"

Scientific labs generate e-waste as equipment breaks down or is phased out for newer technology. The waste can accumulate in stockpiles destined for landfills, as proper handling is often an afterthought. This was the case at our university, where an eclectic assortment of discarded lab equipment could be found in a hallway outside the Integrated Science Center’s loading dock.

The goal of my research was to use this collection of half-broken equipment and other spare parts to build hardware for a synthetic biology research lab. A bioreactor array was prototyped with a scrapped fan and heating sheet, then built using a microcontroller and pumps from previous projects. Auxiliary devices and outreach projects were built using spare parts and open-source electronics. This work demonstrates technical feasibility and material savings, offering laboratories a pathway to embed sustainable engineering practices into student training through equipment reuse and adaptation. 

Student Major(s)/Minor: Engineering Physics Major, Bioengineering Minor

Advisor: Dr. Margaret Saha

Alexis Savage, "Behavioral Analysis of Necrotizing Enterocolitis in a Murine Model Using a DeepLabCut and SimBA Workflow"

Necrotizing enterocolitis (NEC) is a serious gastrointestinal disease that primarily affects premature infants and can lead to long-term health complications. While NEC is characterized by intestinal inflammation and perforation, its effects on neurological development and behavior currently remain less understood. This study investigates whether experimental NEC is associated with measurable behavioral differences in mice. Mice were tested using behavioral assays designed to measure general locomotion, anxiety-related behavior, and social activity. Video recordings were analyzed using an automated workflow incorporating DeepLabCut, a machine-learning tool for tracking animal movement, and SimBA, a software platform used to quantify behavioral patterns. Though more testing is necessary, our findings suggest increased anxiety-related behavior and non-significant change in locomotor ability in mice induced with greater severites of NEC. Identifying behavioral consequences associated with NEC may improve our understanding of the relationship between gastrointestinal disease and neurological development, helping guide future investigations into the long-term outcomes of NEC.

Student Major(s)/Minor: Physics (Medical Concentration) Major

Advisor: Dr. Jenny Rahn

Jason Shen, "Phytoplankton Distribution Pattern Along Main Channel of Chesapeake Bay: A Bayesian Modeling Study"

Phytoplankton are important indicators of aquatic ecosystem health, with growth influenced by nutrient availability, light, temperature, and physical transport. Transport time regulates the balance between nutrient supply and the time available for phytoplankton growth. Previous studies suggest that phytoplankton biomass in estuaries follows a non-monotonic spatial pattern, increasing to a maximum at an intermediate location before declining as nutrient availability becomes limiting. However, this relationship remains difficult to verify using observational data. We use salinity as a surrogate for transport and develop Bayesian models to simulate chlorophyll-a (Chl-a) distributions from approximately 40 years of observations. Results indicate that transport plays an important role in shaping phytoplankton distribution along the Chesapeake Bay main channel. PCA identified a dominant non-monotonic distribution pattern with a mid-Bay peak, with PC1 and PC2 explaining approximately 80% of the variance. Posterior distributions indicate that mean salinity and log(salinity) are the most influential predictors of chlorophyll, while quadratic salinity, DIN, and DIP contribute less.

Student Major(s)/Minor: Biology Major

Advisor: Dr. M. Drew LaMar

Amelia Spitz, "Cyp2c Knockout Mice Model Human Like Bile Acid Dysregulation and Inflammatory Signatures in  Intrahepatic Cholestasis of Pregnancy"

Intrahepatic cholestasis of pregnancy (ICP) is a disorder having to do with bile acid levels in the liver. Current mouse models are limited because mice produce a type of bile acid not present in humans that alter bile acid signaling. This study aimed to evaluate the Cyp2c knockout (Cyp2cKO) mouse (Cyp2c gene removed) as a more humanized model of ICP. Pregnant Cyp2cKO mice were evaluated for plasma and liver markers of liver injury, bile acid concentrations and composition using mass spectrometry, lipid processing, and liver RNA alterations. During pregnancy, Cyp2cKO mice developed ICP-like features, including increased liver weight, elevated liver enzyme levels, increased bile acid concentrations, and altered bile acid signaling. There was also a strong innate immune and inflammatory signature in pregnant Cyp2cKO livers. Together, these findings support the Cyp2cKO mouse as a promising model for studying the interactions between bile acid metabolism, inflammation, and immune adaptation in ICP.

