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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- ItemA Therapeutic Evaluation of a Creative Reaching Game in Immersive Virtual Reality(University of Delaware, 2022-12) Baron, LaurenVirtual Reality (VR) has several applications beyond entertainment, e.g., architectural planning, surgical procedure assistance, and physical therapy. These implications are important and require the most accuracy for users, especially when their healthcare is involved. Users can lose accuracy immersed in a virtual environment (VE) from inaccurate depth perception. Often, people underestimate distant objects and overestimate close objects in VR, which concerns software developers and healthcare providers. VR Therapy systems also rely on information from VR hand controllers, which do not fully capture the movement from the rest of the limb. While VR games have shown much potential for rehabilitation, research on creative virtual therapy is still growing. Considering many possibilities for therapeutic interventions in VR, my goal is to create activities with an appropriate balance between the intensity level of therapy intervention with enjoyment and entertainment. I will also capture the limb's movement both from the arm and hands with a noninvasive elbow sleeve sensor. I propose a creative line art drawing game in an immersive VR environment as a tool for both upper extremity therapy and vision therapy using enjoyable multi-dimensional reaching tasks. To examine the validity of the proposed virtual therapy system, I conducted two preliminary human-subjects experiments: a mixed design varying the drawing content (Easy vs. Hard; a between-subjects factor) and the user’s position (Seated vs. Standing; a within-subjects factor) on 16 non-clinical participants; and a withinsubjects design varying the drawing content dimension (2D vs. 3D) and the content’s orientation (Vertical vs. Horizontal) on 12 non-clinical participants. My results of the first experiment (SUI 2021) show that the change of drawing content objectively influenced participants’ drawing performance, e.g., the completion time and the number of mistakes, while they did not feel the difference in the difficulty level between the contents subjectively. Interestingly, participants reported more enjoyment from drawing the Hard Chicken content than the Easy Fish content and more substantial body stretches in the Seated setting than the Standing setting. The results of the second experiment (submitted to ACM/IEEE CHASE 2023) show that for all levels, there was no significant difference between subjective easiness, comfortability, and enjoyment and between objective measures for task completion time and the number of mistakes. This finding suggests that all versions are at the same therapeutic intensity level, with no model being more prone to longer time or more mistakes and are all usable/feasible. This leads to the customization of therapy to the user with any of these configurations and orientations while keeping the same level of intensity; for example, if a patient has restricted lower limb mobility and requires to be seated, they can use the horizontal orientation interchangeably. However, there was significance with elbow resistance change, which shows how data collection from just the hands and not throughout the arm is insufficient for VR rehabilitation, particularly for the upper extremities. There is a need to improve depth perception, visual cues, and reaching capabilities in VEs, especially for 3D objects.
- ItemCharacterization of molecular and metabolic phenotypes of Clostridium syntrophic co-culture(University of Delaware, 2022-05) Zou, YinHistorically, Clostridium species were used in Acetone-Butanol-Ethanol (ABE) fermentation. However, the ABE fermentation processes face competition from petroleum based processes, thus fermentation processes need to evolve to produce a higher valued chemical efficiently. Clostridium species are known to metabolize a range of sugar molecules and produce valuable chemicals such as hexanol and octanol. To achieve this goal, utilization of co-culture allows each species of bacteria to specialize in one task and avoids complex metabolism engineering. In this thesis, optimization of the bioreactor performance of syntrophic Clostridium co-culture for medium chain alcohol or fatty acid production utilizing Clostridium kluvyeri and Clostridium saccharolyticum. And the characterization of the molecular interactions and localization of proteins of interest related to cell-to-cell interaction was investigated. In the bioreactor investigation, the optimized C. kluyveri monoculture yielded 173 mM of hexanoate. In comparison the co-culture yielded 123 mM of hexanote. The result exhibits promising industrial value for Clostridium co-culture, and the insufficient supply of ethanol from C. saccharolyticum could be the major drawback for this co-culture system, which may be improved by incorporating a third species into the system such as Clostridium ljungdahlii. Direct cell-to-cell material exchange between Clostridium acetobutylicum and C. ljungdahlii has been previously shown by our lab 1 This phenomenon greatly improves the productivity and carbon utilization in the co-culture, thus understanding the mechanism of cell-to-cell material exchange is critical to improve the performance of the co-culture and bring more industrial and economical significance. It is possible that C. ljundahlii could be actively seeking CO2 rich source and therefore fused with C. acetobutylicum to consume CO2 waste produced by C. acetobutylicum. To further investigate this phenomenon, the localization pattern of the proteins of interest such as carbonic anhydrase (CA) and methyl-accepting chemotaxis protein (MCP) could be helpful. These proteins may be involved in CO2 metabolism and CO2 sensing respectively. To visualize the localization of these proteins, Halotag was fused with the two proteins of interest. The preliminary testing of the fluorescence of both MCP Halotag and CA-Halotag under the microscope in Escherichia coli and under the flow cytometry in C. ljungdahlii shows the strong fluorescent intensity of the fluorescent fused protein. Visualizing the proteins in C. ljungdahlii under the microscopy, uniform membrane localization of MCP-Halotag and uniform cytoplasmic localization were observed. Future experiment of fluorescent imaging C. acetobutylicum and C. ljungdahlii utilizing the MCP-Halotag and CA-Halotag could provide more information about the proteins involved in the cell-to-cell direct material exchange.
