Doctor of Philosophy, Case Western Reserve University, 2024, Physics

The goal of this work is to investigate magnetic materials (MM) and the influence of magnetic field on different shapes and types of MM with innovative magnetic devices. Using magneto-optical detection devices, we examined the physical science of two MM systems: malarial hemozoin (a paramagnetic crystal) in rod-like form, and synthetic magnetic particles with iron oxide cores in spherical form. The second study focuses on capturing and imaging targeted cells using a newly developed CAPGLO device that combines magnetic and fluorescent mechanisms. Due to their magnetic properties, the crystalline hemozoin shows unique alternation in the presence of a magnetic field. Using a light beam, we were able to detect and verify the changes in the direction of the crystal by measuring the polarization-dependent optical absorption when the magnetic field is alternated between on and off. Our results show a factor of two increase in absorption as it grows with light polarization along the easy-axis crystallographic direction compared to polarization along the hard-axis (ax/az = σx/σz = 2), which shows a correlation between the basic physics and the chemical structure of the crystal. The characteristics of magnetophoresis – that is, motion under a gradient magnetic field of magnetic particles (MP) suspended in fluid – are analyzed. As the MP migrate from the center of the sample toward the magnets, we measure the changes in the photodiode detector voltage for the light beam over time. Our results show the effect of different concentrations and MP sizes. In addition, we notice a universal pattern that displays multiple phases that are correlated with the motion of fluid, the chain formation of MPs, and the complete separation of the MPs. Lastly, CAPGLO is an original magnetic detector designed to capture the composite made up of an MP binding to a cell. The cancer cell example has concentrations corresponding to biopsies. The composites are imaged using a fluorescence technique. (open full item for complete abstract)

Committee: Robert Brown (Committee Chair); Michael Martens (Committee Member); Robert Deissler (Committee Member); Susann Brady-Kalnay (Committee Member); Gary Chottiner (Committee Member) Subjects: Experiments; Physics

Doctor of Philosophy (PhD), Ohio University, 2022, Chemistry and Biochemistry (Arts and Sciences)

Antibiotic resistance is a global threat beside the ongoing pandemic by SARS-CoV-2. The number of deaths due to antibiotic-resistant infections is increasing at an alarming rate. The COVID-19 pandemic has already claimed millions of deaths worldwide. Fighting against antibiotic-resistant superbugs and the SARS-CoV-2 has become a challenge. A significant amount of research is going on to develop the vaccine and small molecule antiviral and antibacterial therapeutics targeting proteins. Fortunately, novel non-coding regulatory RNA targets have been identified for developing new antibacterial and antiviral drugs such as bacterial T-box riboswitch, RNA thermometers, and viral stem-loop II motif. T-box riboswitch can control the transcription or translation of amino acid-related genes in bacteria by forming unique interactions between tRNA and mRNA. RNA thermometers (RNATs) are temperature-responsive riboswitches that control the translation based on temperature sensing thus controlling the interaction with the mRNA and 16S rRNA. In Shigella dysenteriae, three RNATs, i.e., ompA, shuT, and shuA, have been discovered. ompA RNAT controls the translation of outer membrane protein A. shuT, and shuA RNAT controls the translation of two proteins that are crucial to the bacterial heme utilization system. The Stem-loop II motif (S2M) is a highly conserved RNA element found in most coronaviruses, astroviruses, and picornaviruses that plays a potential role in viral replication and invasion. The RNA structure plays a significant role in its regulatory function for all of these potential therapeutic targets. Consequently, it is essential to examine the factors that affect the RNA structure and RNA-RNA interaction. Despite having limited building blocks, RNA has diverse functions in the cells. Base protonation and protonated base pairs often occur in RNA when interacting with other biomolecules, thus could play a critical role in vital biological processes. Diff (open full item for complete abstract)

Committee: Jennifer Hines (Advisor) Subjects: Biochemistry; Biology; Genetics

Master of Science in Biomedical Engineering (MSBME), Wright State University, 2020, Biomedical Engineering

High cognitive workload occurs when excessive working memory resources have been deployed to resolve sensory and cognitive processing, resulting in decremented task performance. The P300 event-related potential (ERP) component has shown sensitivity to cognitive load, and it was hypothesized that an attenuated P300 amplitude could be indicative of high cognitive load. We tested this hypothesis by having eight participants complete two continual performance tasks at increasing workload levels while simultaneously performing an oddball task, evoking P300 ERPs in either the auditory or tactile sensory channel. In our experiment, electroencephalographic recordings were collected over the parietal region to observe the P300 component. Our results show a downward trend in P300 amplitude as workload increased when performing auditory oddball tasks, although P300's elicited by the tactile oddball tasks produced no consistent trend. These results suggest cognitive load indexing is possible in select sensory channels, though additional investigation is required.

