Biology

Session I

Boston Andrew, Jacob Diaz, "The Kinase SPE-55 is Required for the Localized Assembly of MSP, the Key Cytoskeletal Protein of Nematode Sperm"

During sperm development, the sperm cells of Caenorhabditis elegans fascinatingly cease transcription, meaning that the sperm must undergo regulated cellular remodeling and regulation with the aid of accessory proteins transcribed prior to the karyosome stage. In the “budding division” that follows anaphase II, spermatocytes discard unnecessary cell components into a waste bag called a residual body. As a result, the mature sperm locomote not via actin or tubulin but via the Major Sperm Protein (MSP) – a cytoskeletal protein that dynamically drives the sperm’s crawling-based cell motility. To ensure MSP arrives properly to the crawling pseudopod, it is sequestered into structures called fibrous bodies (FBs). In our current model the Casein Kinase 1 (CK1) SPE-6 is required for MSP polymerization, whereas the intrinsically disordered protein SPE-18 ensures that MSP polymerizes and bundles specifically at the cytosolic face of the Membranous Organelle (MO). Our immunofluorescence microscopy analysis of the kinase SPE-55 suggests that FB formation is primarily important for ensuring that MSP and other FB components are "packaged" for proper segregation to the spermatids. Further studies into the interactions of SPE55 kinase with SPE6 and SPE18 will unfold novel mechanistic insights into localized MSP assembly. 

Student Major(s)/Minor: Boston: Biology Major, Art & Art History Minor; Jacob: Biology Major, Chemistry Minor

Advisor: Dr. Diane Shakes

Brendan Anselmo, "The Benefits of Low Carbon Strategy on Healthcare Spending" 

Transboundary pollutants, including carbon dioxide, sulfur dioxide, particulate matter, and others, are emitted by various US industries and contribute to health complications and mortalities, increasing healthcare spending. In the context of an ever increasing federal deficit and rising health care spending, it's valuable to consider how low carbon strategy, which aims to reduce these pollutants, can reduce spending on healthcare. In order to analyze the potential of low carbon strategy, my research analyzed the economic impacts of pollutants, and then used a costs benefit analysis to look at how different models of low carbon strategy could reduce impacts while keeping costs down. In doing so, I have found that a moderate input of various low carbon technologies (hydrogen energy, CCS, nuclear, wind and solar, etc.), provide the most cost effective solution while also being feasible and beneficial to a strong US energy market.

Student Major(s): Biology and Environmental Science

Advisor: Dr. Mayank Chugh

Madeleine Babcock, "Fiddling Around: the effects of invasive root masses on the burrowing activity of Leptuca pugliator"

This project addresses how burrowing activity of the Atlantic Sand Fiddler, Leptuca pugilator, is affected by the dense, rhizomatic, root structure of the invasive reed, Phragmites australis. Burrows in strands of Phragmites and the native Spartina alterniflora are counted and casted to analyze burrow depth and shape characteristics. Crabs are then placed under enclosures to assess capability and willingness to burrow in Phragmites and Spartina root masses. The complexity of shape in burrows among Phragmites should increase due to the “trial-and-error” approach a crab must take to avoid the barrier that large, dense roots present. With increasing complexity may come decreasing depth as the energy expenditure from navigating the dense root mass could result in a tradeoff with depth. Fiddler crabs depend on burrows for reproductive and safety purposes, so a crabs ability to burrow correlates with its fitness. Therefore, understanding the effect of an invasive plant on Leptuca pugilator's burrowing ability could have significant conservation implications.

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

Advisor: Dr. Matthias Leu

Aarthi Bharathan, "Evaluating Candidate Genes for a Role in E. coli Cell Division" 

The stress signaling molecule" ppGpp and its complementary transcription factor DksA indirectly activate FtsZ, an important component of the protein machinery responsible for cell division. However, the pathway of FtsZ regulation is unknown. Dr. Anderson identified 89 genes with differential expression in dksA mutants. We hypothesized that at least one of these genes directly regulates FtsZ. The microbiology lab screened 36 of the most promising genes by deleting them in cells with the ftsZ84 mutation (heat sensitive allele of ftsZ) and determining heat sensitivity. Nine of these genes appeared to affect the phenotype of ftsZ84 or gave inconclusive results. This summer, the heat sensitivity of these genes were evaluated. Our results demonstrate that none of the genes have an effect on bacterial cell division. We also confirmed 33 of the 36 gene knockouts by PCR. 

