Barrett, The Honors College Thesis/Creative Project Collection

Polyketides are a wide ranging class of natural microbial products highly relevant to the pharmacological industry. As chemical synthesis of polyketides is quite challenging, significant effort has been made to understand the polyketide synthases (PKSs) responsible for their natural production. Native to Streptomyces, the aln biosynthetic gene cluster was recently characterized and encodes for an iterative type I polyketide synthase (iT1PKS). This iT1PKS produces both , and ,-double bond polyketides named allenomycins; however, the basis in which one bond is chosen over the other is not yet clear. The dehydratase domain, AlnB_DH, is thought to be solely responsible for catalyzing double bond formation. Elucidation of enzyme programming is the first step towards reprogramming AlnB_DH to produce novel industrially relevant products. The Nannenga lab has worked as collaborators to the Zhao lab at the University of Illinois at Urbana-Champaign to unravel AlnB_DH’s structure and mechanism. Here, mutant constructs of AlnB_DH are developed to elucidate enzyme structure and provide insight into active site machinery. The primary focus of this work is on the development of the mutant constructs themselves rather than the methods used for structural or mechanistic determination. Truncated constructs were successfully developed for crystallization and upon x-ray diffraction, a 2.45 Å resolution structure was determined. Point-mutated constructs were then developed based on structural insights, which identified H49, P58, and H62 as critical residues in active site machinery.

The concept of rape has been a prominent part of historical U.S. criminal law, and legislation and statutes have changed significantly over time. Despite numerous reforms, however, there is still a lack of reporting, arrests, and convictions for sexual assault cases. This is due to several factors influencing the judgement of criminal justice actors, such as how cases are handled by police officers and prosecutors, who decide whether to further investigate a case, send the case to prosecution for sentencing, or bring the case to trial. Some of these influences include legal and extra-legal factors and certain beliefs or assumptions about sexual assault victims, which affect these officials’ discretionary decisions. As a result, criminal justice officials tend to dismiss or unfound a sexual assault case, especially with acquaintance rape, contributing to the substantial lack of arrests and convictions. These facts, which are examined in the paper, emphasize the need to reassess our criminal justice system's current response to sexual assault cases. This includes adjusting the evaluation markers for prosecutors, improving the communication between the relevant criminal justice actors, and implementing evaluations of prosecutorial ethics and community satisfaction.

Ketone levels give an insight into the bodies metabolism. People with epilepsy or people dieting may want to keep their levels high, whereas type one diabetics or those recovering from eating disorders may want to keep their levels low. Current ketone detection methods involve blood samples or urinalysis. A ketone (acetone) biosensor was fabricated to detect levels in human breath, providing a noninvasive way to quickly and accurately detect ketone levels in the body.

Stoicism is a philosophy that emerged in the Hellenistic Age, between 323 BCE and 30 BCE in the Eastern Mediterranean and Middle East (Irvine, 2009). Stoicism was born into an exceptionally transitional social and political time period, and three major philosophers, Marcus Aurelius, Seneca, and Epictetus, rose to fame and established this manner of interacting with the world around them. These teachings and writings, still read throughout the world today due to their practicality and effectiveness, provide a major framework for “(It is [Stoicism]) the power of the mind to be unconquerable,” (Seneca, The Stoic Letters). Stoicism can be used as a tool in the pursuit of perseverance, wisdom, self control, and self mastery, which can ultimately lead to a more fulfilling and happy life. This philosophy is a practical one, and is designed with the intention to help those who practice it live well rather than just provide a theoretical understanding of the teaching of the world. Stoicism is a way to interact with others and the world in a way that reduces the amount of suffering experienced and can increase the capacity for joy. As a high achieving college student, it may not be feasible or entirely practical to live as Stoics did in the ancient world. Yet, aspects of ancient Stoicism can still be applied to modern-day living and can be used to make college students more resilient, happier, and allow them to live a fuller, more satisfied life. In this 7 week asynchronous program designed for high achieving college students, we will explore the most common barriers to happiness that college students face and explore what Stoic philosophies offer to help remedy these barriers.

Graph neural networks (GNN) offer a potential method of bypassing the Kohn-Sham equations in density functional theory (DFT) calculations by learning both the Hohenberg-Kohn (HK) mapping of electron density to energy, allowing for calculations of much larger atomic systems and time scales and enabling large-scale MD simulations with DFT-level accuracy. In this work, we investigate the feasibility of GNNs to learn the HK map from the external potential approximated as Gaussians to the electron density 𝑛(𝑟), and the mapping from 𝑛(𝑟) to the energy density 𝑒(𝑟) using Pytorch Geometric. We develop a graph representation for densities on radial grid points and determine that a k-nearest neighbor algorithm for determining node connections is an effective approach compared to a distance cutoff model, having an average graph size of 6.31 MB and 32.0 MB for datasets with 𝑘 = 10 and 𝑘 = 50 respectively. Furthermore, we develop two GNNs in Pytorch Geometric, and demonstrate a decrease in training losses for a 𝑛(𝑟) to 𝑒(𝑟) of 8.52 · 10^14 and 3.10 · 10^14 for 𝑘 = 10 and 𝑘 = 20 datasets respectively, suggesting the model could be further trained and optimized to learn the electron density to energy functional.

The nonprofit sector exists as one of three working groups which contribute to the flow of the economy and society. Unlike the government and for-profit sectors, the nonprofit world has faced a growing responsibility alongside a lack of emphasis on the sector’s importance. Nonprofits have often faced a lack of resources needed to combat these gaps. However, since Covid-19, resources have been diminishing even further. These resources can be identified as a variety of elements, from volunteers and paid staff to funds and access to overseas goods and services. A case study of the world-renowned Make-A-Wish Foundation and its Arizona Chapter perfectly illustrates the journey back to full mission-accomplishment in present times through their actions taken to combat common sector struggles. This case study proves importance of the nonprofit sector, accompanied by a call for education and re-emphasis of the nonprofit sector.