Committee: Sherif Elbasiouny Ph.D. (Advisor); Ulas Sunar Ph.D. (Committee Member); Matthew Sherwood Ph.D. (Committee Member) Subjects: Biomedical Engineering; Neurosciences

Master of Arts, The Ohio State University, 2016, Psychology

Moderation analysis is used throughout many scientific fields, including psychology and other social sciences, to model contingencies in the relationship between some independent variable (X) and some outcome variable (Y) as a function of some other variable, typically called a moderator (M). Inferential methods for testing moderation provide only a simple yes/no decision about whether the relationship is contingent. These contingencies can often be complicated. Researcher often need to look closer. Probing the relationship between X and Y at different values of the moderator provides the researcher with a better understanding of how the relationship changes across the moderator. There are two popular methods for probing an interaction: simple slopes analysis and the Johnson-Neyman procedure. The Johnson-Neyman procedure is used to identify the point(s) along a continuous moderator where the relationship between the independent variable and the outcome variable transition(s) between being statistically significant to nonsignificant or vice versa. Implementation of the Johnson-Neyman procedure when X is either dichotomous of continuous is well described in the literature; however, when X is a multicategorical variable it is not clear how to implement this method. I begin with a review of moderation and popular probing techniques for dichotomous and continuous X. Next, I derive the Johnson-Neyman solutions for three groups and continue with a partial derivation for four groups. Solutions for the four-group derivation rely on finding the roots of an eighth-degree polynomial for which there is no algebraic solution. I provide an iterative computer program for SPSS and SAS that solves for the Johnson-Neyman boundaries for any number of groups. I describe the performance of this program, relative to known solutions, and typical run-times under a variety of circumstances. Using a real dataset, I show how to analyze data using the tool and how to interpret the results. I co (open full item for complete abstract)

Committee: Andrew Hayes (Advisor); Michael Edwards (Committee Member); Duane Wegener (Committee Member) Subjects: Applied Mathematics; Behavioral Sciences; Biostatistics; Experimental Psychology; Psychology; Quantitative Psychology; Statistics

Doctor of Philosophy, The Ohio State University, 2012, Soil Science

Methane (CH4) is a critical greenhouse gas with ~ 25 times greater global warming potential than carbon dioxide. As the largest natural source of CH4, wetlands have faced a setback in the global warming scenario. Manipulation of wetland hydrology can be a potential management strategy to enhance CH4 consumption (by microbial oxidation) from constructed and managed wetlands. Although work in pure cultures have shown the importance of methane oxidizing bacteria (methanotrophs) in regulating net CH4 flux, few field based studies have been done on the microbial ecology of these CH4 oxidizing communities and how they respond to differing land management systems. For example, there is considerable interest in enabling current wetlands and creating wetlands that have hydrologic pulsing that is driven by seasonal rainfall and watershed dynamics. However, little is known about the ecology of methanotrophs in the “pulsing fringe” - the oxic sediment-water interface of wetlands. The objective of this study was to characterize the functionally active methanotroph communities and link them to potential methane oxidation rates in response to pulsing wetland hydrology and seasonally induced changes in redox conditions. 13C-CH4 stable isotope probing of biomarker Phospholipid Fatty Acids (PLFAs) was successfully used to track the 13C flow into the methanotroph community. Identification and quantification of methanotrophs was effectively achieved to link bacterial structure and function. The results show that, in addition to methanotrophy being controlled by environmental factors such as soil water content, oxygen and methane availability, the physiology of the microorganisms themselves can be uniquely adapted to extant conditions and potentially influence process rates. Results from this study demonstrate that seasonally pulsed wetlands have greater diversity of methanotrophs under elevated methane concentrations. In comparison, methane oxidation in the permanently flooded site (open full item for complete abstract)

Committee: Richard Dick (Advisor); Warren Dick (Committee Member); William Mitsch (Committee Member); Brian Lower (Committee Member) Subjects: Biochemistry; Biogeochemistry; Ecology; Environmental Science; Geochemistry; Microbiology; Soil Sciences

Doctor of Philosophy (PhD), Ohio University, 2007, Molecular and Cellular Biology (Arts and Sciences)

Bacillus subtilis tyrS is an aminoacyl-tRNA synthetase gene that is a member of the T box family of genes, which are found in many Gram-positive bacteria. This family includes aminoacyl-tRNA synthetase, amino acid biosynthetic and amino acid transport genes, and these genes are characterized by a highly-conserved sequence of nucleotides known as the T box sequence. Expression of these genes is regulated by the interaction of uncharged cognate tRNA with the 5' untranslated region of the nascent mRNA. One feature of this interaction is the base pairing of the tRNA acceptor end with four bases of the antiterminator, a conserved mRNA structural element that contains a seven-nucleotide bulge flanked by two helices. The tRNA-antiterminator base pairing prevents the formation of an alternative terminator element and results in complete transcription of the gene. This research investigates binding of tRNA and small molecules to the T box antiterminator using two antiterminator models, AM1A and AM1A(C11U) which represent the wild type aniterminator and a reduced function variant, respectively. From chemo-enzymatic probing and fluorescence studies data, the structural changes occurring in AM1A upon the binding of the acceptor end tRNA to only the first four nucleotides of the bulge and the greater flexibility of AM1A(C11U) compared to AM1A indicate that binding of tRNA occurs via tertiary structure capture and induced fit. Native gel mobility shift, fluorescence studies, and nucleotide analog interference mapping (NAIM) indicated that the integrity of the A2 helix and Mg2+ concentration play an important role in binding of tRNA to antiterminator. The functional groups probed by NAIM of absolutely conserved A10 (A223 of B. subtilis tyrS) were not essential for the binding of tRNA, but the presence of a methyl group on the amino functionality of A10 may sterically hinder binding. Using fluorescence resonance energy transfer and enzymatic probing, neomycin B and two oxazolidinon (open full item for complete abstract)

Committee: Jennifer Hines (Advisor) Subjects: