Digital Commons Network^™

Sampling Techniques For Research And Management Of Cichlid Species In Lentic Systems, Jason Matthew Bies

Theses and Dissertations

Introduced cichlid species are increasingly more common in tropical freshwater systems and expanding in range, often with negative consequences to receiving systems. To better understand, monitor, and manage these populations, improved cichlid sampling protocols are required. The goal of this study was to (1) evaluate diel electrofishing and gill netting sampling catch efficiency, and (2) compare two non-lethal methods for extracting stomach contents from Butterfly Peacock Bass Cichla ocellaris. This study suggests that electrofishing, particularly at night, may be a more appropriate gear for sampling cichlid species in the littoral zone of reservoirs, as gill nets were more time intensive, …

Design And Synthesis Of 5-Oxo-Ete Receptor Antagonists; And Synthesis Of Neuroprostanes As A Biomarker For The Diagnosis Of Alzheimer’S Disease, Rui Wang

Theses and Dissertations

1) 5-Oxo-ETE (7, Scheme 1) is the most potent eosinophil chemoattractant among all lipid mediators and it can also stimulate a late-phase asthma attack. It is formed by the biotransformation of arachidonic acid (AA, 1, Figure 1). 5-Oxo-ETE (7) elicits eosinophil migration both in vitro and in vivo when injected intradermally in humans, acting via the highly selective OXE receptor (OXE-R). Our group postulated that a selective OXE-R antagonist might be a useful therapeutic agent in late phase asthma. As a result, the first and only series of OXE receptor antagonists which are structural mimics of 5-oxo-ETE (7) have been …

Relative Importance Of Ions And Particles In Silver Nanoparticle Uptake And Accumulation In Keystone Estuarine Organisms; Prorocentrum Minimum And Crassostrea Virginica, Shelby Victoria Butz

Theses and Dissertations

In marine systems, silver is regarded as being one of the most toxic and readily accumulated metals, and is known to be taken up and accumulate within marine invertebrates, fish, phytoplankton and seaweeds. Reported open ocean concentrations of silver range from 0.1 – 2 ng L-1 while silver concentrations in coastal waters are typically 5 to 10 times higher than open ocean values (0.1 - 50 ng L-1). The determination of silver in marine and coastal waters presents several challenges including low concentrations and matrix complexity of seawater, which creates interferences and other challenges for many instrumental techniques creating a …

Green Synthesis/Biosynthesis Of Silver Nanoparticles By Using Orange Peel Extract, Leela Joshi

Theses and Dissertations

Joshi, Leela, Green Synthesis/Biosynthesis of Silver Nanoparticles by Using Orange Peel Extract. Master of Science (MS), December, 2018, 40 pages, 23 figures, references, 36 titles. In this work, we report synthesis of silver nanoparticles (AgNPs) with an average size of ~6 nm. The aqueous solution of Ag+ ions is reduced using an aqueous extract from orange peel (Citrus Sinensis) at varying pHs. Reduction of Ag+ ions in solution was monitored using UV-visible absorption spectroscopy, and the corresponding surface plasmon resonance of AgNPs at 435 nm. The solution changed color from yellow to reddish-brown upon bioreduction of silver nitrate in orange …

Measuring The Interaction And Cooperativity Between Ionic, Aromatic, And Nonpolar Amino Acids In Protein Structure, Mason Scott Smith

Theses and Dissertations

Protein folding studies have provided important insights about the key role of non-covalent interactions in protein structure and conformational stability. Some of these interactions include salt bridges, cation-π, and anion-Ï€ interactions. Understanding these interactions is crucial to developing methods for predicting protein secondary, tertiary, quaternary structure from primary sequence and understanding protein-protein interactions and protein-ligand interactions. Several studies have described how the interaction between two amino acid side chains have a substantial effect on protein structure and conformational stability. This is under the assumption that the interaction between the two amino acids is independent of surrounding interactions. We are interested …

The Diversity Found Among Carbapenem-Resistant Bacteria, Galen Edward Card

Theses and Dissertations

This work will look at two factors that add to the diversity of carbapenem resistant bacteria. First, it focuses on the diversity of carbapenemase resistance plasmids. 446 plasmids were characterized by size, gene content and replicon groups. We identified that on average, over 30% of the encoded proteins on each plasmid have an unknown function. Plasmid sizes ranged from 1.6kb to 500kb, with an average of around 100kb and median of 80kb. Additionally, six replicon groups account for 80% of all the carbapenemase resistance plasmids. We also highlight the lack of data available for carbapenemase carrying plasmids from bacterial genera …