Student Major(s)/Minor: Biology Major

Advisor: Dr. Srijani Basu

Jonah Spotts, "Identifying Genes Enabling Pantoea Stewartii Utilization of Individual Nitrogen and Carbon Sources During In Planta Corn Infection"

Pantoea stewartii subsp. stewartii (Pnss) is a bacterium that infects corn plants and decreases crop yield. Pnss secretes WtsE, an effector protein, into the interior of plant cells. Effectors perturb host cells to promote pathogenicity. For example, WtsE alters host physiology to increase water and nutrient availability in the apoplast. The apoplast is the extracellular space within the leaf that is colonized by Pnss. A twofold approach was used to better understand Pnss nutrient utilization within this niche. Through an indirect approach, we used Random Barcode Transposon Sequencing (Rb-TnSeq) to quantify fitness of strains within a genome-wide mutant library in single nitrogen or carbon sources. Simultaneously, our direct approach involved engineering knockouts of Pnss genes previously shown to be important for utilization of two of those nutrients. We hypothesize that mutants unable to use these nutrients will be less fit during an in planta infection. A longer-term project will identify an exhaustive list of genes important for individual metabolite usage, followed by generation of mutant Pnss strains. Due to the short time frame of this project, we are still in the process of generating three mutants yet have established a clear workflow for additional mutant engineering. The Rb-TnSeq approach was carried through to the point of data collection. Our results will allow us to better understand how the bacterial genes are required for nutrient utilization during infection, which is a key process necessary for pathogenicity.

Student Major/Minor: Biology Major, History Minor

Advisor: Dr. David Mackey, The Ohio State University Department of Horticulture and Crop Science 

Maisie Wang, "Investigating the Regulation of Tumor Suppressor Gene PXR1 During G2/M Phase Arrest in Saccharomyces cerevisiae"

PINX1 is a human tumor suppressor that inhibits telomerase activity and regulates telomere length. To bypass the genomic complexity of human cells, this project investigates PXR1, the yeast ortholog of PINX1, using Saccharomyces cerevisiae (Sc). We examined PXR1 protein localization during G2/M cell cycle arrest and post-release using fluorescence microscopy combined with machine learning-based image processing, data visualization, and quantitative analysis. By measuring the nucleolus-to-cytosol intensity ratio, we observed that proteins preferentially localize to the nucleolus during G2/M arrest, but migrated toward the cytosol upon cell cycle release. Because PINX1 plays a crucial role in regulating cell proliferation, characterizing PXR1 behavior right before division offers valuable insights into fundamental mechanisms relevant to cancer research. Further investigation is required to clarify the molecular mechanisms driving this dynamic redistribution.

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

Advisor: Dr. Oliver Kerscher, Dr. Xyrus Maurer-Alcalá

Carol Yang, "Shaping Muscle: STYXL2 Variants and Regulation of C2C12 Muscle Cells"

Cells rely on protein signaling networks to regulate growth, differentiation, and function. Phosphatases normally remove phosphate groups from proteins, while pseudophosphatases lack catalytic activity but can retain regulatory roles. Serine/threonine/tyrosine-interacting-like protein 2 (STYXL2) is a pseudophosphatase involved in skeletal muscle development whose cellular function remains unclear. This study examined how STYXL2 and its catalytic-site variants affect C2C12 myoblasts (muscle) cell morphology. Cells overexpressing STYXL2, STYXL2 S224H, STYXL2 S225C, or STYXL2 S224H/S225C were fixed and analyzed by fluorescence microscopy. For each construct, 100 randomly selected cells were scored for elongated, muscle-like morphology. One-way ANOVA showed significant differences among groups, and post-hoc tests identified significant differences between the control and STYL2 and each STYXL2 variant. These findings suggest that STYXL2 influences morphological changes associated with C2C12 differentiation. Future studies will quantify extension length and examine cellular responses to external stimuli to further investigate STYXL2 function.

Student Major(s)/Minor: Biology and Computational & Applied Mathematics & Statistics Major

Advisor: Dr. Shantá D. Hinton

Session II

Elena Benson, "Developing a 4× Expansion Microscopy Protocol to Study the FB–MO During C. elegans Spermatogenesis"

Spermatogenesis is the process of sperm cell development that produces healthy, motile sperm. While the motility of mature sperm has been well studied, the earlier stages of this development are far less understood. Mature sperm in many species are unable to make new proteins, requiring all necessary motility proteins to be produced during early spermatogenesis and be correctly partitioned into later cells. Recent findings reveal that in the model organism Caenorhabditis elegans, the kinases TTBK-8.1/2 are required for proper sperm motility. This research project will identify the pattern of proteins TTBK-8.1and TTBK-8.2 in developing spermatocytes before the meiotic divisions and how they are subsequently distributed to individual sperm. Immunofluorescent labeling will be used to track the subcellular location of TTBK-8.1/2 throughout these stages. Because developing spermatocytes contain densely organized structures, expansion microscopy will be used to physically enlarge the samples and improve visualization of TTBK-8.1/2 localization and

co-localization with other known sperm proteins. Characterizing these patterns may

clarify how sperm motility proteins are organized during early development and provide insight into fertility.​

