Undergraduate Senior Theses

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A senior thesis is a paper which highly-motivated senior undergraduates may write to present the results of a major, independent research or creative project. Unlike most term projects, papers, and lab reports written in undergraduate courses, a senior thesis addresses questions or issues for which no known or generally accepted answers exist.

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VIABILITY OF AZIDE-ALKYNE CLICK CHEMISTRY ON POLYELECTROLYTE-ANTIBODY CONJUGATION
(University of Delaware, 2025-12) Barden, Margaret F.
Current at-home, lateral flow immunoassays rely on visual interpretation of small lines to communicate a result to users. While this method of testing is considered generally accessible due to ease of use, it significantly limits independent usage by users suffering from visual impairment, a demographic including ~10% of individuals worldwide. The necessity for help from a sighted individual or electronic interpreter compromises patient confidentiality, introduces potential to spread disease, and remains inaccessible for those facing economic disparities. While Bluetooth devices offering audio readouts have been developed, these still require access to technology and a power source. Our aim is to create a low-tech at home-testing method that can be read by touch instead of sight. Prior research in the field of tactile interfaces has shown that humans are capable of discriminating small molecular differences between surfaces through monolayer ordering and changes in mesoscale friction. Polyelectrolytes offer an interesting method of achieving surface alterations given their high degree of charge repulsion. Poly(styrene sulfonate), PSS, is a well studied polyelectrolyte known for its water solubility, stability, and negative charge repulsion. Due to these desirable properties, we are developing methods to conjugate PSS chains to a mouse IgG antibody. These attempts were approached using various bioconjugation techniques, namely click mechanisms copper-mediated azide alkyne cycloaddition (CuAAC) and strain-promoted azide alkyne cycloaddition (SPAAC). Click chemistry offers a reliable mechanism for conjugation due to its neutral charge transition state which results in quick reaction times, solvent flexibility, broad functional group tolerance, and selectivity. NuPAGE was used to assess the successful extent of conjugation. Polymers were synthesized via RAFT polymerization and functionalization was attempted through an end-chain approach. Polymerization was assessed by ¹H NMR and FTIR and results have suggested hydrolysis of the synthesized polymers results in the loss of azide functionality. Given this, current work is focused on the synthesis of an ester-free RAFT agent to ensure azide alkyne cycloaddition can occur in future conjugation attempts.
EVALUATING ROADKILL HOTSPOTS IN NORTHERN NEW JERSEY
(University of Delaware, 2025-12) Kalb, Isabella
Millions of mammals are killed each year by vehicles, and while there is oftentimes bias in recording larger mammalian roadkill, these species have become crucial in analyzing roadkill hotspots. With the growing human population and increased pressures of urban development, the state of New Jersey provides an excellent opportunity to understand the factors that affect roadkill events. I examine American black bear, white-tailed deer, and coyote roadkill events in combination with randomly generated roadkill points in northern New Jersey. We focused on seven different covariates, including NAACC terrestrial passage score, nearby agriculture and urban habitat, nearby core and corridor habitat, distance to the nearest core/corridor area, and distance to the nearest culvert or underpass structure. My findings suggest that the percent agricultural and percent urban habitat within a 10km2 radius of each event point were most significant in describing roadkill events. In all six models, the percent urban area was negatively correlated with roadkill events, while the percent agricultural area was also negatively correlated with roadkill events, but only significant in the first model. For bear roadkill events, the percent core and corridor showed a significant positive relationship, with more roadkill events occurring near core and corridor areas. In these same bear models, the distance to the nearest core or corridor was negatively correlated with roadkill events. The distance to the nearest culvert and NAACC terrestrial passage scores were not good indicators of roadkill events for any of the three species, most likely due to culverts rarely explaining roadkill on their own. These findings can be used to better evaluate landscape and habitat importance in roadkill events and evaluate existing underpass placements to facilitate terrestrial species movement across the state of New Jersey.
