Barrett, The Honors College Thesis/Creative Project Collection

Mutations in the DNA of somatic cells, resulting from inaccuracies in DNA<br/>replication or exposure to harsh conditions (ionizing radiation, carcinogens), may be<br/>loss-of-function mutations, and the compounding of these mutations can lead to cancer.<br/>Such mutations can come in the form of thymine dimers, N-𝛽 glycosyl bond hydrolysis,<br/>oxidation by hydrogen peroxide or other radicals, and deamination of cytosine to uracil.<br/>However, many cells possess the machinery to counteract the deleterious effects of<br/>such mutations. While eukaryotic DNA repair enzymes decrease the incidence of<br/>mutations from 1 mistake per 10^7 nucleotides to 1 mistake per 10^9 nucleotides, these<br/>mutations, however sparse, are problematic. Of particular interest is a mutation in which<br/>uracil is incorporated into DNA, either by spontaneous deamination of cysteine or<br/>misincorporation. Such mutations occur about one in every 107 cytidine residues in 24<br/>hours. DNA uracil glycosylase (UDG) recognizes these mutations and cleaves the<br/>glycosidic bond, creating an abasic site. However, the rate of this form of DNA repair<br/>varies, depending on the nucleotides that surround the uracil. Most enzyme-DNA<br/>interactions depend on the sequence of DNA (which may change the duplex twist),<br/>even if they only bind to the sugar-phosphate backbone. In the mechanism of uracil<br/>excision, UDG flips the uracil out of the DNA double helix, and this step may be<br/>impaired by base pairs that neighbor the uracil. The deformability of certain regions of<br/>DNA may facilitate this step in the mechanism, causing these regions to be less<br/>mutable. In DNA, base stacking, a form of van der Waals forces between the aromatic<br/>nucleic bases, may make these uracil inclusions more difficult to excise. These regions,<br/>stabilized by base stacking interactions, may be less susceptible to repair by<br/>glycosylases such as UDG, and thus, more prone to mutation.

The COVID-19 pandemic has resulted in preventative measures and has led to extensive changes in lifestyle for the vast majority of the American population. As the pandemic progresses, a growing amount of evidence shows that minority groups, such as the Deaf community, are often disproportionately and uniquely affected. Deaf people are directly affected in their ability to personally socialize and continue with daily routines. More specifically, this can constitute their ability to meet new people, connect with friends/family, and to perform in their work or learning environment. It also may result in further mental health changes and an increased reliance on technology. The impact of COVID-19 on the Deaf community in clinical settings must also be considered. This includes changes in policies for in-person interpreters and a rise in telehealth. Often, these effects can be representative of the pre-existing low health literacy, frequency of miscommunication, poor treatment, and the inconvenience felt by Deaf people when trying to access healthcare. Ultimately, these effects on the Deaf community must be taken into account when attempting to create a full picture of the societal shift caused by COVID-19.

As the return to normality in the wake of the COVID-19 pandemic enters its early stages, the necessity for accurate, quick, and community-wide surveillance of SARS-CoV-2 has been emphasized. Wastewater-based epidemiology (WBE) has been used across the world as a tool for monitoring the pandemic, but studies of its efficacy in comparison to the best-known method for surveillance, randomly selected COVID-19 testing, has limited research. This study evaluated the trends and correlations present between SARS-CoV-2 in the effluent wastewater of a large university campus and random COVID-19 testing results published by the university. A moderately strong positive correlation was found between the random testing and WBE surveillance methods (r = 0.63), and this correlation was strengthened when accommodating for lost samples during the experiment (r = 0.74).

In this thesis paper, the mental health consequences of the COVID-19 pandemic are discussed. Chapter 1 discusses what inspired me to write this thesis and follows with a discussion of social isolation during the COVID-19 pandemic. Chapter 2 takes a step back and discusses biological effects of social isolation in general. Chapter 3 discusses the psychological effects of social isolation. Finally, this thesis concludes with a discussion of what can be done to help those experiencing social isolation during the pandemic.