Student Major(s): CAMS Mathematical Biology Track

Advisor: Dr. Sarah Anderson

Nina Bugg, "Decoding Cold Tolerance: The Role of ppGpp and its Targets in E. coli"

ppGpp, an alarmone conserved across bacteria, decreases growth and induces stress responses at transcriptional and post-translational levels. ppGpp is critical for survival during long-term refrigeration, but the exact mechanism remains unclear. The Anderson Lab focused on identifying putative cold-tolerant ppGpp0 mutants through spontaneous selection. We screened 194 different potential cold-tolerant mutants by growing cultures for 2.5 hours, serially diluting, and comparing survival following 0 or 21 days of incubation at 4°C. We discovered 11 strains exhibiting increased survival. Candidates were further tested using exponential-phase cultures normalized to the same concentration and incubated for 0, 7, and 21 days at 4°C, ultimately confirming more cold-tolerance compared to ppGpp0cells. Additionally, we evaluated the cold tolerance of WT and ppGpp0 cells using liquid cultures, using propidium iodide (PI) staining. We discovered that cells lacking ppGpp showed notable death and damage. This research enhances our understanding of ppGpp’s role in bacterial adaptation to stress and bacterial survival in long-term refrigeration.

Student Major(s)/Minor: Human Health and Physiology Major; Biology Minor

Advisor: Dr. Sarah Anderson

Madison Danese, "Hatching and Development in Gastropod Mollusks"

Softshell clams are a major resource in Maine, with a commercial value of $23M in 2015. Euspira triseriata moon snails are significant predators of softshell clams, so it is possible to increase softshell clam populations (and economic output in Maine) by reducing the E. triseriata population. One method of controlling the population is through removing their eggs (case-like structures called sand collars) from mudflats. However, this method may only be successful when the sand collars are likely to hatch as crawl-away juveniles, rather than dispersive larvae. Therefore, this project observed sand collars to determine when they may be more likely to hatch as crawl-away juveniles. This project also investigated the feeding patterns of Doris pseudoargus sea lemon larvae to understand how they thrive as an invasive species in the Gulf of Maine and learn more about their life history strategies. 

Student Major(s): Biology

Advisor: Dr. Jonathan Allen

Naomi Heilen, "Quantifying the Response of Aquatic Fungal Communities to Dam Removal using Environmental DNA (eDNA)"

Dams are a common anthropogenic feature that shift the environment of rivers and reduce fungal biomasses and taxa richness upstream and downstream of dams. Fungi play pivotal roles in many biological processes, so these shifts may have large-scale impacts on the aquatic ecosystem (Bai et al 2018, Colas et al 2016). Dam removals are becoming increasingly popular, however, reversal of the dams’ negative effects may not be timely or complete after removal (Stanley et al 2003). This project will investigate (1) if aquatic fungal communities return to “pre-dam” conditions following removal and (2) the timeline of recovery. The project will employ new non-invasive environmental DNA (eDNA) sequencing and bioinformatics methods to assess fungal taxonomic and functional diversity at dammed, undammed, and dam-removal sites across Virginia. As fungi are both highly sensitive to anthropogenic environmental stressors and predictive of ecosystem functioning decline, they may serve as a powerful metric for understanding the cascading effects of dam removals on aquatic ecosystem function and recovery. 

Student Major(s): Marine Science, Biology

Advisor: Dr. James Skelton

Samuel Li, "Ulp2 SUMO Protease Mutation Induces Thermosensitivity in Kluyveromyces Marxianus Yeast"

SUMO is a small protein modifier that plays important roles in essential cellular pathways including transcription, cell cycle progression, and DNA repair. To understand whether SUMO plays a role in stress tolerance we investigated the functional role of the SUMO protease Ulp2 in the thermotolerant yeast strain Kluyveromyces marxianus. Ulp2 plays a key role in the SUMO pathway by cleaving chains of SUMO in the nucleus. We created a novel CRISPR targeting construct to knockout Ulp2 in K. marxianus. After generating a ulp2* knockout strain, we used spotting assays with various temperature treatments to compare its thermotolerance to other yeast ulp2* mutants and wild type strains. These spotting assays showed a slight increase in thermosensitivity of our new mutant as well as an older ulp2* mutant. Understanding the mechanisms that can lead to decreased stress tolerance in yeast may help us understand similar processes in cancer cells and fungal pathogens.