Characterization of spe-43 homologs: K05F1.1 and F57A8.6
(University of Delaware, 2025-12) Pheris, Julianne
Sexual reproduction relies on the presence of a viable sperm cell, which fuses with an egg cell in the process of fertilization. To increase understanding of the molecular processes involved in sexual reproduction, a reverse genetics method can be utilized to learn the role of specific proteins in fertility. C. elegans are an excellent organism to model these processes with, as they reproduce through sexual reproduction. C. elegans exhibits two sexes: hermaphrodites, which can self-fertilize, as well as males, which produce sperm to fertilize eggs from the hermaphrodites. Sperm activation is the process through which post-meiotic spermatids are altered to become sperm suitable for fertilization. In C. elegans, the process is triggered through two different pathways: TRY-5 and SPE-8. The TRY-5 pathway and the SPE-8 pathway are active in the male reproductive tract, while only the SPE-8 pathway is active in hermaphrodites. Hermaphrodites with mutations in genes required for the SPE-8 pathway experience self-sterility. In contrast, males with non-functional TRY-5 pathway components show no fertility defect unless the SPE-8 pathway is also disabled. spe-43 is a protein-encoding gene required for sperm activation through the SPE-8 pathway. spe-43 has three different paralogs: K05F1.1, F57A8.6, and T10E9.4. All three paralogs are protein-encoding genes hypothesized to be involved in sperm activation. To study the role of K05F1.1 and F57A8.6 in C. elegans fertility, deletion mutants were made to knock out the genes’ function. Quantitative experiments, including hermaphrodite self-fertility assays and male fertility assays, display no significant difference in progeny produced by K05F1.1(syb4161) deletion mutants compared to wild type organisms. Similarly, imaging such as DAPI staining and sperm dissections have shown that loss of K05F1.1 has no visible impact on sperm production, localization, and sperm morphology. When knocking out K05F1.1 and spe-8 together, males were able to produce viable progeny. The result implies that the K05F1.1 protein is neither part of the TRY-5 pathway, nor the SPE-8 pathway. In contrast, F57A8.6(syb4189) deletion mutants had significantly fewer progeny produced compared to wild type organisms in quantitative experiments.
CHARACTERIZATION OF BACTERIOPHAGE AND MACROPHAGE INTERACTIONS FOR APPLICATIONS IN PULMONARY DRUG DELIVERY
(University of Delaware, 2025-12) Anilkumar, Adhya
Lower respiratory infections (LRIs) remain a leading global health burden, with bacterial infiltration and biofilms that can limit antibiotic efficacy. Bacteriophages are a promising alternative to antibiotics, capable of lysing bacterial pathogens. Their nanoscale size enables deposition in the lower respiratory tract and interaction with innate immune cells. However, the development of inhalable phage therapies is underexplored due to a limited understanding of phage-lung interactions. This work explores a workflow for administering purified phages to macrophage models to evaluate their potential as therapeutic vectors and macrophage immunomodulating effects. First, crude T4 phage lysates were purified from endotoxins using spin columns (SP) and 1-Octanol organic phase extraction (OP). Endotoxin concentrations were quantified via Limulus Amebocyte Lysate assay, and phage DNA concentrations were measured by absorbance spectroscopy. Both purification methods reduced the endotoxin concentration by 10,000-fold using spin columns and 26-fold using organic solvent extraction. However, the spin column purification resulted in a 3-4 fold reduction in phage DNA and a significant reduction in phage titer. The second aim of this thesis is to compare purified phage preparations and crude phage lysate in a macrophage model to evaluate phage internalization and clearance, effects on mammalian cell metabolic activity, and modulation of macrophage inflammatory responses and antigen presentation. SYBR Gold-stained phages were visualized in RAW 264.7 stained with Hoechst and CellMask Plasma membrane stain, where phages localized in the cytoplasm and surrounded the nucleus of cells. Macrophage metabolic activity post-phage treatment was measured using Cell Titer-Glo. Flow cytometry was conducted to assess macrophage polarization and immune response. RAW 264.7 cells treated with purified lysates demonstrated significantly higher metabolic activity at 24 hours compared to lipopolysaccharide (LPS controls, indicating that purified phages are non-cytotoxic to macrophage function. The crude and purified T4 phages were then co-administered with LPS to mimic an LRI inflammatory environment. RAW 264.7 cells activated with LPS show greater internalization of T4 phages. Macrophages dosed with purified T4 phages expressed minimal CD40+, a pro-inflammatory marker, compared to crude T4 phage lysate and LPS. Maximal phage internalization and CD40+ expression were observed at 24 hours, followed by phage clearance by 72 hours, corresponding with a resolution of inflammation. These findings demonstrate that endotoxin-free phage samples can exhibit dynamic immunomodulatory effects in macrophages. Future work will focus on improving endotoxin purification methods that minimize phage loss. Additionally, complex in-vitro models, including air-liquid interface cultures, diverse phage types and immune cell populations, and bacterial co-culture systems, will be developed to evaluate phage lytic activity within mammalian cells and understand how macrophage clearance may limit therapeutic efficacy in the respiratory system.