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

Advisor: Dr. Diane Shakes

Aarthi Bharathan, "Linking Transposase Domestication to Patterns of Eukaryotic Evolution"

Mobile genetic elements (MGEs) are DNA sequences that move within genomes and have played a fundamental role in genome evolution. Ciliates are a group of microbial eukaryotes possessing separate germline and somatic genomes in distinct nuclei. Following sexual reproduction, precise excision of germline-limited DNA is performed by domesticated MGEs during somatic genome development, providing a unique model for investigating the evolution of natural gene-editing systems. Using comparative genomics and phylogenomics, this project examines the evolutionary history of wild and domesticated PiggyBac transposases across ciliates and diverse eukaryotic lineages. High-performance computing pipelines integrate sequence similarity searches (DIAMOND), protein domain identification (HMMER), and structural homology prediction (ESMFold2, Foldseek, TM-align) to identify conserved transposases in publicly available genomes and transcriptomes. By reconstructing the evolutionary history of PiggyBac transposases, this work provides insight into the origins of eukaryotic genome editing and the evolutionary processes shaping eukaryotic genomes.

Student Major(s)/Minor: Computational & Applied Mathematics & Statistics (Mathematical Biology) Major, Data Science Minor

Advisor: Dr. Xyrus Maurer-Alcala

Lucy Brennan, "Understanding the Basic Life Cycle of Heliophrya Through Microscopy"

The focus of eukaryotic biology typically is limited to complex multicellular organisms, specifically humans. Due to its one sided nature, single cell eukaryotes and their unique life cycles and histories are underresearched despite their importance  in ecosystems (oxygen production, aquatic food webs, and recycling nutrients) and health (parasitism and toxic algal blooms impacting shellfish toxicity). Despite their importance in our water works and as bioindicators of water quality, we poorly understand the life history of ciliates, such as Heliophrya,  a pin cushion-like ciliate. This summer research aims to develop a comprehensive life history of this bioindicator ciliate, including expanding on the structure of its nucleus, and morphological changes it goes through during growth and mating. Given the most recent descriptions are from >30 years prior,  the hope of this summer research is to draw connections between the more obvious stages through captured proof of their transitions using advanced microscopy techniques (confocal microscopy). The overall scientific process will facilitate creation of other lab protocols: microscopy, cell culture maintenance, and proof of concept.

Student Major(s)/Minor: Neuroscience Major, Biochemistry Minor

Advisor: Dr. Xyrus Maurer-Alcala

Isabelle Cleaveland, "Monitoring of Nesting Diamondback Terrapins on Long Beach Island, NJ"

The Diamondback Terrapin is a species of special concern and is the only fully estuarine turtle in North America. Each summer, female terrapins emerge from tidal

marshes to nest, but much of their historic nesting area is now occupied by coastal development. This project will assess the occurrence, frequency, and success of nesting forays by female diamondback terrapins on Long Beach Island, NJ, where a study of terrapins has been ongoing for more than a decade. Daily monitoring of nesting areas will be completed; new terrapin captures will be marked using passive transponder (PIT) tags to allow for future identification. Nest site locations, frequency of nesting (females nest three or more times per year), and whether the nests are predated or survive to hatching will be determined, thereby adding to the ongoing study. The PIT tagging technology will be transferred to W&M for future research on Virginia terrapin populations.

Student Major(s)/Minor: Chemistry Major

Advisor: Dr. Randolph Chambers

Juliana Corallo, "Diagnosing Genetic Disorders: A Case Study of Somatic Mosaicism in the Brain"

Somatic mosaicism is a rare genetic disorder where a mutation occurring after fertilization causes cells to have different sets of genetic information. While this type of genetic mutation can occur in any part of the body, it can be extremely harmful when it occurs in the brain, frequently causing epilepsy. However, diagnosing somatic mosaicism in the brain can be challenging due to the location of the tissue required to be sampled for examination. This literature review explores the diagnostic process for somatic mosaicism in the brain through a case study of epileptogenic cortical dysplasia. Using databases such as Pubmed, a comprehensive search of recent publications assessed data from primary studies involving next generation sequencing. This data was synthesized and used to review current diagnostic techniques and investigate emerging techniques and their impacts on clinical decisions and patient outcomes.