Student Major(s): Biology, Data Science

Advisor: Dr. Oliver Kerscher

Bennett Low, "Female Song on the Nest in Northern Cardinals and Its Fitness Costs"

Female bird song is a trait that has been lost in many temperate bird species. However, the potential fitness costs of female song that may have led to this loss are not well understood. However, here in Virginia there are two species two species in which this trait is still very much present that still have female song are, the Northern Cardinal, Cardinalis cardinalis, and the Northern Mockingbird, Mimus polyglottos. Females in both of these species are known to sing on the nest which could serve as communication between the male and the female to coordinate feedings for when they are needed most but may also attract predators by alerting them to the location of the nest. Studying  these two species can provide valuable information as to why this trait might have been lost. Evaluation of nest failure and predation rates in relation to female song can clue in the potential costs of female song can provide valuable information as to why this trait might have been lost. This study aims to use northern cardinals and mockingbirds as a model species to evaluate possible costs of female song that may have led to its loss diminution as a trait in many bird species.

Student Major(s): Biology

Advisor: Dr. Michelle Moyer

Bella Mack, "Characterization of Mecillinam Resistance Mechanisms in Escherichia coli MG1655"

β-lactams are the most widely prescribed class of antibiotics. Overproduction of the alarmone ppGpp confers resistance to the β-lactam mecillinam, which targets penicillin-binding protein 2 (PBP2) and disrupts cell wall synthesis. This resistance requires PBP1B, a related synthase. Measuring minimum inhibitory concentrations (MICs) of PBP1B separation-of-function mutants revealed that full enzymatic activity is essential for resistance. Overproduction of ppGpp upregulates the PBP1B activator LpoB. An LpoB-bypass PBP1B mutant revealed that LpoB expression partially mediates resistance. Additional mutants revealed that the transcriptional regulator DksA acts within the same pathway as PBP1B. We also report the first evidence of mecillinam heteroresistance (HR), a subpopulation-driven resistance phenotype, detected by E-tests and measured with population analysis profiling (PAP). Mutants lacking ppGpp, DksA, and PBP1B exhibited reduced HR. These findings highlight ppGpp, DksA, and PBP1B in mecillinam resistance and uncover HR as an additional survival pathway.

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

Advisor: Dr. Sarah Anderson

Elias Mitrokostas, Joseph Nizza, Srija Upadhyay, "Sing at Your Own Risk: The Relationship Between Puerto Rican Oriole Song and Parasitic Bird Presence"

Why does a bird sing? This research investigates the function of Puerto Rican Oriole (PROR) song, particularly the conditions for sex-specific song and how song may trigger a parasite bird species to lay eggs in PROR nests. Motion-activated cameras, playback tapes, and audio recordings near confirmed presence of PROR were used to understand the relationship between PROR song and its parasite species. Field observations indicate a relationship between PROR song and increased parasite bird presence. Preliminary results imply that female PROR song has a separate and unique function from male PROR song. Improving knowledge on song frequency within the species will allow for more accurate population abundance estimates. Additionally, this work endeavors to overturn a longstanding research bias against female birds, beginning to remedy the discrepancy in research attention between the two sexes.