CHARACTERIZATION OF CELL-MIMETIC DRUG CARRIERS FOR SUSTAINED DELIVERY OF THERAPEUTICS
(University of Delaware, 2025-05) Zucaro, Katherine
Metastatic cancer is a challenging disease to treat. One contributing factor to consider is the selective permeability of the lymph nodes, which enables them to act as a safe haven for cancer cells in the body. One approach is to utilize a Trojan horse strategy, where cryo-shocked T-lymphocytes (CSTLs) act as an engineered cell-mimetic drug carrier to home to the lymph node. CSTLs loaded with small-molecule drugs resulted in rapid release kinetics, which limited achievable doses at the target sites. To follow on, it was hypothesized that by incorporating a hydrogelated core into the CSTLs system, modifying the CSTLs would provide controlled, delayed, sustained release of the therapeutic agents. This version of the carriers is called hydrogelated T-lymphocytes (HTCs), utilizing DOX-laden poly(ethylene glycol)-based gelation solution (PEG-diacrylate (PEG-DA), initiated with 2-hydroxy-4'-(2-hydroxyethoxy)-2 methylpropiophenone). Three aims were researched for the hypothesis: (1) characterization of loading efficiency and max loading of CSTLs and HTCs, (2) determination of the release kinetics of CSTLs and HTCs loaded with Doxorubicin, and (3) test target efficiency of loaded drugs against cancer cells in vitro. To characterize loading efficiency and max loading of CSTLs and HTCs, the ability for HTCs to be loaded with doxorubicin had to be assessed, both visually with an epifluorescence microscope and utilizing a plate reader. The CSTLs have an average loading efficiency of 74.27 ± 6.61%. 10% and 20% PEG-DA in HTCs had average loading efficiencies of 3.95 ± 3.42% and 28.76 ± 10.52%. When testing for maximum loading, respectively for each concentration 0.525 mg/ml, 0.7 mg/ml, and 0.8 mg/ml, the efficiencies were 3.95 ± 3.42%, 12.93 ± 3.42%, and 17.19 ± 2.25%. This aim helped to better understand the loading efficiencies of HTCs and how to increase their loading abilities. To investigate the release kinetics of CTSLs and HTCs, release experiments of all drug delivery vehicles were completed. The release profiles were analyzed utilizing one and two-phase decay, and the rates of release were determined, after varying controlled release compared to CSTL’s rapid release. Both 20% and 10% PEG-DA HTCs drug delivery vehicles have similar trends, exhibiting one-phase decay graphs. 10% PEG-DA HTCs have a rate of release (K=1.16*102), whereas 20% PEG-DA HTCs have a lower rate (K=7.87*10-5). The 20% PEG-DA HTCs have a higher percentage released than the 10% PEG-DA HTCs. With a lower loading efficiency, the 20% PEG-DA has less to release than the 10% PEG-DA HTCs. To test the target efficiency of the HTCs loaded with the drug, the loaded HTCs were tested on 4T1s cancer cells. An assay was run to determine the viability of the cancer cells to see how efficiently the drug-loaded vehicles treated them. The viability of the 4T1s on the bottom of the well was analyzed after 20% PEG-DA HTCs released DOX from a transwell directly on the 4T1s. The viability of the 4t1's was 90.7 % after 7 days, compared to the positive and negative controls, which were respectively 100% and 58.5%. This study demonstrated that the encapsulation of small-molecule drugs inside a hydrogel core (HTCs) produced a drug delivery vehicle with tunable properties that will enable a delayed and controlled release of small-molecule payload. This study supports the hypothesis that incorporating a hydrogelated core into the CSTLs system would provide controlled, delayed, sustained release of the therapeutic agents. This new delivery system potentially creates formulations that enable sustained release of therapeutics locally within the lymph node. Optimizing the amount of drug at the site of the disease, decreasing dosing frequency, and less off-target accumulation leads to lower systemic toxicity for the patient.
NEURAL CORRELATES OF OBJECT-BASED WARPING
(University of Delaware, 2025-05) Zoe Cronin
Object-based warping is a visual illusion in which space within an object appears expanded when points are located within the object and compressed when points are located on or just beyond the boundaries of an object. Other studies have used functional imaging to investigate the neural mechanisms of visual illusions, but this has yet to be done for object-based warping. In the current study, we tested feasibility of measuring positions of small stimuli (N = 5), a prerequisite for studying object-based warping using functional imaging; then, we delineated visual regions in subjects (N = 3) using probabilistic atlases and conducted multivoxel pattern analysis (MVPA) to determine which of these visual regions may hold representations of object-based warping based on classifier errors in position estimation. We trained classifiers on activity when a dot stimulus is isolated, when the dot is on a perceived figure region, and when the dot is on a perceived ground region. The classifier estimated locations above chance for nearly all visual regions in all subjects and tests, with greater accuracy for early than late visual regions. However, accuracy drops dramatically on runs with figure-ground displays, and early visual regions did not consistently exhibit systematic errors in estimates that would demonstrate expansion and compression effects involved in object-based warping. Our results do not support our hypothesis that early visual regions hold representations of position that are subject to object-based warping. We have demonstrated that this approach to studying object-based warping is ineffective, perhaps due to a limited amount of data and the use of figure-ground stimuli that are too high contrast and complex. Future work is needed to more precisely investigate the neural mechanisms of object-based warping.