Automated vehicles are becoming more prevalent in the modern world. Using platoons of automated vehicles can have numerous benefits including increasing the safety of drivers as well as streamlining roadway operations. How individual automated vehicles within a platoon react to each other is essential to creating an efficient method of travel. This paper looks at two individual vehicles forming a platoon and tracks the time headway between the two. Several speed profiles are explored for the following vehicle including a triangular and trapezoidal speed profile. It is discovered that a safety violation occurs during platoon formation where the desired time headway between the vehicles is violated. The aim of this research is to explore if this violation can be eliminated or reduced through utilization of different speed profiles.

In my undergraduate honors thesis, I strive to convey my idea that dance is more than just movement, it’s one of the many artistic tools used to express emotions; which therefore has the power to storytell without words. It is my hope to create a captivating form of art that you not only view, but can interact and interpret.

Stardust grains can provide useful information about the Solar System environment before the Sun was born. Stardust grains show distinct isotopic compositions that indicate their origins, like the atmospheres of red giant stars, asymptotic giant branch stars, and supernovae (e.g., Bose et al. 2010). It has been argued that some stardust grains likely condensed in classical nova outbursts (e.g., Amari et al. 2001). These nova candidate grains contain 13C, 15N and 17O-rich nuclides which are produced by proton burning. However, these nuclides alone cannot constrain the stellar source of nova candidate grains. Nova ejecta is rich in 7Be that decays to 7Li (which has a half-life of ~53 days). I want to measure 6,7Li isotopes in nova candidate grains using the NanoSIMS 50L (nanoscale secondary ion mass spectrometry) to establish their nova origins without ambiguity. Several stardust grains that are nova candidate grains were identified in meteorite Acfer 094 on the basis of their oxygen isotopes. The identified silicate and oxide stardust grains are <500 nm in size and exist in the meteorite surrounded by meteoritic silicates. Therefore, 6,7Li isotopic measurements on these grains are hindered because of the large 300-500 nm oxygen ion beam in the NanoSIMS. I devised a methodology to isolate stardust grains by performing Focused Ion Beam milling with the FIB – Nova 200 NanoLab (FEI) instrument. We proved that the current FIB instrument cannot be used to prepare stardust grains smaller than 1 𝜇m due to lacking capabilities of the FIB. For future analyses, we could either use the same milling technique with the new and improved FIB – Helios 5 UX or use the recently constructed duoplasmatron on the NanoSIMS that can achieve a size of ~75 nm oxygen ion beam.

For my creative project, I explored using natural sound to create a sound score or song. I used contrasting natural sounds to create the sound scores. Most of the sound recordings are from the New York City subways as well as other recordings around different cities in the United States. I created new sounds using sound manipulation techniques. I explored the use of electronic music production to translate the natural noise into the patterns, repetition and other elemental musical techniques to create a song. I used Ableton as the music production platform to develop the three songs.

Enzyme-induced carbonate precipitation (EICP) is a biocementation technique that produces comparatively fewer carbon dioxide emissions than traditional cementation. However, the use of synthetic reagents for EICP is costly, and the process produces an ammonium byproduct which is a harmful pollutant. This study utilizes fresh urine as a source of urea and calcium-rich zeolites as an ammonium adsorbent and a source of calcium ions for the EICP cementation technique. Batch hydrolysis and adsorption experiments were conducted to determine the effects of zeolite type, zeolite form, and solution composition on ammonium adsorption and calcium release. Cementation experiments were then conducted to determine the effects of different hydrolysis and adsorption times on ammonium adsorption and calcium carbonate precipitation. The results showed that calcium-rich chabazite could be used as a source of calcium ions and as an effective adsorbent of ammonium for EICP. Additionally, synthetic, fresh urine and real, fresh urine had comparable ammonium adsorption and calcium release trends. Finally, inclusion of a pre-hydrolysis step reduced the ammonium adsorption and calcium release, but longer adsorption times lead to calcium carbonate precipitation outside of the sand column, which is an undesirable outcome for soil biocementation; even with this limitation, the calcium carbonate content of sand columns ranged from 0.48% to 0.92%, which signifies the potential of the proposed process for cementation, given a higher initial concentration of urea.