Student Major(s)/Minor: Chemistry Major

Advisor: Dr. Patricia Habersham

Annabel Coxon, "Genome Architecture in Parasitic Kinetoplastids"

Kinetoplastids are a species-rich group of microbial eukaryotes (protists) that encapsulate a number of parasitic lineages with human health implications (e.g., Trypanosoma and Leishmania, the causative agents of “African sleeping sickness” and leishmaniasis). The diseases caused by this diverse lineage of parasites result in thousands of deaths annually, and while several pharmaceutical treatments exist, there are no vaccines. These parasites have unique methods of host immune system evasion based on the distribution and functions of their genes. This study focuses on the evolutionary characteristics of parasitic Kinetoplastid species that provide insight into their infectious tendencies. We use bioinformatic tools such as OrthoFinder and IQTree to infer the phylogenetic relationships between these species. We find that the genes in these species are non-randomly distributed along chromosomes, and analyze the numbers and percentages of genes that belong to orthogroups. The findings from this study will allow for further research into these species’ unique genes.

Student Major(s)/Minor: Biology Major

Advisor: Dr. Xyrus Maurer-Alcala

Samantha Di Santi, "Impact of Select Disease-Associated Mutations on Thyroid Hormone Receptor Cellular Localization and Function"

This project will analyze thyroid hormone receptor alpha 1 (TRα1), a protein that helps cells respond to thyroid hormone (T3) and regulates gene expression. A rare genetic condition, Resistance to Thyroid Hormone syndrome alpha (RTHα), is

caused by TRα1 mutations that prevent the body from responding properly to T3. This results in tissue specific hypothyroidism especially in brain, heart, and skeletal

muscle tissue. Previous research demonstrated that an RTHα mutant missing the end of the T3 binding region (C392X) was still tagged appropriately for breakdown within the cell. This project will examine several other mutations (A263S, A263V, and I170V) to see whether they affect protein localization, stability, and the breakdown process. The goal is to determine whether these mutations disrupt TRα1 function through shared or distinct mechanisms. Linking these molecular mechanism defects to disrupted T3 signaling can help explain how particular mutations lead to clinical symptoms of RTHα.

Student Major(s)/Minor: Biology Major

Advisor: Dr. Lizabeth Allison

Kamna Kalkunte, "Visualizing Endosymbiotic Gene Transfers in Eukaryotes"

Eukaryotes represent an incredible biological diversity, from singular cells to large multicellular animals possessing complex abilities and adaptive potential to extreme environments. While most studied eukaryotes undergo oxygenic respiration, like most plants, animals, and fungi, numerous lineages of eukaryotes are solely found in environmental conditions lacking oxygen (i.e., animal guts, anaerobic muds and water). Some eukaryotes have the ability to respire nitrogen in addition to oxygen, providing them with a unique metabolic flexibility. However, the origin, evolution, and distribution of genes involved in non-oxygenic respiration pathways in eukaryotes is extremely understudied. This project laid the foundation for exploring the genetic origins of non-oxygenic respiration by confirming the genetic transfer of photosynthetic abilities among eukaryotes. This was done through protein sequence analysis of thousands of taxa and construction of phylogenetic trees that display known endosymbiotic gene transfers between eukaryotes. Using Photosynthesis as a positive control, various computational methods were developed to filter large datasets of taxa, protein sequences, and shared genes. These programs will be used on larger datasets containing both eukaryotic and prokaryotic taxa to investigate the hypothesized lateral gene transfers that led to non-oxygenic respiration in eukaryotes. Ultimately, this project aims to provide insight into the evolution of metabolic flexibility in eukaryotes, which is increasingly important considering the consequences of climate change, which includes major deoxygenation events in our oceans.

Student Major(s)/Minor: Computational & Applied Mathematics & Statistics (Mathematical Biology) and Biology Major

Advisor: Dr. Xyrus Maurer-Alcala

Olivia Kerr, "Characterizing the Meiotic Arrest Phenotype of spe-6(null) Caenorhabditis elegans Spermatocytes"

Spermatogenesis, male-specific meiosis through which parental genetic material is split amongst spermatocytes, is essential for many organisms to reproduce effectively. Understanding this process and its potential downfalls can provide insight into male infertility. Previous studies by Varkey, et al. (1993) show that an absence of SPE-6, a specific type of essential protein for spermatogenesis known as a kinase, results in early meiotic arrest and subsequent infertility in C. elegans. The present study aims to characterize the spe-6 meiotic arrest phenotype by comparing it to related human proteins that when knocked out result in distinct meiotic arrest phenotypes. We visualized proper chromosomal detachment from the nuclear envelope in both wild type and spe-6 male gonads. Our findings establish our capability to conduct future investigations, such as microtubule dynamics and chromosomal separation from the kinetochore, to understand the mechanism of meiotic arrest in C. elegans lacking SPE-6.