EFFECTS OF PRIVATE MILITARY CONTRACTORS ON CONTEMPORARY RUSSIAN GRAND STRATEGY OBJECTIVES
(University of Delaware, 2025-05) Zoe Byer-Wein
The Wagner Group, Russia's premier private military outfit, defined Russian grand strategy doctrine for over a decade acting on the behalf of the Kremlin. After the fiery end of the Wagner Group as a private actor following an attempted mutiny in 2023 on the Kremlin by the group's leader, Evgeny Prigozhin, scholars and Russia-watchers around the world documented the vast myriad of effects that the Wagner group has had on proxies and regions of interest abroad. However, the use of Wagner contractors has also had a remarkable impact on Russia itself. In this paper I argue that Russia's pervasive use of the Wagner Group and semi-state contractors has been one of the biggest weaknesses of contemporary Russian grand strategy, and that even Wagner's marginal wins in a few of these proxies have contributed to the failure or stalling of other Russian objectives in the same states. Despite the mutiny ending Prigozhin's tenure as Wagner's leader, the group is still active in everything but name, and will affect how Russia conducts grand strategy in the future.
FORMING GENOME TO PHENOME CONNECTIONS: BACTERIOPHAGE REPLICATION GENES
(University of Delaware, 2025-05) Victoria Barbone
Viruses are the most genetically diverse and environmentally abundant biological entities, however they are vastly understudied. Viral impacts on host communities and ecosystems can be differentiated by distinct infection dynamics. Lytic viruses lyse the host during infection, affecting nutrient cycling and community composition. Temperate viruses incorporate their genomes into hosts during infection, contributing to horizontal gene transfer and affecting host biology. DNA polymerase I (PolA) is carried by many bacteriophages (bacterial viruses) and may be linked with infection dynamics phenotypes. Variations in the PolA 526 residue (T7 numbering) influence the speed and accuracy of DNA replication, a vital infection process. Three previously identified 526 residues—phenylalanine, tyrosine, and leucine—influence enzyme biochemistry and phage infection phenotypes. Faster replicating Phe526 or Tyr526 PolAs tend to be found in lytic phage, while slower replicating Leu526 PolAs are largely found in temperate phage. A novel histidine 526 variant has been identified in oceanic viral metagenomes (viromes). In vitro biochemical analysis and in vivo mutagenesis studies showed that His526 PolAs have hindered processivity and phage T7 mutants encoding the His526 variant replicate slower. Bioinformatic analysis of viromes show contextual differences in His526 PolAs that predominate in different depths in oligotrophic ocean samples by sequence variation, as well as different requirements for additional replication proteins. This study aims to strengthen the PolA genome to phenome hypotheses and aid in predicting the infection strategies of His526 viral populations to understand their impacts on ecosystem.
AMERICAN BLACK BEAR (URSUS AMERICANUS) USE OF HIGHWAY UNDERPASSES IN NORTHERN NEW JERSEY
(University of Delaware, 2025-05) Victoria Alves
The state of New Jersey balances a large human population with associated transportation infrastructure and urban development with an ecological diversity that encompasses many species and habitat types. One key member of that ecological diversity is the American black bear (Ursus americanus), a quintessential omnivore found throughout the state despite many major roadways that could pose barriers to movement and habitat connectivity. Here I examine black bear movement dynamics at existing underpass structures of major roadways in Northern New Jersey. We monitored 37 potential crossing structures along State Route 1, Interstate 78, Interstate 80, Interstate 95, State Route 202, and State Route 206, using trail cameras. My findings suggest that the current North Atlantic Aquatic Connectivity Collaborative metric used to assess underpasses for bear use may not accurately predict bear use, and that habitat related factors, specifically the amount of core habitat in the area surrounding each underpass, may provide a stronger predictive basis for where a bear crossing might occur. These findings can be used to better inform the future placement or enhancement of crossing structures for use by black bear. This will be important in the continued management of human-wildlife conflict in the most densely population state in the nation.
Modeling River Otter (Lontra canadensis) Habitat Suitability using Citizen Science Data
(University of Delaware, 2025-05) Victor Kowalski
The North American river otter (Lontra canadensis) has undergone population decline and recovery due to historical overharvesting, habitat loss, and recent reintroduction efforts. My study models river otter habitat suitability using Maxent in four Mid-Atlantic states—Pennsylvania, Maryland, Delaware, and New Jersey—using citizen science presence-only data from iNaturalist. I incorporated environmental variables (wetlands, forests, and stream density) and anthropogenic factors (harvest rates and human population density) to assess their relative contributions. The full model, which included all five covariates, performed best (AUC = 0.812), with an increasing harvest rate as the strongest predictor. Environmental-only (AUC = 0.731) and anthropogenic-only (AUC = 0.785) models performed less effectively, supporting the hypothesis that both types of variables improve predictive accuracy. Wetlands and moderate human population density positively influenced habitat suitability, while detectability biases affected remote or heavily urbanized areas. These results demonstrate the value of combining citizen science data with spatial modeling to assess habitat use for semi-aquatic mammals like the river otter in human-dominated landscapes.
