Physical Sciences and Mathematics Commons^™

Variation In Personality Among Semi-Wild Myanmar Timber Elephants, Sateesh Venkatesh

Theses and Dissertations

This study examines two personality traits: exploration and neophobia, which could influence human-elephant conflicts. Thirty-one semi-wild elephants were tested over two trials using a custom novel puzzle tube containing three tasks and three rewards. Our studies show that elephants do vary significantly between individuals in both exploration and neophobia.

Machine Learning Applications For Drug Repurposing, Hansaim Lim

Dissertations, Theses, and Capstone Projects

The cost of bringing a drug to market is astounding and the failure rate is intimidating. Drug discovery has been of limited success under the conventional reductionist model of one-drug-one-gene-one-disease paradigm, where a single disease-associated gene is identified and a molecular binder to the specific target is subsequently designed. Under the simplistic paradigm of drug discovery, a drug molecule is assumed to interact only with the intended on-target. However, small molecular drugs often interact with multiple targets, and those off-target interactions are not considered under the conventional paradigm. As a result, drug-induced side effects and adverse reactions are often neglected …

Small Molecule Synthetic Carbohydrate Receptors, Marcelo F. Bravo Carranco

Dissertations, Theses, and Capstone Projects

Carbohydrate – receptor interactions are often involved in the attachment of viruses to host cells, and this docking is a necessary step in the virus life cycle that precedes infection and, ultimately, replication. Despite the conserved structures of the glycans involved in docking, they are still considered “undruggable”, meaning these glycans are beyond the scope of conventional pharmacological strategies. Recent advances in the development of synthetic carbohydrate receptors (SCRs) – small molecules that bind carbohydrates – could bring carbohydrate-receptor interactions within the purview of druggable targets. Here we discuss the role of carbohydrate-receptor interactions in viral infection, the evolution of …

Pointing The Zinc Finger On Protein Folding: Energetic Investigation Into The Role Of The Metal-Ion In The Metal-Induced Protein Folding Of Zinc Finger Motifs, Inna Bakman-Sanchez

Dissertations, Theses, and Capstone Projects

Interactions between inorganic metal-ion cofactors and organic protein scaffolds are important for the proper structure and function of metalloproteins. Zinc finger proteins (ZFPs) are an example of proteins with such crucial metal-protein interactions. Incorporation of the Zn(II)-ion into ZFPs allows for their correct folding into structures that can carry out vital biological functions which include gene expression and tumor suppression. In addition, engineered ZFPs have shown to be promising genetic therapeutics in the clinic. And yet, there is still a gap in a quantitative understanding of the energetic contribution of the metal-protein interactions towards the structure and function of these …

Snow-Albedo Feedback In Northern Alaska: How Vegetation Influences Snowmelt, Lucas C. Reckhaus

Theses and Dissertations

This paper investigates how the snow-albedo feedback mechanism of the arctic is changing in response to rising climate temperatures. Specifically, the interplay of vegetation and snowmelt, and how these two variables can be correlated. This has the potential to refine climate modelling of the spring transition season. Research was conducted at the ecoregion scale in northern Alaska from 2000 to 2020. Each ecoregion is defined by distinct topographic and ecological conditions, allowing for meaningful contrast between the patterns of spring albedo transition across surface conditions and vegetation types. The five most northerly ecoregions of Alaska are chosen as they encompass …

Method Development For Identifying Counterfeit Cigarettes Using Environmental Pollen Analysis, Tiffany Chan

Student Theses

Cigarette counterfeiting negatively impacts government revenue and undermines tobacco control policies. Tracking geographical origins and potential trade routes of counterfeit cigarettes is important for investigation illegal trade in tobacco products. Traditional pollen extraction techniques provide clear residues of pollen trapped on tobacco leaves and used for geographical identification; however, such methods are time-consuming and utilize concentrated chemicals. This study developed a simple, fast and environmentally friendly method for extraction of pollen grains used in differentiating genuine and counterfeit cigarettes. Experimental factors that may affect pollen recovery including number of cigarettes, extraction solution, and extraction temperature, were optimized. The optimum parameters …

Proton Pumping Mechanism In Cytochrome C Oxidase, Xiuhong Cai

Dissertations, Theses, and Capstone Projects

Cytochrome c Oxidase (CcO), is the terminal electron acceptor in the membrane bound aerobic respiratory chain. It reduces O₂ to water. The energy released by this reaction is stored by pumping protons from the high pH, N-side of the membrane to the low pH, P-side. The generated proton gradient provides the motive force for synthesis of ATP by the ATP synthase.