The Economics Of Skin Tone In Nineteenth-Century Maryland, Yuree Kim

Theses and Dissertations

I analyze the effect of subtle differences in skin complexion on heights of free blacks in Maryland during the nineteenth century. I propose that lighter-skinned blacks were taller (indicating better nutrition) than their darker counterparts. I find the hypothesis holds - 15.9% taller for males and 16.5% taller for females.

Characterization Of Ambient Noise, Rachel C. Ramirez

Theses and Dissertations

An Air Force sponsor is interested in improving an acoustic detection model by providing better estimates on how to characterize the background noise of various environments. This would inform decision makers on the probability of acoustic detection of different systems of interest given different levels of noise. Data mining and statistical learning techniques are applied to a National Park Service acoustic summary data set to find overall trends over varying environments. Linear regression, conditional inference trees, and random forest techniques are discussed. Findings indicate only sixteen geospatial variables at different resolutions are necessary to characterize the first ten ⅓ octave …

Resolution Of Proximal Oxidative Base Damage And 3′-Phosphate Termini For Nonhomologous End Joining Of Free Radical-Mediated Dna Double-Strand Breaks, Sri Lakshmi Chalasani

Theses and Dissertations

Clustered damage to DNA is a signature mark of radiation-induced damage, which involves damage to the nucleobases and/or DNA backbone. Double-strand breaks created by damaging agents are detrimental to cell survival leading to chromosomal translocations. Normal cells employ Non-homologous end-joining because of its faster kinetics, to suppress chromosomal translocations. However, the presence of complex DNA ends constitutes a significant challenge to NHEJ. Location of Thymine glycol (Tg) at DSB ends was a potential hindrance to end joining. The substrate with Tg at the third position (Tg3) from the DSB joined better than when present at the fifth position (Tg5). However, …

Climate Metric Coherence: Stationarity Of The Relationships Between North Pacific Climate Indices And Ecological Processes In The Gulf Of Alaska, Michael Opiekun

Theses and Dissertations

The Pacific Decadal Oscillation (PDO) has been used to characterize the dominant basin-scale climate variability, in the North Pacific. The PDO index has been correlated to Pacific salmon (Oncorhynchus spp.) population dynamics in the Gulf of Alaska (GOA) during the late 1900s, but the stationarity of the statistical relationships between salmon production and the basin-scale index (and between the regional physical processes and the basin-scale index) has not been quantified. A change in the relationship between the PDO and salmon catches has been noted during the late 1980s, motivating further investigation of variability in climate and ecosystem properties during this …

Insects As Metaphors For Post-Civil War Reconstruction Of The Civic Body In Augustan Age Rome, Olivia Semler

Theses and Dissertations

Early Augustan Age literature saw a focus on recovery from a period steeped in the tragic losses of civil war; Vergil, in his Georgics, and Ovid, in his Metamorphoses, employed insects likened to, or transformed into, humans as a way to suggest possible models for recovery. While these models have been studied throughout classical scholarship for their value in proposing a new Roman Golden Age and its tenability, scholars have long overlooked the importance of the insects used in such models, and the ways in which they can substantially alter our understanding of these metaphors. As structures for cultural understanding …

The Development Of Novel Inhibitors Of The Nlrp3 Inflammasome, Jacob W. Fulp

Theses and Dissertations

Inflammasomes are intracellular multimeric protein complexes that regulate inflammation by controlling the maturation of cytokines, interleukin-1β (IL-1β) and interleukin-18 (IL-18). Additionally, activation of these inflammasome complexes has been implicated in an inflammatory form of death known as proptosis. Of the known inflammasomes, the NOD-like receptor family pyrin domain containing 3 (NLPP3) inflammasome, is the most elucidated. Under physiological conditions, NLRP3-mediated inflammation promotes healing and the elimination of cellular debris and pathogens. However, the dysregulation of IL-1β, IL-18 and pyroptosis are instrumental in the development of multiple pathologies. Furthermore, studies suggest that the NLRP3 inflammasome mediates detrimental neuroinflammation and …

An Investigation Of Electronic Cigarette Aerosol Mixture On Craniofacial Development In Mouse Embryos, Suraj Kandalam

Theses and Dissertations

E-cigarette (e-cig) use has increased in recent years among teenagers and young adults. E-cigs are battery-powered nicotine delivery systems that vaporize e-liquids, a solution composed of propylene glycol (PG), vegetable glycerin (VG), nicotine, flavoring, and coloring agents. The aim of this study was to determine the effects of exposure to e-cig aerosol mixtures (e-cigAMs) on proliferation, migration, and differentiation of NCCs in vitro and craniofacial development in mouse embryos in vivo. E-cigAM was produced by bubbling e-cig aerosol into saline. E-cigAMs were generated for unflavored e-liquid of increasing PG: VG ratio. Metabolic activity (MA), gene expression, migration, and proliferation …

An Analysis Of Signaling Processes Leading To A Defense Response In Soybean, Brandon Trey Mcneece

Theses and Dissertations

Plant-parasitic nematodes are the cause of devastating yield loss in vital agricultural crops around the world. Heterodera glycines, also referred to as soybean cyst nematode, is the main pathogen of Glycine max (soybean) causing more loss than all other pathogens of G. max combined. The resultant economic impact due to H. glycines in United States soybean production alone is estimated to account for an annual one-billion-dollar loss. Natural resistant genotypes have been found in trials to combat this pathogen. Of the resistant varieties identified, G. max[Peking/PI 548402] and G. max[PI 88788] are the major sources of resistance. Identification of genes …

Metastable-State Nh Photoacids And Organic Photo Carbon Monoxide Releasing Materials, Aluthwatte Rallage Nawodi Madhusanka Abeyrathna

Theses and Dissertations

The recently discovered metastable-state photoacids (mPAHs) can produce a large proton concentration with high efficiency and good reversibility upon irradiation with visible light with moderate intensity. Therefore, mPAHs can be conveniently incorporated in to different systems to control various proton-transfer processes. Recently, several applications of mPAHs have been demonstrated. However, none of the previously reported mPAHs can function at a pH 7.4. Thus, biological applications of mPAHs are limited. In this work, mPAHs that can reversibly release a proton in PBS buffer (pH = 7.4) under visible light are designed and synthesized. NH-PAH-1 is the first of this type of …

High Throughput Analysis Of The Penetration Of Iron Oxide/Polyethylene Glycol Nanoparticles Into Multicellular Breast Cancer Tumor Spheroids, Jonathan Robert Gabriel

Theses and Dissertations

The purpose of this study was to design and optimize a system for the high-throughput analysis of multicellular tumor spheroids (MCTS), and validate the system through the study of a complex biological model. The system was successfully created and optimized, allowing the histological recovery of MCTS at rates up to 90% for microarrays of 24-spheroids. Arrays of 96-spheroids were recovered at rates up to 86%. The system was used to study the penetration of 5k Da-polyethylene coated superparamagnetic iron-oxide nanoparticles (5k-PEG SPIONs) into HTB-126 breast cancer spheroids cultured to a mean diameter of 486 micrometer (± 25.2 micrometer). Results were …

Development Of New Routes For The Synthesis Of Carbaporphyrins And Carbachlorins, Navneet Sahota

Theses and Dissertations

Carbaporphyrins and carbachlorins are porphyrin analogs in which one of the nitrogens is replaced with a carbon atom within a porphyrin-like cavity. These systems form stable organometallic derivatives and exhibit unusual chemical reactivity. In the monocarbaporphyrinoids such as benzocarbaporphyrins, one of the pyrrole rings is replaced by an indene unit. Although syntheses of monocarbaporphyrins with fused rings have been widely investigated over the past 20 years, a few examples of carbaporphyrins without fused rings have been reported in the literature.

In this thesis, two projects were conducted to further explore carbaporphyrin and carbachlorin chemistry. The first project utilized a ‘3+1’ …

Decentralized Algorithm Of Dynamic Task Allocation For A Swarm Of Homogeneous Robots, Maha Alshawi

Theses and Dissertations

The current trends in the robotics field have led to the development of large-scale swarm robot systems, which are deployed for complex missions. The robots in these systems must communicate and interact with each other and with their environment for complex task processing. A major problem for this trend is the poor task planning mechanism, which includes both task decomposition and task allocation. Task allocation means to distribute and schedule a set of tasks to be accomplished by a group of robots to minimize the cost while satisfying operational constraints. Task allocation mechanism must be run by each robot, which …

Hydrogen Sulfide Regulation Of Kir Channels, Junghoon Ha

Theses and Dissertations

Inwardly rectifying potassium (Kir) channels establish and regulate the resting membrane potential of excitable cells in the heart, brain and other peripheral tissues. Phosphatidylinositol- 4,5-bisphosphate (PIP2) is a key direct activator of ion channels, including Kir channels. Gasotransmitters, such as carbon monoxide (CO), have been reported to regulate the activity of Kir channels by altering channel-PIP2 interactions. We tested, in a model system, the effects and mechanism of action of another important gasotransmitter, hydrogen sulfide (H2S) thought to play a key role in cellular responses under ischemic conditions. Direct administration of sodium hydrogen sulfide (NaHS), as an exogenous H2S source, …

A Roadmap For Development Of Novel Antipsychotic Agents Based On A Risperidone Scaffold, Urjita H. Shah

Theses and Dissertations

Schizophrenia is a chronic psychotic illness affecting ~21 million people globally. Currently available antipsychotic agents act through a dopamine D₂ receptor mechanism, and produce extrapyramidal or metabolic side effects. Hence, there is a need for novel targets and agents. The mGlu₂/5-HT_2A receptor heteromer has been implicated in the action of antipsychotic agents, and represents a novel and attractive therapeutic target for the treatment of schizophrenia. A long-term goal of this project is to synthesize bivalent ligands where a 5-HT_2A receptor antagonist is tethered to an mGlu₂ PAM via a linker.

The goals of the …

Improving Peptide Identification By Considering Ordered Amino Acid Usage, Ahmed Al-Qurri

Theses and Dissertations

Proteomics has made major progress in recent years after the sequencing of the genomes of a substantial number of organisms. A typical method for identifying peptides uses a database of peptides identified using tandem mass spectrometry (MS/MS). The profile of accurate mass and elution time (AMT) for peptides that need to be identified will be compared with this database. Restricting the search to those peptides detectable by MS will reduce processing time and more importantly increase accuracy. In addition, there are significant impacts for clinical studies. Proteotypic peptides are those peptides in a protein sequence that are most likely to …

Investigate Genomic 3d Structure Using Deep Neural Network, Yan Zhang

Theses and Dissertations

The 3D structures of the chromosomes play fundamental roles in essential cellular functions, e.g., gene regulation, gene expression, evolution and Hi-C technique provides the interaction density between loci on chromosomes. In this dissertation, we developed multiple algorithms, focusing the deep learning approach, to study the Hi-C datasets and the genomic 3D structures.

Building 3D structure of the genome one of the most critical purpose of the Hi-C technique. Recently, several approaches have been developed to reconstruct the 3D model of the chromosomes from HiC data. However, all of the methods are based on a particular mathematical model and lack of …

Developing The Three Dimensional Tumor Model For Melanoma Drug Screening, Guochang Ye

Theses and Dissertations

Two-dimensional (2D) Tissue Culture Treated Plastic (TCTP) is widely used for cancer drug screening and has dominated the field for a long time. Compared with traditional two dimensional cell culture, a three dimensional tumor model may able to provide more reliable experimental results related to drug screening and discovery. With the development of nanoparticle chemotherapies, there is a need for ways to better investigate and characterize the effect of the 3D tumor environment. Cerium oxide nanoparticles, Nanoceria, is one of the potential solutions being explored for treating melanoma in the future in combination with conventional chemotherapies. This is attributed to …

Structural And Dynamic Analysis Of Wild And Splice Variants Human Μ-Opiod Receptors In Complex With Morphine And Ibntxa And Human Topoisomerase Ii Alpha Mutational Basis Of Amsacrine Resistance, Safaa Sader