Quantifying Diel Change in the Metabolic Rate of the Clearnose Skate (Rostroraja eglanteria)
(University of Delaware, 2025-05) Trinity Clifford
In this study, we measured the routine metabolic rate (RMR) for the Clearnose Skate (Rostroraja eglanteria) throughout the diel cycle to understand activity levels. Intermittent flow respirometry measured oxygen consumption of skates, a proxy for metabolic rate, during the day and night. Subtracting the day and night RMR’s, two skates saw higher RMR’s during the day phase (Skate 1 - average difference of 63 mg O2/hr/kg and standard deviation of 31.1 mg O2/hr/kg, Skate 3 - average difference of 21 mg O2/hr/kg and standard deviation of 37.1 mg O2/hr/kg) while one saw higher RMR’s at night (Skate 2 - average difference of -50 mg O2/hr/kg and standard deviation of 68.7 mg O2/hr/kg). There was no significant difference between phases. To observe acclimation influence, the first RMR conducted was removed from each skate. Two skates showed contradicting patterns (Skate 2 - average difference of 9.5 mg O2/hr/kg and standard deviation of 2.1 mg O2/hr/kg, Skate 3 - average difference of -11 mg O2/hr/kg and standard deviation of 4.24 mg O2/hr/kg). No significant statistical difference was found. The first trial RMR’s suggest that skates were stressed when introduced to the system, thus future applications should increase acclimation time and decrease animal handling.
RELATIONSHIP BETWEEN IRON MINERALS AND CARBON IN MARSH-FORESTED TRANSITIONS
(University of Delaware, 2025-05) Tara Metters
Marsh-forested transitions, or interfaces between upland forest systems and tidal creeks, are dynamic coastal systems that play an important role in carbon sequestration and mineral cycling. As the Delmarva Peninsula experiences increased rates of relative sea level rise, it is increasingly urgent to understand biogeochemical cycling within these critical areas. In this study, we investigated variability and relationships of crystalline iron (Fe) oxides, short-range order Fe oxides, and water extractable organic carbon (WEOC) along three marsh-forested transitions located in Delaware, Maryland, and Virginia. To assess Fe mineral concentrations in soils, we used acid ammonium oxalate extractions for short-range order Fe oxides and citrate dithionite-bicarbonate to extract crystalline Fe oxides. For carbon in soils, we used water extractions to determine WEOC concentrations and CHNS combustion analysis to quantify total carbon. We observed variability in Fe oxide and WEOC concentrations at site, subsite, and depth. In contrast with previous literature indicating positive relationships between short-range order Fe oxides and carbon concentrations, our results showed no statistically significant relationships. We did, however, see significant negative relationships between crystalline Fe oxides and carbon at upland forest subsites. The lack of correlation between short-range order Fe oxides and carbon concentrations may be influenced by the dynamic redox conditions of marsh forested systems, which can prevent formation of Fe-organic complexes. Negative relationships between crystalline Fe oxides and carbon indicate limited carbon sequestration abilities of upland forests. These findings highlight the complex nature of biogeochemical cycling along marsh-forested transitions and demonstrate the influence that site-specific factors like redox conditions, salinity, and microbial communities could have on these cycles. Our research had limited scale due to sampling regime. Future research should emphasize additional sampling at the spatial and temporal scale to fully understand Fe-carbon interactions and carbon cycling in these critical systems.
THE INFLUENCE OF MECHANICAL PROPERTIES ON CARTILAGE SUPERLUBRICITY
(University of Delaware, 2025-05) Tanmayee Joshi
Articular cartilage supports near frictionless joint movement over a lifetime of hundreds of millions of articulation cycles because of a complex interaction between its mechanical properties and tribomechanics. Only recently has cartilage’s unmatched superlubricating frictional capacity been replicated on benchtop, using the convergent stationary contact area (cSCA) explant testing configuration(in the presence of synovial fluid). However, the relationship between cartilage mechanical properties and the tissues capacity for superlubricity remains unclear. In articular cartilage, the superficial zone and the progressively stiffer middle and deep zones create a depth-dependent mechanical property gradient that supports load distribution and maintains fluid pressurization, both thought critical for superlubricity. Changes in this zonal structure may compromise lubrication, though the precise relationship between depth-varying mechanics and frictional behaviors remains unknown. Osteoarthritis, a degenerative joint disease, is characterized by collagen network degeneration, proteoglycan loss, and cartilage swelling, which alter the tissue’s mechanical properties. To better understand the relationship between mechanical properties and cartilage lubricity, cSCA configured osteochondral explants were free swollen in baths of varying tonicity (isotonic and hypotonic; 400 to 55mOsm) before being mechanically characterized via indentation and tribologically characterized in the cSCA. Overall, this thesis aimed to investigate the effect of osmotically induced, and reversible changes in bulk and depth-dependent mechanical properties and how (if at all) they influence cartilage superlubricity. In Aim I, a novel micro-indentation protocol was developed to evaluate effective contact moduli at varying tissue depths and indentation speeds, allowing for analysis of zonal mechanical properties of articular cartilage when subjected to free swelling in varying tonicities (isotonic and hypotonic; 400 to 55mOsm). These results were compared with macro-indentation derived “bulk” material properties. The study revealed that near surface measures of effective moduli at both fast and slow indentation rates appear more sensitive to hypotonic bath influences than bulk mechanical properties, indicating localized, tonicity (hypoosmolality)-induced mechanical changes. Such findings indicated that bulk cartilage stiffening is also associated with localized mechanical changes within the tissue (i.e., near surface stiffening) that may impact its ability to sustain a low-friction performance. In Aim 2, cartilage explant samples were subjected to a speed sweep tribological characterization in the presence of PBS and hyaluronic acid (HA) to determine if there exist relationship(s) between cartilage stiffening and frictional behavior. Cartilage explant tribology testing, under the cSCA configuration, showed that cartilage lubricity remained largely unaffected by hypotonic-driven tissue stiffening. Interestingly, correlations between cSCA friction coefficients and indentation-based mechanical properties were lubricant and speed-dependent, underscoring complex surface and hydration interactions. This finding suggests that cartilage’s frictional behavior is influenced by both the lubrication environment and sliding speed, highlighting the dynamic nature of cartilage mechanics and its capacity for low-friction performance under varying physiological conditions.
ANALYZING BIOGEOGRAPHICAL TRENDS OF BENTHIC HABITATS IN GUAM USING WORLDVIEW-2/3 IMAGERY INTEGRATED WITH ADVANCED DEEP LEARNING
(University of Delaware, 2025-05) Talha Mahmood
Benthic habitatss—ecological communities inhabiting seafloor environments— such as seagrass meadows and coral reefs, are vital components of coastal ecosystems but face increasing threats from anthropogenic and climatic stressors. Traditional remote sensing methods for mapping these habitats often struggle with fine-scale het erogeneity, label scarcity, and computational inefficiency. This study addresses these challenges by integrating high-resolution WorldView-2/3 multispectral imagery with an optimized deep learning framework to analyze biogeographical trends in the ecologically distinct coastal zones of Guam. We propose Tiny-UNet—a lightweight U-Net-based architecture tailored for benthic habitat segmentation, incorporating channel-wise at tention mechanisms and bilinear upsampling to enhance spectral-spatial feature extrac tion while minimizing computational complexity. The model was trained on a dataset of nine labeled images that span two regions: Angana Bay and Manell Geus, annotated with seven habitat classes. Strategic patch-based preprocessing and deterministic data augmentation are applied to mitigate class imbalance and environmental variability, such as sunglint, radiometric inconsistency, and clouds. We conducted experiments and evaluated the performance of our proposed solution, which exhibits outstanding performance for segmenting and classifying each of seven benthic classes, as well as in its broader adaptability, when compared to the original U-Net design. The efficiency of our framework (214K parameters vs 31M in the original U-Net) and the preservation of the boundaries underscore its potential for scalable coastal monitoring. However, persistent challenges in transitional zones—driven by environmental noise and spectral ambiguities—require hybrid physics-AI models to disentangle overlapping signatures, active learning for label efficiency, and multi-sensor fusion to address dynamic condi tions. Integrating synthetic data generation and transformer architectures could fur ther mitigate class imbalance and sensor artifacts, balancing computational efficiency, model generalizability, and ecological precision for scalable coastal monitoring. This work advances AI-driven marine conservation by balancing computational efficiency with ecological precision, o↵ering a pathway for adaptive management in data-limited coastal ecosystems.