Student Major(s) Elias: Coastal and Marine Sciences, Biology; Joseph: Biology; Srija: Biology, French/Francophone Studies

Advisor: Dr. Michelle Moyer

Ishbel Neil, "Liaisons Dangereuses: Insect Vectors of Harmful Microbes Among Pollinators of Common Milkweed"

The aim of this summer research project was to deepen our understanding of the microbial and animal interactions which impact the seed production of an important plant species, Asclepias Syriaca, common milkweed. Common milkweed is considered a keystone plant as it is the sole food source for numerous insect species and provides vital support of biodiversity in many regions. Changes to the microbiome brought by visiting insects may impact the reproductive success of common milkweed by altering the sugar concentration of the nectar. The aim of this project was to investigate the microbiome composition of milkweed pollinators and potentially determine rates of microbial transmission via pollination by hand collecting insects observed to inoculate a sterile artificial nectar solution in an artificial flower using milkweed nectar as an attractant. Microbes will be cultured from the collected insects and plated alongside the inoculated artificial nectar to compare the microbial communities of pollinator bodies to their contributions to plant microbiomes through the act of pollination.

Student Major(s): Biology 

Advisor:  Dr. Harmony Dalgleish 

Grace Parker, "Pining for Diversity: Understory Restoration in a Longleaf Pine Ecosystem"

Longleaf pine ecosystems originally ranged from east Texas to Southern Virginia, but due to the economic value of longleaf pine timber and the suppression of fires critical to these ecosystems, this range dwindled to less than 1% of the original as of 1995. Previous research and restoration work on longleaf pine ecosystems has focused on the pines themselves. This summer research project focused instead on the understory plants that constitute much of this ecosystem’s species diversity, asking how best to restore the understory of a longleaf pine ecosystem. Specifically, both grasses and herbaceous plants transplanted as seedlings, as well as directly seeded. This research will increase understanding of how planting methods affect the survivorship and establishment of understory plants.

Student Major(s)/Minor: Biology Major, Integrative Conservation Minor

Advisor: Dr. Harmony Dalgleish

William Rice, "Yeast Glutton Alert: A Custom Objection Detection Program for Yeast-Amoeba Predation"

Many microbes that cause disease do not do so by necessity; rather, they develop incidental traits that happen to lead to increased likelihood of causing disease in humans. For example, yeast which have evolved to resist predation ("being eaten") by amoebas may also incidentally develop resistance to being engulfed by human immune cells, leading to pathogenicity in human populations (Casadevall, 2007). To understand and test this resistance, a series of 9000 images was taken of amoeba co-cultured with 1000 natural isolates of yeast . The images must now be quantified to measure the overall predation-resistance of the yeast. Being too numerous to quantify manually, a program will be written to automatically detect the number of amoebas per image and how many yeast they have each engulfed. Overall, this helps to understand the broader process linked to the indirect evolution of microbes which cause disease and death in human populations.

Student Major(s): Computational and Applied Mathematics

Advisor: Dr. Helen Murphy

Alexis Savage, "Optimization of Techniques to Study Neurodevelopmental Changes due to Necrotizing Enterocolitis"

Necrotizing enterocolitis (NEC) is a debilitating gastrointestinal disease that affects about 7% of premature infants each year, with 30-50% of these patients requiring surgical intervention. Patients who survive NEC have severe long-term consequences that include neurodevelopmental delay, yet its causes remain largely unknown. Using a graded mouse model of NEC that recapitulates the three different clinical severity stages, our lab found trends between disease severity and clinical phenotype, inflammatory marker levels, and immune cell activity in the brain. From these findings, we hypothesized that these acute changes in the brain would lead to long-lasting impacts on cognitive function. Therefore, to build upon these studies, I optimized techniques to assess long-term behavior and motor function in mice, using Open Field, Elevated Plus Maze, and Social Interaction tests, and mouse activity was analyzed using DeepLabCut and SimBA. To observe neurobiological changes resulting from NEC induction, I optimized immunohistochemistry protocols for both IBA-1 and BrdU staining to visualize microglia and cellular proliferation, respectively. Finally, I acquired data from a cytokine-treated cell culture models, optimizing dendritic spine and IBA-1 cell counting methods. Training mouse behavior videos in DeepLabCut and SimBA allowed successful recognition of regions of interest, velocity, distance, and poses to be used in future experiments. Optimization of immunohistochemistry and cell counting protocols revealed ideal sample processing and data analyzing to acquire information that provide insight into the neurobiology of our model. Incorporating many different neurological outcomes in our mouse model allows a comprehensive understanding of the long-term effects of NEC many possibilities for future findings.

Student Major(s): Physics (Pre-Med Concentration)

Advisor: Dr. Jenny Rahn

Annie Yan, "Mobility of Postdoctoral Researchers in the United States and South Africa"

My research compares the mobility patterns of postdoctoral researchers whose prior education was in the United States or South Africa, using 2024 ORCID data (a global researcher identifier database). I employed quantitative analysis of 856,000 ORCID records, focusing on postdoctoral employment and education histories. The results show that postdoctoral researchers from both countries have high retention rates in academia, but the United States remains more attractive for both advanced training and employment. This result, if combined with qualitative analysis of immigration policies, research utilities, and university funding structures in the United States and South Africa, may further reveal the challenges postdoctoral researchers face in building sustainable careers. Such an integrated perspective would also point to what constitutes a more supportive environment for early-career scholars. These findings highlight persistent global academic inequalities and can inform policy making aimed at improving mobility opportunities and retention strategies for postdoctoral researchers worldwide.

Student Major(s): Biology, Classical Studies 

Advisor: Dr. Mayank Chugh 

Tal Zach, "Urolithin A Ameliorates Chemotherapy Induced Gut Integrity in Pancreatic Cancer"

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer with a poor prognosis. In PDAC, KRAS mutations are present in approximately 93% of cases, with the G12D variant being the most prevalent. MRTX1133, a selective KRASG12D inhibitor, has demonstrated strong therapeutic potential by targeting the MAPK pathway. However, its clinical use is limited by gastrointestinal (GI) toxicity, including gut barrier disruption, and other symptoms. Urolithin A (Uro A), a gut-derived microbial metabolite, has shown anti- inflammatory activity and the ability to inhibit PI3K/AKT/mTOR signaling, suggesting it may help alleviate these GI related adverse effects. This study aims to investigate the role of Urolithin A in modulating MRTX1133-induced inflammation and gut barrier dysfunction in the colon epithelial tissue in a genetically engineered mouse model (GEMM) Ptf1aCre/+;LSL-KrasG12D/+;Tgfbr2flox/flox (PKT) of PDAC. Mice were treated with vehicle, MRTX1133, Uro A, or a combination of MRTX1133 and Uro A. Western blotting was performed on mouse pancreatic cancer cell lines treated with MRTX1133, Uro A, or their combination for 3 and 24 hours to assess downstream MAPK and PI3K pathway activity. Levels of phosphorylated ERK1/2 (T202/204), total ERK1/2, and phosphorylated AKT (s473), total AKT were measured. Histological staining was performed to evaluate the tissue structure of pancreas. Gut barrier function was assessed by measuring colon length and validated intestinal permeability using FITC-dextran. Treatment with MRTX1133 successfully reduced pERK levels, confirming inhibition of the RAS mediated MAPK pathway, but also led to shortened colons and compromised gut integrity. In contrast, co-treatment with Uro A preserved colon length and significantly reduced intestinal permeability. In summary, our studies highlight the ability of Uro A to reduce drug-induced inflammation and gut barrier disruption. 

Student Major(s)/Minor: Biology Major, Judiac Studies Minor

Advisors: Dr. Varunkumar Krishnamoorthy, Principal Investigator: Dr. Nagaraj Nagathihalli 

Session II

Elena Benson, Jenna Jablonski, 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. TTBK-8.1/2 is not required for the proper localization of other pseudopod-localized proteins such as NSPH-2. 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. During sperm activation, wildtype sperm extend filopodia-like spikes and subsequently a motile pseudopod, while 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): Elena: Chemistry; Jenna: Biology; Olivia: Computational Mathematics and Statistics on the Biology track

Advisor: Dr. Diane Shakes

Ean Casey, "Microscopic Mapping: Viral Classification in Agricultural Soil Samples"

Viruses are the most numerous organisms on the planet, and can be found in every environment imaginable. While aquatic ecosystems have been heavily investigated, our understanding of the abundance, diversity, and roles of viruses in soil systems lags behind. Software packages and open-source pipelines have been developed that allow for sequence analysis of entire viral populations in environmental samples, allowing for determination of both the amount and type of viruses present in soil samples. By analyzing the whole viral populations of agricultural soil samples, we can unearth relationships between management practices, the soil microbiome - including viruses - and productivity, which may inform more efficient and sustainable farming practices in the future.