Theses and Dissertations

Morphine prescribing is limited by its high addiction tendency and other serious effects. Recent animal’s biological studies on Mu 6TM splice variants, which mainly include G1, G2 and Mu3, supported a high safety and potency profiles of IBNtxA as potential alternative of Morphine. Nevertheless, there is no high-resolution structures of these 6TM variants, and the detailed structural features and dynamic characteristics of these splice variants remain elusive. We applied homology modeling and MD simulation to probe the structural, dynamic and ligand binding differences between the wild type (7TM) and two major truncated 6TM variants (G1 and G2). MD results underscored …

Lebanon's Shouf Biosphere Reserve: A Protected Area And Sport Hunting, Robert Watkins Bowdoin Greeley

Theses and Dissertations

Fortress conservation, the act of setting aside for conservation goals and protecting them through sanction, coercion, and violence, towards local users has became the paradigmatic understanding of how protected areas are created and maintained. The fortress conservation critique is marked by a preoccupation with the negative livelihood impacts of these areas, portrays animosity and social conflict between local users and the protected areas, is primarily concerned with national parks and clearly defined protected areas, and places state power at the center of the creation and maintenance of protected areas. This dissertation takes the tenants of fortress conservation to task by …

Integration Of Multispectral Camera Systems For Enhanced Visualization Biological Studies Using Uas, Subin Shahukhal

Theses and Dissertations

The purpose of this research is to enhance visualization of warm-blooded animals and analyze the vegetation in which they are located using a camera system mounted on Unmanned Aircraft System (UAS). The results are coherently displayed in a single image at the same spatial location so that biologists will have accurate animal counts along with vegetation conditions. Application of aerial imagery has been used to analyze the vegetation health and determining the number of the animals by the wildlife service. However, a major obstacle of the research is to combine the two imaging systems to obtain the same spatial image …

Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions, J. Harry Caufield

Theses and Dissertations

The emergence of genomics as a discrete field of biology has changed humanity’s understanding of our relationship with bacteria. Sequencing the genome of each newly-discovered bacterial species can reveal novel gene sequences, though the genome may contain genes coding for hundreds or thousands of proteins of unknown function (PUFs). In some cases, these coding sequences appear to be conserved across nearly all bacteria. Exploring the functional roles of these cases ideally requires an integrative, cross-species approach involving not only gene sequences but knowledge of interactions among their products. Protein interactions, studied at genome scale, extend genomics into the field of …

Curcumin/Melatonin Hybrids As Neuroprotective Agents For Alzheimer's Disease, John Saathoff

Theses and Dissertations

Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the leading cause of dementia, affecting ~5.2 million Americans. Current FDA approved medications provide mainly symptomatic relief and there are no agents available to delay or cure this disease. Multiple factors such as amyloid-β aggregates, dyshomeostasis of biometals, oxidative stress, and neuroinflammation have been implicated in the development of AD. Even though significant advances have been made in understanding the mechanisms leading to AD, the exact etiology still remains elusive. Given AD’s multifactorial nature, a multifunctional strategy of small molecule design would help to identify novel chemical templates. Recently our lab …

Momentum Clinic For Teen And Young Adult Cancer Patients, Merian O'Neil

Theses and Dissertations

This study explores the needs of teen and young adult cancer patients undergoing long-term chemotherapy treatments and the design of an outpatient clinic that accommodates this population’s unique needs. Most teens endure long-term treatments in a pediatric facility targeted primarily for children, while others are treated in adult facilities. Teens have different privacy and social needs than children, and while they are not adults, they are involved in their own treatment decisions, unlike children. The target age group for this study is teens and young adults, ages thirteen to twenty-two. A common theme emerged from research and interviews conducted in …

A Study Of The Action Of Risperidone At 5-Ht2a Receptors, Supriya A. Gaitonde

Theses and Dissertations

Risperidone is an ‘atypical’ antipsychotic and is approved by the USFDA mainly for the treatment of schizophrenia and symptoms of bipolar disorder. Risperidone (an SDA or serotonin-dopamine antagonist) has ~20-fold higher affinity at 5-HT_2A receptors over dopamine D₂ receptors, which makes it more efficacious against the negative symptoms of schizophrenia and less liable to causing extrapyramidal side effects than ‘typical’ antipsychotics.

The major goal of the current investigation was to study the structure of risperidone and to identify the minimum structural features required for 5-HT_2A receptor affinity that retain antagonist action. The structure of risperidone was systematically …