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

Advisor: Dr. Diane Shakes

Nathan Kulp, "The Effect of Milkweed-Found Microbes on Pollen Tube Germination of other Local Plants at Blandy Experimental Farm"

Many common milkweed- found bacteria and fungi have been shown to be detrimental to the pollen tubes of common milkweed pollen packets (pollinia). This project examined whether selected microbial species that had been studied in common milkweed exhibited the same effects onto other local plant species’ pollen at Blandy Experimental Farm in Boyce, VA. Pollen from six non-milkweed plant species, a mix of native, non-native, invasive, and agricultural plants, were exposed to 19 microbial species studied in Milkweed. While a full analysis is pending, pollen from across the six plant was often sterilized or experienced reduced germination in the presence of the 19 selected microbial species, indicating that the selected plants might have a similar response to common Milkweed. The six plant species examined were predominantly bee-pollinated species. This means that the flowers would likely be exchanging microbial communities, making this work significant in demonstrating potential impacts of this exchange. 

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

Advisor: Dr. Harmony Dalgleish

Daniel Li, "Antisense Oligonucleotides Targeting SPIN4"

Skeletal dysplasias are a diverse group of genetic disorders affecting 1 in 4,000 live births and resulting in extreme short stature and altered bone quality. While hyperactive WNT/β-catenin signaling is a known feature of many skeletal dysplasias, no therapies are currently available. We previously reported a new epigenetic reader gene, Spindlin Family Member 4 (SPIN4), where mutations can cause enhanced bone growth and overgrowth syndrome by suppressing WNT/β-catenin signaling. We developed human and mice antisense oligonucleotides (ASOs) targeting SPIN4 and tested their ability to suppress SPIN4 in cell and mice models. Cells treated with ASOs showed reduced SPIN4 expression, reduced WNT signaling, and increased cell proliferation, including in disease models. Mice treated with ASOs showed inconclusive results and further analysis with a larger sample will be necessary. Our results show a novel potential approach to treat bone disorders caused by WNT/β-catenin hyperactivation. 

Student Major(s)/Minor: Biology Major

Advisor: Dr. Oliver Kerscher

Samuel Li, "Stopping HIV-1 at Cellular Baggage Claim: Achieving Homogeneous Assembly of the HIV-1 Gag-RNA Nucleation Complex for Cryo-EM Structural Characterization"

HIV-1 is a retrovirus affecting more than 40 million individuals worldwide. One promising drug target is the interaction between the viruses’ Gag protein and its RNA genome that is necessary to form the viruses’ protein shell. Our ultimate goal is to solve the 3D structure of this Gag/RNA complex. To do this, our lab is using a technique called cryo-EM single-particle analysis (SPA). SPA takes thousands of images of the complex then averages them all together to create a 3D model. We want to create as many complexes that look exactly the same as possible so there’s less noise during averaging leading to a high resolution model. My project focused on different methods to get homogenous-looking complexes. Determining the 3D structure of the complex will allow us to understand how HIV forms its protein shells and potentially lead to the development of a new class of HIV drugs.

Student Major(s)/Minor: Biology Major

Advisor: Dr. Oliver Kerscher

Harika Mandava, "The ABC’s of Microeukaryotic Transcriptomics: Assessing By-Catch in Publicly Available Datasets"

Microbial eukaryotes (protists) represent a significant yet understudied proportion of eukaryotic diversity, encompassing diverse lifestyles and organismal interactions. Thousands of protist transcriptome assemblies are available in public repositories (such as NCBI’s Short Read Archive), with this number rapidly growing due to the widespread adoption of single-cell transcriptomic and genomic approaches. Traditionally, non-host sequences arising from bacterial and eukaryotic associations have been treated as contamination. Current contamination-screening approaches predominantly rely on sequence identity comparisons, which cannot reliably distinguish true contamination from biologically meaningful associations and interactions, which we refer to as “by-catch.” Here, we present a bioinformatic pipeline that integrates rapid phylogenomic screening and sequence-composition metrics to identify actionable by-catch across ~2,400 unique protist transcriptomes. By combining this diagnostic approach with an existing machine-learning-based sequence classification tool, we provide a unique opportunity to explore overlooked biologically meaningful relationships (including incipient symbioses and kleptoplasty) within complex transcriptomic datasets.

