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In intracranial aneurysms, multiple factors and biochemical pathways are believed to be involved in the event of a rupture. The epidermal growth factor receptor (EGFR) activation pathway is of particular interest as a way to understand and target the mechanism of rupture due to its established role in cellular proliferation

In intracranial aneurysms, multiple factors and biochemical pathways are believed to be involved in the event of a rupture. The epidermal growth factor receptor (EGFR) activation pathway is of particular interest as a way to understand and target the mechanism of rupture due to its established role in cellular proliferation and inflammation. Furthermore, unfolded protein responses in vascular cells’ endoplasmic reticulum (ER), known as ER stress, have emerged as a potential downstream mechanism by which inflammatory EGFR activation may lead to aneurysm rupture. The purpose of this project was to investigate the role of EGFR inhibition on the aneurysm rupture rate in a preclinical model, investigate the role of ER stress induction on the aneurysm rupture rate, and confirm which cellular phenomenon lies upstream in this mechanistic cascade. Based on analyses of aneurysm rupture rate and gene expression in the Circle of Willis, ER stress and inflammatory unfolded protein responses were found to be downstream of initial EGFR activation, which may be an effective therapeutic target for preventing aneurysm rupture in a clinical setting.

ContributorsPolen, Kyle (Author) / Van Horn, Wade (Thesis director) / Martin, Thomas (Committee member) / Hashimoto, Tomoki (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor) / School of Human Evolution & Social Change (Contributor)
Created2022-12
Description
Voluntary participation is a common teaching practice used to engage students and is often used in undergraduate STEM classrooms. The body of literature is growing regarding participation, specifically how it can be used and what it can include (e.g., letting students ask questions and/or answer questions during class). Since the

Voluntary participation is a common teaching practice used to engage students and is often used in undergraduate STEM classrooms. The body of literature is growing regarding participation, specifically how it can be used and what it can include (e.g., letting students ask questions and/or answer questions during class). Since the body of literature is growing, there is also increasing potential for there to be variation in how participation is defined or interpreted by researchers, educators, etc. To my knowledge, there is no study that has explored the extent to which there is variation in 1) the term voluntary participation across STEM peer-reviewed articles, 2) the definition of the terms used by investigators in articles regarding voluntary participation, and 3) the examples used by investigators regarding voluntary participation. The data set in this study consists of a multi-step literature review and nine peer-reviewed research articles regarding voluntary participation in science undergraduate courses from 2010 to 2022. The analysis revealed that: 1) 78% of articles use the term and of those, 44% of articles clearly define the term in the context of the research; 2) 22% do not use the term and instead use an umbrella term (e.g., active learning). This study provides insight into how voluntary participation is used across different contexts, and how it can be conceptualized in a variety of spaces, which can allow for instructors and educators to make informed decisions before using it as a teaching practice.
ContributorsWinton, Makena (Author) / Collins , James (Thesis director) / Nadile, Erika (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Molecular Sciences (Contributor)
Created2022-12
Description

In cold chain tracking systems, accuracy and flexibility across different temperatures ranges plays an integral role in monitoring biospecimen integrity. However, while two common cold chain tracking systems are currently available (electronic and physics/chemical), there is not an affordable cold chain tracking mechanism that can be applied to a variety

In cold chain tracking systems, accuracy and flexibility across different temperatures ranges plays an integral role in monitoring biospecimen integrity. However, while two common cold chain tracking systems are currently available (electronic and physics/chemical), there is not an affordable cold chain tracking mechanism that can be applied to a variety of temperatures while maintaining accuracy for individual vials. Hence, our lab implemented our understanding of biochemical reaction kinetics to develop a new cold chain tracking mechanism using the permanganate/oxalic acid reaction. The permanganate/oxalic acid reaction is characterized by the reduction of permanganate (MnVII) to Mn(II) with Mn(II)-autocatalyzed oxidation of oxalate to CO2, resulting in a pink to colorless visual indicator change when the reaction system is not in the solid state (i.e., frozen or vitrified). Throughout our research, we demonstrate, (i) Improved reaction consistency and accuracy along with extended run times with the implementation of a nitric acid-based labware washing protocol, (ii) Simulated reaction kinetics for the maximum length reaction and 60-minute reaction based on previously developed MATLAB scripts (iii) Experimental reaction kinetics to verify the simulated MATLAB maximum and 60-minute reactions times (iv) Long-term stability of the permanganate/oxalic acid reaction with water or eutectic solutions of sodium perchlorate and magnesium perchlorate at -80°C (v) Reaction kinetics with eutectic solvents, sodium perchlorate and magnesium perchlorate, at 25°C, 4°C, and -8°C (vi) Accelerated reaction kinetics after the addition of varying concentrations of manganese perchlorate (vii) Reaction kinetics of higher concentration reaction systems (5x and 10x; for darker colors), at 25°C (viii) Long-term stability of the 10x higher concentration reaction at -80°C.