- ItemThe Effect of Nicotinamide Riboside on LDL-Cholesterol Induced T-Cell Dysfunction(University of Delaware, 2022-05) Ward, HoustonAging is associated with chronic low-grade inflammation (“inflammaging”) and is a significant risk factor for multiple chronic diseases, including cardiovascular disease, Alzheimer’s disease, and cancer. Inflammaging is caused by the deterioration of the innate and adaptive immune systems, often accompanied by immunosenescence. T-lymphocytes (T-cells), primarily known for their role in the adaptive immune system responding to foreign antigens, are increasingly recognized as contributors to inflammaging via immunosenescence and impaired mitochondrial function. Age-related declines of cellular nicotinamide adenine dinucleotide (NAD+) levels may be the trigger of immunosenescence and mitochondrial dysfunction. However, the mechanisms leading to T-cell mediated inflammaging and mitochondrial dysfunction are not fully known. One mechanism which might contribute to age related T-cell dysfunction is an increase in endogenous low-density lipoprotein cholesterol (LDL-C) in blood plasma. Increased endogenous LDL-C occurs with aging and has been linked, cross-sectionally, to mitochondrial damage and dysfunction, reduction of ATP synthesis, and increased reactive oxygen species. Subsequently, this damage can lead to various cellular consequences, rapid aging, and disease onset. Supplementation with nicotinamide riboside (NR), a precursor to nicotinamide adenine dinucleotide (NAD+), might be a novel therapeutic to protect T-cells from the deleterious effects of high LDL-C. In addition to its role as a regulator of cellular reoxidation-reduction reactions, NAD+ is a critical co-substrate for several energy-sensing and stress-resistance enzymes. These enzymes are referred to as “NAD+- consuming enzymes” and include the silent mating type information regulation of two homologs (sirtuins; SIRTs), poly adenosine diphosphate (ADP) ribose polymerases (PARPs), cyclic ADP (cADP)-ribose synthases, and CD38/156 ectoenzymes. These enzymes contribute to a multitude of homeostatic processes including the maintenance of biological stress resistance, DNA damage repair, and the regulation of immune cell function. Supplementation with NR has been shown to increase NAD+ bioavailability. NAD+ has emerged as a vital and intriguing cofactor for maintaining mitochondrial fitness by up-regulating enzymes that repair mitochondrial DNA. However, whether NAD+ can protect T-cell mitochondria from immunosenescence is unknown. This study aimed to investigate the efficacy of exogenous NAD+ supplementation in protecting young T-cells from the effects of hypercholesterolemic conditions associated with aging. I hypothesized that treatment with LDL-C would impair T-cell mitochondrial respiration and induce T-cell inflammation and that NR would exert a protective effect on T-cells, preserving mitochondrial respiration and reducing the inflammatory response. Seven adults (6 female/ 1 male) between the ages of 22 and 26 participated in this study. Blood samples were collected in EDTA coated vacutainer tubes from all 7 participants. Peripheral Blood Mononuclear Cells (PBMCs), isolated from whole blood, were further isolated into a pan T-cell sample. The isolated T-cells were later treated and used for the Seahorse XF Analyzer. The supernatant was isolated and frozen to use for the quantification of cytokines. Pan T-cells were treated with high (4.9 mMol/L) physiologic concentrations of LDL-C and co-incubated with high LDL C and NR compared to control (Serum-free media, 0 mMol/L). T-cell mitochondrial function and inflammatory cytokine production were assessed by measuring mitochondrial respiration using an extracellular flux analyzer (Seahorse XFe96 Analyzer) and multi-plex protein quantification (Luminex Magpix), respectively. Concentrations of pro-and anti-inflammatory cytokines, specifically interleukin-6 (IL 6) and interleukin-10 (IL-10), were measured across the three treatment groups of the pan T-cell samples. Proinflammatory cytokines up-regulate the production of radical oxygen species (ROS) and anti-inflammatory cytokines reduce the production of ROS. Contrary to our hypothesis, LDL-C non-significantly augmented T-cell mitochondrial respiration during