Student Major(s)/Minor: Chemistry Major

Advisor: Dr. Xyrus Maurer-Alcala

Matthew Mercer, "RNAi Knockdown of EcR in Gryllus lineaticeps"

We were attempting to perform an RNAi knockdown of the Ecdysone receptor gene to reduce the expression of ecdysone in crickets and analyze its role in wing length determination. However, it was unsuccessful, as the gene was not knocked down. Ecdysone is a gene heavily involved with molting and is believed to have a role in the determination of a cricket's wing length, so we attempted to reduce, not eliminate, the expression of the Ecdysone receptor gene. Methods included quantitative PCR to measure RNA concentration and gene expression, and double-stranded RNA injection. Despite the lack of knockdown in our methods, revisions could be made to achieve the desired result, such as increasing the amount of double-stranded RNA injected, increasing the volume of fluid injected, and/or increasing the number of times injections are performed.

Student Major(s)/Minor: Biology Major

Advisor: Dr. Lisa Treidel

Caitlin Murphy, "In Search of Gynaecotyla: A Spatial Observation of Trematode Infections of the Eastern Mudsnail, Iylanassa obsoleta"

This project examines how trematode parasite prevalence varies among Eastern mudsnail (Ilyanassa obsoleta) populations across five coastal field sites in Virginia. Trematodes are parasitic flatworms that utilize different host species—such as mollusks, crustaceans, and vertebrates—throughout their life history, making them useful indicators of community structure. While this study initially sought to identify a particular trematode species, Gynaecotyla adunca, substantial data were collected on Ilyanassa obsoleta trematode infections as a whole. During field sampling, mudsnails were collected from each site and dissected to identify infections based on their cercarial life stage. This approach provided spatial data on parasite communities within mudsnail populations, which can uncover additional information about definitive host ecologies at the different sites. Comparison of infection patterns across locations revealed differences in parasite prevalence and species composition, which can also aid in further research on parasite dynamics in coastal Virginia.

Student Major(s)/Minor: Coastal & Marine Sciences Major

Advisor: Dr. Jeff Shields

Hao Ni, "Phenotypic Analysis of a Federally Threated Coastal Plant"

Aeschynomene virginica (sensitive jointvetch) is a federally threatened annual plant found in tidal freshwater and brackish marshes of the mid-Atlantic coast. Despite its conservation status, relatively little is known about the phenotypic variation present within and between populations of this species. A. indica is a closely related and more widespread species that occurs in similar habitats and shares similar floral characteristics with A. virginica. Characterizing phenotypic differences between these species can provide insight into traits that distinguish A. virginica and may contribute to its ecological and reproductive biology. This project investigates phenotypic variation in A. virginica and compares selected morphological and reproductive traits with those of A. indica. Plants of both species were grown under controlled conditions, and phenotypic traits were measured to characterize differences in vegetative and floral morphology. Controlled pollinations were also conducted between and within species to investigate reproductive compatibility. By documenting phenotypic variation in A. virginica and comparing it with a closely related species, this research provides a broader characterization of the biology of a federally threatened coastal plant and establishes a foundation for understanding its reproductive and conservation biology.

Student Major(s)/Minor: Biology Major

Advisor: Dr. Joshua Puzey

Elena Ottens, "Phenotypic Analysis of a Federally Threated Coastal Plant"

Aeschynomene virginica (sensitive jointvetch) is a federally threatened annual plant found in tidal freshwater and brackish marshes of the mid-Atlantic coast. Despite its conservation status, relatively little is known about the phenotypic variation present within and between populations of this species. A. indica is a closely related and more widespread species that occurs in similar habitats and shares similar floral characteristics with A. virginica. Characterizing phenotypic differences between these species can provide insight into traits that distinguish A. virginica and may contribute to its ecological and reproductive biology. This project investigates phenotypic variation in A. virginica and compares selected morphological and reproductive traits with those of A. indica. Plants of both species were grown under controlled conditions, and phenotypic traits were measured to characterize differences in vegetative and floral morphology. Controlled pollinations were also conducted between and within species to investigate reproductive compatibility. By documenting phenotypic variation in A. virginica and comparing it with a closely related species, this research provides a broader characterization of the biology of a federally threatened coastal plant and establishes a foundation for understanding its reproductive and conservation biology.