VALIDATING DIFFERENTIALLY EXPRESSED GENES IN MET-2 DELETION MUTANTS AND IDENTIFICATION OF GENES RESPONSIBLE FOR SPERMATOGENIC DEFECTS REGULATED BY H3K9 METHYLATION
(University of Delaware, 2025-05) Sydney Bradley
One important mechanism of genetic regulation is through post-translational histone modifications. A histone methyltransferase known as MET-2 is an enzyme responsible for such modifications. Specifically, MET-2 is responsible for dimethylation of lysine 9 of histone H3 (H3K9me2), thus promoting heterochromatin structure and resulting in repression of gene expression (Bessler et al., 2010). Consequently, the absence of H3K9me2 leads to the overexpression of various genes, threatening germline integrity, which is vital for proper embryonic development (Delaney et al., 2019). The function of H3K9me2 has been previously studied in oogenesis. However, these germline effects may also impact spermatogenesis in C. elegans. This is evidenced by data indicating met-2 deletion males have significantly reduced fertility. The goal of this research is to explore if misregulation of specific genes is responsible for the spermatogenic defects seen in met-2 mutants. RNAseq was performed on control and met-2 male germ lines and data was collected on differentially expressed genes. Based on previous characterization for functions in meiotic progression or fertilization I am investigating eight of the met-2 differentially expressed genes that were found to be upregulated. My first project goal was to validate upregulation of transcripts in met-2 males compared to control by performing qPCR to analyze mRNA levels of the genes of interest. Analysis of qPCR results did not verify differential expression of the genes of interest in male enriched samples of met-2 versus control worms. The second project goal was to explore in more depth the function of one gene of interest, rmd-1, and how misregulation of gene expression contributes to the spermatogenic defects seen in met-2 mutants. The gene rmd-1 is involved in spindle organization and microtubule attachment to the kinetochore. Preliminary data of RNAi knockdown of rmd-1 shows reduced percent embryonic viability, meanwhile having no effect on brood size. Although both gametogenesis and fertilization occur in rmd-1 knockdown animals, these results indicate that proper expression of rmd-1 may be necessary for the production of gametes of high quality. I have also begun examining spermatogenesis-specific effects of rmd-1 RNAi knockdown via male Embryonic Viability Assays and DAPI staining of the dissected male gonads. Thus far, rmd-1 RNAi knockdown males may have an extended transition zone. More replicates of male EVAs, as well as additional staining and imaging of the gonads in the future will help further elucidate details of the possible role of rmd-1 in spermatogenic defects regulated by H3K9 methylation.
IMMUNOMODULATORY DRUG DELIVERY SYSTEM FOR NEONATAL HYPOXIC ISCHEMIC ENCEPHALOPATHY
(University of Delaware, 2025-05) Sudha Anilkumar
Occurring in 1.5 per 1000 live births, hypoxic ischemic encephalopathy (HIE) is a leading cause of death and long-term disability in children born at term. Interleukin-33 (IL-33), a nuclear cytokine released in response to injury, has emerged as a potent immunomodulator capable of reprogramming microglia toward a reparative phenotype. However, systemic IL-33 delivery can cause off-target effects, highlighting the need for localized therapeutic strategies. To address this, we developed an injectable alginate-based hydrogel system incorporating laponite nanoclay to enable tunable, intracranial delivery of IL-33. The hydrogel was engineered for optimal viscosity and release kinetics compatible with small-gauge needle injection into brain tissue. Using this platform, we evaluated microglial responses to IL-33 under control, Maternal Immune Activation (MIA), and HIE conditions in vitro. IL-33 treatment induced morphological changes consistent with a reparative (M2-like) phenotype and significantly enhanced phagocytic activity across all conditions, particularly rescuing deficits observed in HIE-exposed microglia. However, IL-33 did not significantly reduce pro-inflammatory cytokine levels (IL-1β, IL-6), suggesting its benefits may occur through phenotype modulation rather than direct cytokine suppression. These results demonstrate the potential of IL-33-loaded hydrogels as a targeted immunotherapeutic strategy for neonatal neuroinflammation.
NETWORK ANALYSIS REVEALS CONSERVED PROTEIN CLUSTERS AND RHIZOSPHERE-DRIVEN BIOGEOGRAPHY IN BRADYRHIZOBIUM PHAGES
(University of Delaware, 2025-05) Spencer Catherine Toth
Bradyrhizobia are nitrogen-fixing bacteria that form symbiotic nodules on the roots of leguminous plants, supplying their hosts with fixed nitrogen in exchange for photosynthetic products. This symbiosis reduces the need for chemical fertilizers, which in excess can lead to eutrophication and toxic algal blooms, ultimately contribute to climate change. Consequently, the Bradyrhizobium-legume relationship is recognized for its economic, ecological, and agricultural significance. However, bacteriophages can shape this mutualistic relationship by regulating host bacterial populations. The impact of bacteriophages on soil nutrient cycles and food web interactions remains poorly understood, therefore contributing to the need for further investigation into soil viral populations and their ecological roles. In this study, we used previously isolated and sequenced Bradyrhizobium phage (bradyphage) population representative genomes from Delaware soybean field soil samples as references. Through metagenomic analysis, we identified uncultivated viral genomes (UViGs) in environmental samples that share significant protein homology with these bradyphages. Our results reveal conserved functional gene groups, especially those involved in phage infection and replication, indicating the essential roles of structural and DNA synthesis proteins. We also found bradyphages to exhibit strong genomic similarity to UViGs from soil and rhizosphere environments, suggesting adaptation to similar ecological niches. By identifying conserved gene clusters and characterizing genome features of bradyphages, this work provides a foundation for future research on viral-host interactions, with implications for engineering phages to enhance nitrogen fixation in sustainable agriculture. Our findings expand the known diversity of soil viruses and highlight the importance of phage research in understanding and managing soil microbial communities.