ContributorsLjungberg, Emil (Author) / Borges, Chad (Thesis director) / Levitus, Marcia (Committee member) / Williams, Peter (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor) / Department of Psychology (Contributor)
Created2022-12
Description

An effort to experiment on the novel Usutu virus in pure in silico methods was made to determine conformational changes with non polar point mutations in the amino acid sequence. The first method consisted of creating a Python program to exhaustively identify codons, amino acids, and dinucleotide bridges & nonbridges,

An effort to experiment on the novel Usutu virus in pure in silico methods was made to determine conformational changes with non polar point mutations in the amino acid sequence. The first method consisted of creating a Python program to exhaustively identify codons, amino acids, and dinucleotide bridges & nonbridges, including viral characteristics defined by Mollentze in 2021. The second method consisted of creating point mutations to non polar amino acids in deemed key sites of the Usutu virus envelope protein and finding the RMSD from the original structure. This resulted in one of two outcomes - either the experiment showed that the Usutu virus envelope protein is highly resistant to point mutations or in silico methods are inconsistent and biased, leading to inaccuracy.

ContributorsBurton, Reilly (Author) / Mills, Jeremy (Thesis director) / Sterner, Beckett (Committee member) / Upham, Nathan (Committee member) / Barrett, The Honors College (Contributor) / Division of Teacher Preparation (Contributor) / School of Molecular Sciences (Contributor)
Created2023-05
Description
Wetlands produce approximately one third of total global methane emissions and sequester significant amounts of CO2. Salt marshes make up 5% of total wetland area, and therefore are key factors affecting global methane and CO2 emissions. Many marshes are anthropogenically managed either by diking, draining, impoundment, or otherwise restricting tidal

Wetlands produce approximately one third of total global methane emissions and sequester significant amounts of CO2. Salt marshes make up 5% of total wetland area, and therefore are key factors affecting global methane and CO2 emissions. Many marshes are anthropogenically managed either by diking, draining, impoundment, or otherwise restricting tidal exchange. This causes marsh freshening, increases methane emissions, and releases sequestered carbon, all of which can lead to a warming effect on the climate by the greenhouse effect. We studied the formerly impounded Old County salt marsh, found in the Herring River Estuary of Wellfleet, Massachusetts, USA. The USGS Woods Hole Coastal and Marine Science Center installed two eddy covariance flux towers in the Herring River Estuary. These showed that Old County had low methane fluxes (17 nmol/m2/s) compared to another site in the same estuary (112 nmol/m2/s). The question became; why did Old County experience lower methane emissions? We then did a focused study on the Old County location to investigate. We sampled various biogeochemical parameters including pH, salinity, ORP, dissolved Fe, sulfate, chloride, CH4, DOC, and DIC from pore water samples taken June 2022. We also measured extractable iron from a 2015 archived sediment core at Old County. Specifically, we explored the role of Fe in reducing methane through Fe coupled anaerobic oxidation of methane (Fe-AOM). The porewater depth profiles ranged from 10cm to 242 cm in depth and showed Old County as acidic (pH of 3-6.5), mostly fresh, anoxic, highly reducing, and high in dissolved organic carbon (DOC; 2,000-10,000 μM). I divided the depth profiles into two distinct zones, one above 50 cm and one below 50 cm. Overall, Fe-AOM was likely to occur below 50 cm because dissolved Fe increased as CH4 decreased, which is the expected pattern for Fe-AOM. Also, because the ratio of the calculated methane flux (-0.552 nmol m-2 s-1) to the dissolved Fe (0.072 nmol m-2 s-1) was 7.6, which closely matched the 1 to 8 stoichiometry of the Fe-AOM reactions.
ContributorsEinecker, Rachel (Author) / Hartnett, Hilairy (Thesis director) / Anbar, Ariel (Committee member) / Eagle, Meagan (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor)
Created2023-12
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Description
The goal of this research was to better understand the knowledge, preparedness, and comfort level of single fathers with daughters regarding menarche and menstruation. To achieve this goal, a Google Forms survey was distributed using social media, and the data from this survey were analyzed using chi-squared tests and a