Student Major(s)/Minor: Biology Major, Creative Writing Minor

Advisor: Dr. Kurt Williamson

Mary Laun, "Terrapins Trapped: Analyzing Blue Crab Catch and Diamondback Terrapin Bycatch in Modified and Unmodified Crab Traps"

Diamondback terrapins are the only estuarine turtle native to Virginia, and frequently drown in crab traps in the Chesapeake Bay. Oval bycatch reduction devices (BRDs) are plastic rings that narrow the entrance to the trap, preventing turtles from entering. Despite legislation in surrounding states, Virginia has not made any laws requiring the use of BRDs due to protest from commercial crabbers. Elastic escape hatches have been designed as a replacement for BRDs, allowing turtles to push out of the trap. Both trap types were tested alongside control traps at two sites off of the York River for seven weeks. Across both sites, BRD traps caught significantly fewer terrapins than the others, however both BRD and escape hatch traps caught significantly fewer crabs as well. Therefore escape hatches may not be an effective reduction method, and future research into finding a BRD with increased crab catch would be beneficial.

Student Major(s): Coastal & Marine Sciences, Biology

Advisor: Dr. Randolph Chambers

Carolyn Payne, "How Does the Pinx-1 Related Protein, Chigno, Regulate Drosophila Testis Stem Cell Behavior?"

Stem cells are essential for organ function. Testes from fruit flies have been used to identify mechanisms controlling stem cell behavior. Chigno is an uncharacterized protein enriched in the nucleolus of fly reproductive stem cells. Our prior work has shown that Chigno inhibition causes defects in testis stem cell behavior leading to tumors and reduced fertility. Chigno also has a human counterpart, PINX1, that is linked to cancer. Yet functions of Chigno and its homologs are not fully characterized. To understand Chigno’s function, a yeast two-hybrid assay identified potential Chigno-interacting proteins. This summer, I assessed the effects of inhibiting these proteins in testes stem cells. If inhibition has similar effects in the testes as Chigno repression, it indicates that these proteins function together in testes. I have also explored the TIE-DYE system as a means to examine changes observed in individual testis stem cells after gene inhibition. 

Student Major(s)/Minor: CAMS-Mathematical Biology Major, Biochemistry Minor

Advisor: Dr. Matthew Wawersik

Brendan Tingley "Investigating Barred Owl Habitat Use Along a Road-Density Gradient" 

Barred Owls (Strix varia) are a widespread species of true owl found in North America. Their habitat spans forests from the Pacific Northwest to the Southeast.  Though they have a wide range, urbanization has threatened their well being and forced them to adapt to living in cities and suburbs. Though they can survive in urban environments, they face many challenges including vehicular collisions and light pollution. This research project aims to study the effects that urbanization has on Barred Owl behavior, breeding, and mortality. Observations will be conducted across a road-density gradient, taking into account traffic capabilities and speed limits.  Overall, the project will describe the current state of Barred Owl populations in and around urban environments within the Hampton Roads region of Virginia.  

Student Major(s): Biology

Advisor: Dr. Matthias Leu 

Colin Wang, "Uncovering the Cryptic: Building an Environmental DNA Database for Freshwater Sponges That Filter Our Lakes and Streams"

Despite their vibrant green color, ecologists are still largely in the dark about freshwater sponges. Freshwater sponges comprise less than 3% of global sponge diversity, but they are critical to the water filtration and community structure of ponds, lakes, and streams. Historically, research on freshwater sponges has been constrained by their small size, cryptic habits, and difficult species identification. Consequently, ecologists today still have a limited understanding of their range, species diversity, and role as key ecosystem water filters. This project will provide a  new DNA sequence database to vastly improve sponge identification by their unique DNA sequence rather than by appearance. This project will also develop a new environmental DNA assay for identifying sponge diversity from analysis of water samples. eDNA is a zero-impact method of species identification that has demonstrated greater scale, diversity, and taxonomic accuracy than traditional collection-based surveys. With an eDNA database, researchers can more easily discern between sponge species, allowing for further study and better protection of the ecosystems they inhabit against anthropogenic stressors and invasive species.