maximal oxygen consumption rate (OCR), while it non-significantly decreased basal OCR and ATP-linked OCR. Further, the addition of NR to LDL-C treated samples exacerbated mitochondrial respiration in all accounts. Anti-inflammatory cytokine production showed a non-significant decrease with the LDL-C and LDL-C+NR treatments. Proinflammatory cytokine production displayed a non-significant increase within the LDL-C and LDL-C+NR treatment groups. The additional NR treatment to LDL-C treated T-cells significantly decreased the basal, maximum, and ATP-linked OCR, but it is unclear if LDL-C treatment alone had a significant effect on T-cell mitochondrial dysfunction. Cytokine production was not significantly affected with either treatment at the current sample size and may require more samples to clarify a relationship.
- ItemImpact of the GTP Binding Protein ARF-6 on the Biogenesis of Multiple Extracellular Vesicle Subpopulations in C. Elegans(University of Delaware, 2022-05) Wagner, KatherineExtracellular vesicles (EVs) are nano-sized, membrane-bound vesicles that play crucial roles in intercellular communication, impacting both physiologic and pathophysiologic pathways. Use of the genetic model organism C. elegans allows us to study and track EVs and their cargoes in vivo, to observe EV biogenesis and shedding. C. elegans EVs contain various different cargoes, including the calcium homeostasis modulator CLHM-1 and the polycystin PKD-2 ion channels. These cargoes are found to be in two different EV subpopulations that bud from different locations on the cilia of male tail sensory neurons. The small GTPase ARF-6 has been suggested to participate in microvesicle shedding via the phospholipase D pathway of signal transduction based on in vitro studies. However, whether ARF-6 plays this role in the release of EVs from cilia in vivo is unknown. Here, we show, using fluorescent protein tagging and TIRF microscopy, that ARF-6 affects both CLHM-1 and PKD-2-containing EVs, indicating that this protein may act in male-tail sensory neurons to impact biogenesis of all EV subpopulations. Loss of ARF-6 results in an approximate 50% reduction in release of both EV populations, opening the door for several future hypotheses and lines experimentation using the arf-6 mutant.
- ItemIllness as Metaphor: Comparing the Transatlantic Representations of Neurological Deviance in the Works of Charles Dickens and Herman Melville(University of Delaware, 2022-05) Sarikonda, AdvithCharles Dickens’ Barnaby Rudge: A Tale of the Riots of Eighty (1841) and Herman Melville’s “Bartleby, the Scrivener: A Story of Wall Street” (1853) are two stories featuring titular protagonists whose neurological conditions mark them as different from the rest of society. The eponymous protagonist in Barnaby suffers from “idiocy,” now formally termed intellectual disability disorder, whereas the eponymous protagonist in “Bartleby” displays traits of autism, a condition characterized by an impairment in language and communicability. Although Dickens and Melville both present characters who are neurologically deviant, the purpose of doing so is diametrically different in each work. Through Barnaby, Dickens expresses a need for paternalistic reform on both a state and communal level to assist the mentally ill, as well as the rest of society’s most vulnerable groups. Barnaby is not an unambiguous censure of British society, however; in the story, Dickens suggests a need for the existing British practice of moral management, which was a technique of non-restraint originally used in state asylums to treat the mentally ill. Melville, on the other hand, uses “Bartleby” to criticize the American medical system’s tendency to institutionalize members of society who are considered to be “deviant”. In the case of “Bartleby”, this deviance is communicated through autism, which manifests itself into seemingly unusual patterns of work and correspondence that confuse the story’s narrator, a lawyer. As such, “Bartleby” and Barnaby represent ideologically opposing perspectives of medicine and its potential to heal society’s outcasts. Whereas Dickens expresses interest in assisting individuals deemed to be non-normative, Melville portrays normativity itself as mercurial and conditional rather than an innate human disposition.