The goal of this research was to better understand the knowledge, preparedness, and comfort level of single fathers with daughters regarding menarche and menstruation. To achieve this goal, a Google Forms survey was distributed using social media, and the data from this survey were analyzed using chi-squared tests and a regression model. Of 446 responses, 387 were included for analysis. It was found that comfort discussing the menstrual cycle significantly positively correlated with knowing their daughters’ menarcheal status and self-rated knowledge about the menstrual cycle, and negatively correlated with selecting parents as a responsible party for menstrual education. Knowledge level was significantly positively correlated with the number of subjects related to the menstrual cycle participants selected as being knowledgeable about, but was not significantly correlated with knowing menarcheal status or considering parents a responsible party for menstrual education. Considering parents a responsible party was also not correlated with having talked to their daughter about the menstrual cycle. Additionally, there was some evidence that comfort discussing menstruation is negatively correlated to age. The information gained from this study indicates that it would be beneficial to increase single fathers’ knowledge and comfort discussing the menstrual cycle in order to ensure the menstrual health of their daughters.
ContributorsAnderson, Waris (Author) / Hinde, Katie (Thesis director) / Loebenberg, Abby (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / School of Molecular Sciences (Contributor) / School of Human Evolution & Social Change (Contributor)
Created2022-05
Description

This paper examines the physics behind cancer treatment and more specifically radiation therapy. A phenomenon known as Compton scattering has played a substantial role in the treatment of breast cancer and improvement of lives of women around the world. Through Compton scattering, radiation therapy has been tremendously improved and has

This paper examines the physics behind cancer treatment and more specifically radiation therapy. A phenomenon known as Compton scattering has played a substantial role in the treatment of breast cancer and improvement of lives of women around the world. Through Compton scattering, radiation therapy has been tremendously improved and has allowed for the most accurate and effective treatment in breast cancer patients today.

ContributorsRombaoa, Matthew Bryce (Author) / Foy, Joseph (Thesis director) / Hines, Taylor (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor) / Department of Psychology (Contributor)
Created2023-05
Description
Heterotrophs such as E. coli contain metabolic pathways with enzymes called carboxylases that are capable of fixing CO2 gas to form metabolites, which has implications for aiding with CO2’s role in climate change. The reductive branch of the tricarboxylic acid (TCA) cycle serves as an important pathway for NAD+ regeneration

Heterotrophs such as E. coli contain metabolic pathways with enzymes called carboxylases that are capable of fixing CO2 gas to form metabolites, which has implications for aiding with CO2’s role in climate change. The reductive branch of the tricarboxylic acid (TCA) cycle serves as an important pathway for NAD+ regeneration in enteric bacteria in anaerobic conditions and leads to the production of succinate, a useful industrial product. The enzyme phosphoenolpyruvate carboxykinase is responsible for fixing CO2 in the conversion of PEP to OAA within this pathway and has potential to be a significant carbon fixation module in heterotrophic organisms. This project explored pck genes from select organisms by transforming plasmids to test if these variants have improved kinetics compared to the native E. coli Pck and to investigate their ability to improve succinate bioproduction.
ContributorsModukuri, Shree (Author) / Wang, Xuan (Thesis director) / Godar, Amanda (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor) / School of International Letters and Cultures (Contributor)
Created2024-05
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ContributorsLuca, Michael (Author) / Yan, Hao (Thesis director) / Stephanopoulos, Nicholas (Committee member) / Blattman, Joseph (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor) / School of Molecular Sciences (Contributor)
Created2024-05
Description
Cell immunotherapies have revolutionized clinical oncology. While CAR T cell therapy has been very effective in clinical studies, off-target immune toxicity limits eligible patients. Thus, NK cells have been approached with the same therapy design since NK cells have a more favorable safety profile. Therefore, the purpose of this research

Cell immunotherapies have revolutionized clinical oncology. While CAR T cell therapy has been very effective in clinical studies, off-target immune toxicity limits eligible patients. Thus, NK cells have been approached with the same therapy design since NK cells have a more favorable safety profile. Therefore, the purpose of this research project is to explore DNA nanotech-based NK cell engagers (NKCEs) that force an immunological synapse between the NK cell and the cancer cell, leading to cancer death. DNA tetrabody (TB) and DNA tetrahedron (TDN) are fabricated and armed with HER2 affibody for tight adhesion to HER2+ cancer cell lines like SKBR3. Overall, relationship between TB-NK treatment and cancer cell apoptosis is still unclear. TB-NK treatment induces an apoptotic profile similar to PMA/IO stimulation. Pilot cell assay needs to be replicated with additional controls and a shortened treatment window. For DNA TDN fabrication, HER2 affibody polishing with Ni-NTA affinity chromatography achieves high purity with 20% to 100% high-imidazole elution gradient. ssDNA-HER2 affibody conjugation is optimal when ssDNA is treated with 40-fold excess sulfo-SMCC for 4 hours. In conclusion, the manufacturing of DNA-based NKCEs is rapid and streamlined, which gives these NKCEs the potential to become a ready to use immunotherapy.
ContributorsLuca, Michael (Author) / Yan, Hao (Thesis director) / Stephanopoulos, Nicholas (Committee member) / Blattman, Joseph (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor) / School of Molecular Sciences (Contributor)
Created2024-05