Physical Sciences and Mathematics Commons^™

Analytical Considerations And Methods For Comprehensive Analysis Of Bacterial Phospholipidomics Using Hilic-Ms/Ms, David Thomas Reeves

Doctoral Dissertations

Omics technologies have rapidly evolved over the last half century through vast improvements in efficient extraction methodologies, advances in instrumentation for data collection, and a wide assortment of informatics tools to help deconvolute sample data sets. However, there are still untapped pools of molecules that warrant further analytical attention. As the frontline defense of the cell against exterior influences, the phospholipid membrane is key in structure, defense, and signaling, but current omics studies are only just now catching up to the potential hidden within cellular lipid profiles. Examination of shifts in phospholipid speciation and character could provide researchers with a …

Antibiotic Sensitivity Testing Of Foodborne Bacteria Using Surface-Enhanced Raman Spectroscopy, Joshua Gukowsky

Doctoral Dissertations

The spread of antibiotic resistant bacteria around the world has become a major public health issue, and it is essential that effective detection methods exist for identifying these organisms and preventing them from spreading throughout our food systems and into the environment. The goal of this research is to develop a novel analytical procedure that is capable of easily identifying antibiotic resistance in bacterial samples, and also provides more information about the biochemical characteristics of the bacteria and their responses to antibiotic exposure. Surface-enhanced Raman Spectroscopy (SERS), an analytical technique that uses light scattering to produce a spectrum based on …

Monitoring Mammals At Multiple Scales: Case Studies From Carnivore Communities, Kadambari Devarajan

Doctoral Dissertations

Carnivores are distributed widely and threatened by habitat loss, poaching, climate change, and disease. They are considered integral to ecosystem function through their direct and indirect interactions with species at different trophic levels. Given the importance of carnivores, it is of high conservation priority to understand the processes driving carnivore assemblages in different systems. It is thus essential to determine the abiotic and biotic drivers of carnivore community composition at different spatial scales and address the following questions: (i) What factors influence carnivore community composition and diversity? (ii) How do the factors influencing carnivore communities vary across spatial and temporal …

Amyloidogenesis Of Β-2-Microglobulin Studied By Mass Spectrometry And Covalent Labeling, Blaise G. Arden

Doctoral Dissertations

Amyloid-forming proteins are implicated in a number of debilitating diseases. While many amyloid-forming proteins are well studied, the early stages of amyloidosis are still not well understood on a molecular level. Covalent labeling, combined with mass spectrometry (CL-MS), is uniquely well suited to provide molecular-level insight into the factors governing the early stages of amyloidosis. This dissertation leverages CL-MS techniques to examine the early stages of β-2-microglobulin (β2m) amyloidosis. β2m is the protein that forms amyloids in the condition known as dialysis-related amyloidosis. An automated CL-MS technique that uses dimethyl(2-hydroxy-5-nitrobenzyl) sulfonium bromide as a labeling reagent was developed and used …

Birds And Bioenergy: A Modeling Framework For Managed Landscapes At Multiple Spatial Scales, Jasmine Asha Kreig

Doctoral Dissertations

This dissertation examines the design and management of bioenergy landscapes at multiple spatial scales given numerous objectives. Objectives include biodiversity outcomes, biomass feedstock yields, and economic value.

Our study examined biodiversity metrics for 25 avian species in Iowa, including subsets of these species related to ecosystem services. We used our species distribution model (SDM) framework to determine the importance of predictors related to switchgrass production on species richness. We found that distance to water, mean diurnal temperature range, and herbicide application rate were the three most important predictors of biodiversity overall. We found that 76% of species responded positively to …

Investigative Mechanisms To Exploit Caspase-Induced Apoptosis Using Polymeric Nanogels, Francesca Edith Anson

Doctoral Dissertations

Cysteine aspartate proteases (caspases) act as the molecular scissors of cell death, disintegrating diverse cellular components necessary for survival and growth via proteolysis. Caspases are tightly regulated through a myriad of mechanisms including proteolytic processing, structural changes, post-translational modifications and metal binding. Correspondingly, cancers have evolved numerous resistance and desensitization mechanisms upstream or within the caspase pathway to avoid death signals. These mechanisms are extremely diverse and are not fully understood however, the field overwhelming suggests caspase activity and caspase inhibition antagonism to be critical for efficacious cancer therapies. Accordingly, exploiting the role of caspases in apoptosis has become an …

Investigation Of Interactions Between 1,3 Dialkyl Imidazolium Ionic Liquids And Lignocellulosic Polymers, Aparna Annamraju

Doctoral Dissertations

Lignocellulosic biomass is a potential energy source for fuels, chemicals and materials production in a sustainable manner. A network of covalent and non-covalent bonds between the three main polymers of biomass, i.e., cellulose, hemicellulose and lignin, results in a compact structure that is resistant to chemical and biological attacks and therefore challenging for the efficient utilization of lignocellulosic biomass. Ionic liquids (ILs) have been reported to disrupt the bonds between these polymers and dissolve biomass at temperatures below 100 ˚C. Research through the years has shown that biomass pretreatment with IL brings out the selective dissolution of biomass polymers and …