Student Major(s)/Minor: Biology and Geology Major

Advisor: Dr. Joshua Puzey

Kiran Rollins, "Vertical Movement of Larvae in Response to Predator Cues in D. excentricus and E. parma"

Predation is crucial to managing the populations, resources and overall health of an ecosystem. Marine invertebrates in an early life stage can alter their behavior and morphology in response to predators, making mortality range from 0% to 100%. We placed sand dollars Dendraster excentricus and Echinarachnius parma into columns with either control filtered seawater or water containing low or high levels of water from benthic, or bottom-dwelling, predators. We recorded the vertical position of the larvae to track if they swam upwards, away from chemical cues left by the benthic predator. Through six different trials on D. excentricus, 17% more larvae were found on top of the column for the high predator cue concentration than the control. Through one trial on E. parma, 15% more larvae were found atop the column. Movement in response to predation indicates that predators can control their environments even without consumption of prey.

Student Major(s)/Minor: Undeclared

Advisor: Dr. Jonathan Allen

Chelsea Swei, "Mechanism for Unstable Mecillinam Resistance in Escherichia coli MG1655"

Escherichia coli exhibits unstable resistance to the antibiotic mecillinam. Three genes known to contribute to other mechanisms of mecillinam resistance, mrcB, ftsZ, and dksA, have an increased copy number in some unstable resistant isolates. Copy number of each gene returns to one when isolates are cultured in the absence of mecillinam. Amplification of mrcB and ftsZ leads to a 4-fold increase in expression of these genes. To determine whether this level of overexpression is sufficient to confer resistance, we used plasmids encoding ftsZ and mrcB to increase expression to the level observed in the unstable resistant strains. We found that overexpressing ftsZ 3.7-fold confers a 62.5-fold increase in resistance, similar to the 37-fold increase in resistance exhibited by the unstable resistant isolates. However, overexpression of mrcB showed inconclusive results. This project will contribute to the growing understanding of resistance mechanisms, in order to aid in combating antibiotic resistance.

Student Major(s)/Minor: Biology Major

Advisor: Dr. Sarah Anderson

Logan Tannenbaum, "From Turbine to Tributary: The Impact of Energy Production on Local Macroinvertebrate Populations"

In the last century, the methods through which we produce energy have diversified; from coal and oil to gas, and then to renewable methods like solar. Previous data demonstrates that nonrenewable sources have detrimental effects on ecosystems. However, research is lacking on the impact of other energy generation on surrounding areas. To answer this question, my research project investigated the impact of multiple types of power generation on the health of local streams and wildlife through sampling of underwater macroinvertebrate populations. Macroinvertebrates include crustaceans, snails, and insects in their larval stages, and are an excellent representative of the health of the stream because each species requires specific pollution levels of the habitat to survive. Therefore, sampling the prevalence of macroinvertebrate species is a clear way to measure stream health. I also took account of other environmental factors such as neighborhoods and conducted water quality testing to generate a holistic picture of each stream. I found difficulty in attributing differences in stream health to a specific factor, but I anticipate my data will demonstrate that renewable sources were healthier than nonrenewable ones.

Student Major(s)/Minor: Environment & Sustainability and Integrative Conservation Major

Advisor: Dr. Kelly Hallinger

Olivia Warren, "C. elegans amoeboid sperm require proteins tau tubulin kinases 8.1 and 8.2 (TTBK-8.1/2) for effective crawling"

Nematode sperm are crawling cells whose motility is powered by the dynamics of the Major Sperm Protein (MSP) within their extended pseudopod. Earlier biochemical studies in Ascaris first identified MSP polymerization-activating kinase (MPAK) as a key regulator of MSP assembly within the pseudopod. Here we investigate the role of MPAK homologs in C. elegans: TTBK-8.1 and TTBK-8.2. Similar to MPAK in Ascaris, TTBK-8.1/2 localizes to the pseudopods of wildtype spermatozoa. Single knockout males have fertility comparable to wildtype males, while double knockout males are infertile. ttbk-8.1/2 males successfully transfer sperm, but their sperm do not crawl to the site of fertilization. Wildtype in vitro activated sperm initially extend filopodia-like spikes and subsequently a motile pseudopod. However, ttbk-8.1/2 sperm initially form spikes but either arrest after spike protrusion or form abnormal pseudopods. Ongoing studies will further characterize TTBK-8.1/2’s molecular interactions and function in sperm motility.