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

Advisor: Dr. James Skelton

Sierra Warden, "A Weird Gut Feeling: Regulatory RNAs impact on Acetone Carboxylase Expression in a Gastric Pathogenic Bacterium"

The acxA gene in Helicobacter pylori encodes for an enzyme acetone carboxylase - which plays a key role in the bacteria’s ability to use acetone as a carbon source. This allows the bacteria to survive in a gastric environment where acetone is present. This gene is important for H. Pylori’s persistence to survive and allows the bacteria to adapt in a gastric ecosystem. HPnc4160 is a regulatory RNA molecule that controls the synthesis of the acetone carboxylase enzyme. When at the 26th nucleotide of this RNA sequence, an adenine, is changed to guanine, HPnc4160 transcripts decline to virtually zero. My experimental plan is to quantify the mRNA and protein levels of acetone carboxylase in both wild-type H. pylori and the HPnc4160 adenine 26 to guanine mutation (3’A) . 

Student Major(s): Biology

Advisor: Dr. Mark Forsyth

Abigail Yang, "Adapting the Tie Dye System to Characterize Chigno Knockdown in Somatic Cell Clones of Drosophila melanogaster"

The Drosophila melanogaster ovary is a valuable model for investigating stem cell behavior. The CG11180 gene “Chigno,” identified by the Wawersik lab, is homologous to mammalian PINX1 and is a key regulator of stem cells. Somatic knockdown of Chigno in the ovaries leads to infertility, decreased proliferation and differentiation, and increased apoptosis. However, the impact of Chigno suppression on individual cell types has not been studied. Work will be presented on adapting a system to track specific somatic cell clones capable of gene knockdown. This system will then enable further research on how suppression of Chigno expression in these cell clones alters ovary function.

Student Major(s): Biology and CAMS

Advisor: Dr. Matthew Wawersik

Nathan Yang, "H105A Peptide as a Potential Therapeutic for Photoreceptor Protection in Macular Degeneration"

Dry age-related macular degeneration (AMD) is a leading cause of untreatable blindness characterized by photoreceptor cell death in the macula, leading to central vision loss. We used cigarette smoke extract to model a common risk factor for AMD and induce pathophysiologically relevant photoreceptor cell death in human retinal organoids, which recapitulate the lamination and structure of the human retina, making them suitable for in vitro research. Previous literature suggests that H105A, a peptide with high affinity for the pigment epithelium-derived factor receptor (PEDF-R), may reproduce PEDF-R’s effect in reducing cell death through modulation of apoptosis, ferroptosis, and the calpain pathway. We investigated H105A’s effect on overall cell survival as well as apoptotic, calcium-mediated, and ferroptotic cell death. We found that H105A promotes cell survival through modulation of apoptosis and ferroptosis, though calcium-mediated cell death was unaffected. These findings further our understanding of the H105A peptide and its potential clinical applications. 

Student Major(s): CAMS Biology and Public Policy Majors

Advisor: Dr. Natalia Vergara

Mariana VanPelt Chan, "Killer Yeast: Investigating Pathogenicity’s Link to Multicellularity in Saccharomyces cerevisiae"

Many non-pathogenic microbes, which normally thrive in the wild, can cause disease once in contact with hosts. To explain this phenomenon, scientists have proposed the 'accidental virulence' theory: some microorganisms contain disease-causing traits because they help them survive in the wild, which coincidentally also aids in their ability to survive in hosts (Smith et al., 2024). Multicellularity is an example of an accidentally virulent trait, defined by the aggregation (or clumping) of multiple cells. For example, multicellular biofilms are important for microbial resistance to environmental stressors, and may in turn, also help resist host immune system attacks, leading to pathogenicity. Previously, the lab had investigated the prevalence of biofilms in a global panel of the biomedical yeast model, Saccharomyces cerevisiae, and found that multicellular traits are more prevalent in pathogenic strains. This current project is investigating the genetic basis of these biofilm traits using gene deletion via PCR, homologous recombination, and transformation followed by phenotyping to understand the multicellular pathogenic phenotype. 

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

Advisor: Dr. Helen Murphy