Synthetic Heterosynaptic Plasticity Enhances The Versatility Of Memristive Systems Emulating Bio-Synapse Structure And Function, William T. Mcclintic

Doctoral Dissertations

Memristive systems occur in nature and are hallmarked via pinched hysteresis, the difference in the forward and reverse pathways for a given phenomenon. For example, neurons of the human brain are composed of synapses which apply the properties of memristance for neuronal communication, learning, and memory consolidation. Modern technology has much to gain from the characteristics of memristive systems, including lower power operation, on-chip memory, and bio-inspired computing. What is more, a relationship between memristive systems and synaptic plasticity exists and can be investigated focusing on homosynaptic and heterosynaptic plasticity. Where homosynaptic plasticity applies to interactions between neurons at a …

Data Driven Models Of Hemlock Woolly Adelgid Impacts And Biological Control, Hannah M. Thompson

Doctoral Dissertations

We present two models of the Adelges tsugae, the hemlock woolly adelgid, an invasive insect pest of Tsuga canadensis, eastern hemlock, in the eastern United States. An A. tsugae infestation often results in the death of T. canadensis within years, and has caused significant changes to hemlock forests. We construct two models composed of systems of ordinary differential equations with time dependent parameters to represent seasonality. The first model captures the coupled cycles in T. canadensis health and A. tsugae density. We use field data from Virginia to develop the model and to perform parameter estimation. The mechanisms …

Physiological Constraints, Mechanisms, And Mineral Transformations Of Iron Reduction In Hyperthermophilic Crenarchaea, Srishti Kashyap

Doctoral Dissertations

Dissimilatory iron reduction by hyperthermophilic archaea occurs in many geothermal environments and typically relies on microbe-mineral interactions that transform various iron oxide minerals. However, the kinds of iron oxides that can be used, growth rates, extent of iron reduction, and the mineral transformations that occur due to this metabolism are poorly understood. This dissertation improves our fundamental understanding of the physiological mechanisms and mineral transformations of hyperthermophilic iron reduction using two model crenarchaea, Pyrodictium delaneyi and Pyrobaculum islandicum. Using growth yields and metabolite production rates, we demonstrated that a broad range of Fe(III) (oxyhydr)oxides of variable thermodynamic stability was …

High Throughput Analysis To Study Emerging Pollutants And Nanoparticle Fate In Biological Systems, Xiaolong He

Doctoral Dissertations

”The increasing applications of emerging and fugitive contaminants (EFCs) and engineered nanoparticles (ENPs) attract significant research interest for their potential risks to human health and the environment. In order to assess the health risks of these emerging contaminants, rapid and reliable analytical methods to measure the concentrations and fates of these contaminants are imperative. This dissertation focuses on the developments of advanced analytical methods and their applications to study those emerging contaminants in crop plant and simulated gastric fluid (SGF). Three types of mass spectrometry based methodologies have been developed, one is freeze-thaw/centrifugation extraction followed by high performance liquid chromatography …

Multimodal Neuroscience Data Modeling And Inference, Sima Azizi

Doctoral Dissertations

“Mathematical models can be combined with deep learning and machine learning methods to provide new insights in neuroscience. The field of neuroscience is characterized by rich datasets that include fluid biomarkers, EEG signals, and advanced neuroimages. Recent advances in natural language processing have led to the opportunity to gain additional insights from rapidly growing text databases as well as electronic health records. In this research, we focus on applying computational intelligence methods to the analysis of three different complex data sources: blood levels of disease biomarkers, EEG signals from schizophrenic patients, and disease phenotypes encoded in electronic health records. First, …

Exposure Assessment Of Emerging Contaminants: Rapid Screening And Modeling Of Plant Uptake, Majid Bagheri

Doctoral Dissertations

"With the advent of new chemicals and their increasing uses in every aspect of our life, considerable number of emerging contaminants are introduced to environment yearly. Emerging contaminants in forms of pharmaceuticals, detergents, biosolids, and reclaimed wastewater can cross plant roots and translocate to various parts of the plants. Long-term human exposure to emerging contaminants through food consumption is assumed to be a pathway of interest. Thus, uptake and translocation of emerging contaminants in plants are important for the assessment of health risks associated with human exposure to emerging contaminants. To have a better understanding over fate of emerging contaminants …

Critical Behavior In Evolutionary And Population Dynamics, Stephen Walter Ordway

Doctoral Dissertations

“This study is an exploration of phase transition behavior in evolutionary and population dynamics, and techniques for predicting population changes, across the disciplines of physics, biology, and computer science. Under the looming threat of climate change, it is imperative to understand the dynamics of populations under environmental stress and to identify early warning signals of population decline. These issues are explored here in (1) a computational model of evolutionary dynamics, (2) an experimental system of decaying populations under environmental stress, and (3) a machine learning approach to predict population changes based on environmental factors. Through the lens of critical phase …