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.

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.

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.

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.

Is there a mismatch between urban farmers’ perceptions of their farm’s environmental sustainability and its actual environmental impact? Focusing on the use of water and nutrients on each farm as described by the farmers through interviews, it is evident that there is some level of disconnect between ideals and practices. This project may aid in bridging the gap between the two in regard to the farmers’ sustainability goals. This project will move forward by continuing interviews with farmers as well as collecting soil and water from the farms in order to more accurately quantify the sustainability of the farms’ practices. This project demonstrates that there is some degree of misalignment between perception and reality. Two farms claimed they were sustainable when their practices did not reflect that, while 2 farms said they were not sure if they were sustainable when their practices indicated otherwise. Samples from two farms showed high concentrations of nutrients and salts, supporting the idea that there may be a mismatch between perceived and actual sustainability.

This research endeavor explores the 1964 reasoning of Irish physicist John Bell and how it pertains to the provoking Einstein-Podolsky-Rosen Paradox. It is necessary to establish the machinations of formalisms ranging from conservation laws to quantum mechanical principles. The notion that locality is unable to be reconciled with the quantum paradigm is upheld through analysis and the subsequent Aspect experiments in the years 1980-1982. No matter the complexity, any local hidden variable theory is incompatible with the formulation of standard quantum mechanics. A number of strikingly ambiguous and abstract concepts are addressed in this pursuit to deduce quantum's validity, including separability and reality. `Elements of reality' characteristic of unique spaces are defined using basis terminology and logic from EPR. The discussion draws directly from Bell's succinct 1964 Physics 1 paper as well as numerous other useful sources. The fundamental principle and insight gleaned is that quantum physics is indeed nonlocal; the door into its metaphysical and philosophical implications has long since been opened. Yet the nexus of information pertaining to Bell's inequality and EPR logic does nothing but assert the impeccable success of quantum physics' ability to describe nature.

This study investigated the difference in biofilm growth between pristine polypropylene microplastics and aged polypropylene microplastics. The microplastics were added to Tempe Town Lake water for 4 weeks. Each week the microplastic biofilms were quantified. Comparing the total biofilm counts, the results showed that the aged microplastic biofilms were larger than the pristine each week. By week 3 the aged microplastic counts had almost doubled in size increasing from 324 to 626 Colony Forming Units per gram in just one week. There was a significant difference in the diversity found from week 1 to week 4. About 40% of the diversity for the pristine microplastic biofilm was seen as light-yellow dots and about 60% of these dots were seen on the aged microplastic biofilms in both weeks. As the microplastics were submerged in the lake water, new phenotypes emerged varying from week 1 to week 4 and from pristine to aged microplastic biofilms. Generally, it was found that as the microplastics stay in the environment there is more biofilm on the particles. The aged microplastics have a larger amount of biofouling, and the pristine microplastic biofilms were found to have more diversity of phenotypes.

The use of enzyme-catalyst interfaces is underexplored in the field of biocatalysis, particularly in studies on enabling novel reactivity of enzymes. For this thesis, the HaloTag® protein tagging platform was proposed as a bioconjugation method for a pinacol coupling reaction using lipases, as a model for novel reactivities proceeding via ketyl radical intermediates and hydrogen-bonding-facilitated redox attenuation. After an initial lipase screening of 9 lipases, one lipase (Candida rugosa) was found to perform the pinacol coupling of p-anisaldehyde under standard conditions (fluorescein and 530nm light, 3% yield). Based on a retrosynthetic analysis for the photocatalyst-incorporated HaloTag® linker, the intermediates haloamine 1 and aldehyde 6 were synthesized. Further experiments are underway or planned to complete linker synthesis and conduct pinacol coupling experiments with a bioconjugated system. This project underscores the promising biocatalytic promiscuity of lipases for performing reactions proceeding through ketyl radical intermediates, as well as the underdeveloped potential of incorporating bioengineering principles like bioconjugation into biocatalysis to overcome kinetic barriers to electron transfer and optimize biocatalytic reactions.