Student Major(s)/Minor: Computational & Applied Mathematics & Statistics (Mathematical Biology) Major

Advisor: Dr. Diane Shakes

Rachel Way, "The Next Generation of Stars: How a Small Sea Star’s Anatomy and Reproduction Support a Solely Fissiparious Lifecycle "

Sea stars are commonly viewed as a keystone species in the habitat they inhabit due to their predatory nature [3]. They are often essential for keeping the ecosystem in check and making sure no one organism begins to take over the area. For this reason, this project will focus on the developmental processes of a small tropical species of sea star that does not grow and reproduce in the normal way. A majority of sea stars go through a planktonic larval stage before settling on the benthos and metamorphosing into a juvenile sea star. However, in Aquilonastera yairi they often rely on asexual reproduction in the form of fissioning to increase their population. The focus of this project was to explore the morphological differences present in A. yairi due to this alternate method of reproduction and the physical process necessary for this method of reproduction. 

Student Major(s)/Minor: Biology Major

Advisor: Dr. Jonathan Allen

Wilson Wicelinski, "Determining the Impact of a Fatty Acid Transporter on E. coli Cold Survival in the Absence of ppGpp."

The signaling molecule ppGpp is required for E. coli to survive at cold temperatures (4C). Cells unable to produce ppGpp (ppGpp0) are more sensitive to cold, but the mechanism of this cold tolerance is unknown. Additionally, ppGpp0 cells which lack a functional fadL gene, which allows molecules known as fatty acids to enter the cell, have increased cold survival compared to unmodified ppGpp0. The first goal of this project is to understand whether the cold tolerance in the nonfunctional mutant is due to a loss of fatty acid transport, or an additional unknown function of FadL. To study this, we worked to make ppGpp0 cells which express a transport-defective version of fadL called fadLA77E,S100R. To determine whether ppGpp regulates levels of fadL during cold exposure, we measured the amount of fadL in cells stored at 4C.  We did not find a clear relationship between ppGpp production and fadL expression.

Student Major(s)/Minor: Biology and Theatre Major

Advisor: Dr. Sarah Anderson

Abigail Yang, "Neuronal Pcf11N Knockdown Alters Transcriptome-wide Alternative Polyadenylation"

Alternative polyadenylation (APA), an RNA processing mechanism, produces transcript isoforms with unique 3’ untranslated regions (3’ UTRs), which regulate mRNA stability and subcellular localization, from a single gene. While dysregulated APA is linked with neurodegeneration and neurodevelopmental disorders, the mechanisms selectively regulating neuronal PAS usage are not fully understood. Pcf11, a conserved component of the cleavage and polyadenylation complex CFIIm, promotes proximal poly(A) site (PAS) usage, inhibiting the otherwise preferred distal PAS usage of the nervous system. Preliminary studies identified Pcf11N, a class of isoforms enriched in Drosophila melanogaster neurons, containing an intrinsically disordered region (IDR). We aimed to further elucidate the in vivo functional impact of Pcf11N isoforms in L3 Drosophila Central Nervous System. We found that neuron-specific Pcf11N knockdown leads to increased distal PAS usage and 3’ UTR lengthening in transcriptome-wide target genes. To identify the neuronal APA targets of PCF11N, we induced neuronspecific Pcf11N knockdown in transgenic flies and characterized the resulting transcriptome-wide APA changes using Long Read RNA sequencing. 3.4% of genes, including those crucial to development and differentiation, showed significantly increased levels of longer isoforms, indicating distal PAS usage. Additionally, we designed an shRNA construct to generate an shPcf11 transgenic line targeting all Pcf11 isoforms. This line will be used for future neuronal knockdown and rescue experiments to test the neuronal requirement of canonical Pcf11 isoforms.

Student Major(s)/Minor: Biology and Computational & Applied Mathematics & Statistics Major

Advisor: Dr. Matthew Wawersik

Nathan Yang, "Characterizing the Meiotic Arrest Phenotype of spe-6(null) Caenorhabditis elegans Spermatocytes"

Spermatogenesis, male-specific meiosis through which parental genetic material is split amongst spermatocytes, is essential for many organisms to reproduce effectively. Understanding this process and its potential downfalls can provide insight into male infertility. Previous studies by Varkey, et al. (1993) show that an absence of SPE-6, a specific type of essential protein for spermatogenesis known as a kinase, results in early meiotic arrest and subsequent infertility in C. elegans. The present study aims to characterize the spe-6 meiotic arrest phenotype by comparing it to related human proteins that when knocked out result in distinct meiotic arrest phenotypes. We visualized proper chromosomal detachment from the nuclear envelope in both wild type and spe-6 male gonads. Our findings establish our capability to conduct future investigations, such as microtubule dynamics and chromosomal separation from the kinetochore, to understand the mechanism of meiotic arrest in C. elegans lacking SPE-6.

Student Major(s)/Minor: Computational & Applied Mathematics & Statistics (Mathematical Biology) and Public Policy Major

Advisor: Dr. Diane Shakes