Building a proton gradient across the membrane requires that proton transport must occur along controllable proton pathways to prevent proton leakage to the N-side. It has been suggested that CcO function requires proton transfer channels in both the …

Identification And Quantification Of Classic, Prescription, And Synthetic Opioids In Hair By Liquid Chromatography Tandem Mass Spectrometry (Lc/Ms/Ms), Natalia A. Platosz

Student Theses

The current use and misuse of synthetic and prescription opioids in the US has reached epidemic status. According to the US Department of Health and Human Services, every day more than 130 people in the US die after overdosing on opioids, and 2.1 million had an opioid use disorder in 2016. Hair is becoming an alternative matrix of increasing interest in forensic toxicology to investigate drug use and abuse patterns due to its long window of detection. The focus of this project was to develop and validate a method that simultaneously detects and quantifies 27 classic, prescription and synthetic opioids …

Advanced Computational Methodologies To Study Binding Free Energies Of Biomolecular Complexes, Rajat Kumar Pal

Dissertations, Theses, and Capstone Projects

Molecular recognition is the basis of biological mechanisms and is a key element to consider while formulating effective and safe drugs. Pharmaceutical drugs are designed so as to bind a target protein even at very low concentrations to alter the diseased conditions without interfering with normal biological processes. In a rational drug design process, this is achieved by acquiring information about the chemical structure and the physical and chemical properties of the target protein receptor to gain insights on how changing the chemical composition of the substrate drug could affect the protein-drug interaction and binding affinities. Computational models are used …

Leveraging Antibodies For Positron Emission Tomography And Near-Infrared Fluorescence Imaging Of Cancer, Kimberly C. Fung

Dissertations, Theses, and Capstone Projects

The high specificity and affinity of antibodies make them attractive for developing drugs to diagnose and treat cancer. The overarching goal of this work is to explore the synthesis and use of antibody-based imaging agents in preclinical models of cancer. This work can be described as two-fold. In the first part, we investigated how the use of a glycans-specific bioconjugation strategy affects Fc gamma RI binding and why it results in improved in vivo performance of immunoconjugates. To do so, we used the clinically relevant positron emission tomography (PET) imaging agent, ⁸⁹Zr-DFO-pertuzumab, in mouse models of human breast cancer. …

Ecosystem Health In Guánica Bay And La Parguera, Puerto Rico: Remote Sensing Of Ocean Color And Metal Analysis Of Coral Tissue And Surficial Sediments, Jahnelle Howe

Dissertations and Theses

Guánica Bay is an estuary located in southwest Puerto Rico, with a coral reef ecosystem at its periphery. This ecosystem is affected by sediments, nutrients, and contaminants from the watershed through the Bay and into the offshore water. This project evaluates Guánica Bay and La Parguera coastal areas through remote sensing and chemical analysis to assess coastal ecosystem health. The concentration of metals in two coral species and their associated surface sediments was were analyzed by X-ray fluorescence (XRF) and Direct Mercury Analyzer (DMA- 80). Ocean color remote sensing was used to estimate nutrient inputs and phytoplankton biomass through chlorophyll- …

Mechanisms Of Value-Biased Prioritization In Fast Sensorimotor Decision Making, Kivilcim Afacan-Seref

Dissertations and Theses

In dynamic environments, split-second sensorimotor decisions must be prioritized according to potential payoffs to maximize overall rewards. The impact of relative value on deliberative perceptual judgments has been examined extensively, but relatively little is known about value-biasing mechanisms in the common situation where physical evidence is strong but the time to act is severely limited. This research examines the behavioral and electrophysiological indices of how value biases split-second perceptual decisions and the possible mechanisms underlying the process. In prominent decision models, a noisy but statistically stationary representation of sensory evidence is integrated over time to an action-triggering bound, and value-biases …