COLLABORATIVE STORYTELLING, NARRATIVE MANAGEMENT, AND THE IMPACT OF INCLUDING GAME MECHANICS AS A STORYTELLING DEVICE
(University of Delaware, 2025-05) Soryn Sundleaf
Tabletop Roleplaying Games, or TTRPGs, are a type of game that combines mechanical interactions and gameplay elements with narrative components and collaboration in storytelling. Due to several factors, such as multiple participants contributing to a singular narrative output or the inclusion of chance, there exists a more complicated relationship between the story, its creator(s), and its viewer(s) than in traditional mediums. Despite this, the narrative opportunities the medium presents are typically a lower priority than the gameplay ones, particularly in discussions of design. This study presents the results of a bespoke TTRPG created with intentional interaction between its gameplay mechanics and plot. This game was designed, created, and conducted for this project, followed by feedback and extensive analysis. This analysis includes both what alterations would need to be included in any similar TTRPG project, as well as showcasing what this project demonstrates about the nature of storytelling. It explores ludonarrative harmony and dissonance, the malleability of authorship, and the ability for a story to surprise those creating it. The game utilizes a horror genre, chosen to exaggerate the relationship between mechanical and narrative tension, and to prioritize the feelings and mindsets of the characters over the progression of the plot itself. The results show that mechanics have an undeniable impact on the reception of a given narrative, able to influence both simple elements such as the tone of a scene, and complex elements such as the way a character solves a particular problem. It also highlights that allowing random elements to influence the outcome of a narrative can create an unexpected ending. TTRPGs are a storytelling medium that have significant depth available to them and can create narrative interactions that are difficult or impossible to replicate in a traditional medium.
TRANSCONTINENTAL CONFUSION: UNVEILING THE IDENTITY OF CIXIUS FRANCISCANUS STÅL (HEMIPTERA: FULGOROMORPHA: CIXIIDAE)
(University of Delaware, 2025-05) Solomon V. Hendrix
The cixiid planthopper Cixius franciscanus Stål, 1859 was described from specimens asserted to be from San Francisco, California. Subsequent authorities have interpreted the species in varied ways, culminating in the assertion that the species is actually South American in origin. Here the species is redescribed and placed in a new genus, Alviarus n. gen. as Alviarus franciscanus n. comb. based on available specimens and the unpublished notes of the late Dr. Frank Mead. Further notes on the American Pentastirini and the significance of preserving the illustrations and notes of entomologists are discussed.
Optimization And Degradation Of Phosphoarginine-Bearing Substrates
(University of Delaware, 2025-05) Skyler Frostrom
Members of the Clp family of ATP-dependent proteases play critical roles in protein turnover in a wide variety of organisms. These enzymes help maintain quality control of cellular proteins and regulate diverse cellular processes [1]. In the globally important human pathogen Mycobacterium tuberculosis (Mtb) the ClpC1P1P2 protease, a member of this family, has been identified as a promising target for novel antibiotics to treat drug-resistant Mtb infections. Like all Clp proteases, ClpC1P1P2 contains two major functional components: a ring-shaped unfoldase (ClpC1) and a barrel-shaped peptidase (ClpP1P2) [2]. The ClpC1 unfoldase selectively recognizes protein substrates. However, the process of substrate recognition is poorly understood, and few specific physiological substrates have been described. This makes it difficult to develop effective screens for ClpC1-targeting antibiotics. Recent studies by the Clausen group (IMP, Austria) have shown that post-translational phosphoarginine modifications (pArg) are recognized by the ClpC unfoldase in Bacillus subtilis (Bsu) and effectively mark substrates for destruction by the ClpCP protease [3]. The specific kinase that catalyzes arginine phosphorylation in Bsu is McsB [4]. A recent study by our group showed that pArg exists in mycobacteria, although the mycobacterial arginine kinase and phosphatase remains unknown [5]. Additionally, we have found that the pArg binding pockets present in Bsu ClpC are conserved across Actinobacterial ClpC1s, suggesting that pArg modifications similarly function as markers for degradation by ClpC1P1P2 in Mtb. In this study, we aimed to optimize the in vitro generation and purification of pArg-bearing model substrates using a panel of McsB arginine kinases from diverse bacterial species, and to identify the most effective kinase for substrate phosphorylation. We found that the psychrophilic kinase from Paenibacillus glacialis (PglMcsB) achieved phosphorylation efficiency comparable to or exceeding that of the previously used Geobacillus stearothermophilus McsB. Furthermore, we established a robust Strep-Tactin affinity purification protocol to obtain highly pure phosphorylated substrates. These advances improve the toolkit for studying ClpC1P1P2 substrate recognition and lay the groundwork for future investigations into pArg-mediated proteolysis in mycobac

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