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Investigating And Expanding The Functionality Of Rna Catalysts: Studies Of The Hepatitis Delta Virus, The Hammerhead, And The Aminoacyl-Trna Synthetase-Like Ribozymes, Ji Chen

Open Access Dissertations

Ribozymes, just like protein enzymes, catalyze diverse chemical reactions. The first goal of this dissertation is to understand the mechanism of ribozyme-mediated phosphodiester cleavage reaction. Biochemical assays and X-ray crystallography were used for probing the active site of two small self-cleaving ribozymes, the hepatitis delta virus (HDV) ribozyme and the hammerhead ribozyme. Results presented here suggest that divalent metal ions play critical roles in the catalytic mechanisms of both the HDV and the hammerhead ribozymes. In the HDV ribozyme, the result is consistent with an active site Mg2+ being directly involved in catalysis. In the hammerhead ribozyme, however, Mg2+ ions …

A New Reality: Funding Formula Changes And Property Tax Caps And Their Effects On The Role Of The School Superintendent In The State Of Indiana, Patrick L. Gentry

Open Access Dissertations

The purpose of this qualitative study was to discover how school superintendents were using general fund referenda to meet their school district’s operational budgets. However, after interviews began it became clear that the superintendents wanted to tell a different story and that was how the current school funding mechanism and property tax caps has changed the job of the school superintendent. The research consisted of one-on-one guided interviews of a mixed qualitative methods framework combining theories of hermeneutics and phenomenology. The interviews combined open-ended, guided questions and conversations and were with superintendents who were leaders of school districts that have …

Onsite Wastewarer Treatment Systems In A Changing Climate: Technology Robustness And Mechanisms, Jennifer Anne Cooper

Open Access Dissertations

Nearly 25% of U.S. households rely on onsite wastewater treatment system (OWTS), or septic systems, to renovate wastewater before it is recharged to groundwater. These systems rely on soil processes as the final step in contaminant removal. Reliance on soil microbial, physical and chemical processes, which are sensitive to environmental perturbations (e.g. changes in pH, temperature, moisture, O₂, presence of toxins), may result in variable wastewater treatment and release of contaminants to groundwater.

The extent of treatment in the soil treatment area (STA; also known as drainfield or leachfield) depends on the volume of unsaturated soil the wastewater …

Oxidative State Of Songbirds During Migration And Best Practices To Communicate The Science, Megan M. Skrip

Open Access Dissertations

Managing oxidative stress is an important physiological function for all aerobic organisms, particularly during periods of prolonged high metabolic activity, such as long-distance migration. However, no previous study has investigated the oxidative status of songbirds at different stages of migration, whether that oxidative status depends on the condition of the birds, how birds use their condition in concert with access to free water to make stopover decisions, or the effects of oxidative challenges like flight on subsequent reproduction. Additionally, scientists undertaking such research are commonly expected to disseminate their results as a Broader Impact of their studies - typically to …

A Study Of The Regulatory And Environmental Factors Affecting Trimethylamine Oxide Accumulation In Marine Organisms, Abigail Brittany Bockus

Open Access Dissertations

Trimethylamine oxide (TMAO) was first described in marine organisms as an osmolyte, involved in the balance of water and solutes. After its discovery, it was found to be part of a subset of osmotic constituents termed counteracting solutes. These solutes exhibit stabilizing properties and can preserve protein functionality against biological and environmental perturbations. TMAO acts as a universal stabilizer, protecting macromolecular structure and function in response to numerous stressors, including urea destabilization, hydrostatic pressure, temperature and salinity. The studies presented in this dissertation address the regulatory and environmental factors affecting TMAO accumulation.

Both exogenous and endogenous sources are involved in …

Development And Validation Of Immunoinformatics Tools For Swine Vaccine Development, Andres H. Guiérrez Núñez

Open Access Dissertations

Immunoinformatics tools have multiple applications in human immunology research. One of their most prominent applications is the prediction of T cell epitopes to accelerate vaccine development. T cell epitopes are short peptides derived from pathogens that are recognized by the cells of the immune system (T cells) when presented on the surface of cells bound to a major histocompatibility complex (MHC) molecule, which results in a specific immune response. For their role as key drivers of the immune response, numerous algorithms have been developed to predict binding of peptides to MHC molecules; however, comparable tools are limited for other species. …

Agonistic Behavior And Costs Of Aggression In Decapod Crustaceans, Niels-Viggo Schou Hobbs

Open Access Dissertations

Animals that engage in aggressive behavior necessarily incur some costs (e.g., energy expenditure) and risk much greater costs (e.g., injury), both of which are presumably weighed against the potential benefits (e.g., refuge, food, or mates). Such costs and benefits directly impact their distribution, life history, and fitness, so an understanding of the role aggression plays is crucial to a complete understanding of a species’ ecological niche. The research presented here evaluates the degree to which aggression has ecological and life history consequences, using several species of co-occurring crabs as models in a combination of laboratory and field experiments. Specifically, we …

Effects Of Hiv Behavioral Interventions For Men Who Have Sex With Men - United States, 1988-2014, H. Elsa Larson

Open Access Dissertations

Men who have sex with men (MSM) in the United States continue to experience disproportionate HIV disease burden. Historically, most HIV prevention research has focused on reducing sexual risk behaviors through individual-level behavior change interventions. To date, behavioral interventions have not reduced HIV incidence among MSM and combination prevention approaches that package behavioral interventions with additive biomedical or structural interventions are now recommended. The last meta-analysis of HIV behavioral interventions for MSM was conducted in 2008. Since then sixteen new rigorous trials have been identified. New evidence and new recommendations justify an updated meta-analysis to identify the most promising and …

Research Into Computer Hardware Acceleration Of Data Reduction And Svms, Jason Kane

Open Access Dissertations

Yearly increases in computer performance have diminished as of late, mostly due to the inability of transistors, the building blocks of computers, to deliver the same rate of performance seen in the 1980’s and 90’s. Shifting away from traditional CPU design, accelerator architectures have been shown to offer a potentially untapped solution. These architectures implement unique, custom hardware to increase the speed of certain tasking, such as graphics processing. The studies undertaken for this dissertation examine the ability of unique accelerator hardware to provide improved power and speed performance over traditional means, with an emphasis on classification tasking.

In the …

The Gas-Phase Oxidation Of Cationic Bioanalytes Via Ion/Ion Reactions, Alice Lindsay Pilo

Open Access Dissertations

Several solution-phase derivatizations have recently been implemented in the gas-phase through the interaction between oppositely charged ions, viz., ion/ion reactions. The work presented here primarily focuses on the oxidation of bioanalytes via ion/ion reactions with periodate and persulfate anions. Methionine and tryptophan residues in simple polypeptides are selectively oxidized upon ion/ion reactions with periodate anion. The oxidative labeling of disulfide bonds is performed via ion/ion reactions and is used to identify intermolecularly disulfide-linked peptides and further probe their primary structure. Non-modified, non-disulfide linked peptides lacking easily oxidized residues (i.e., methionine and tryptophan) can also undergo oxidation. Peptides containing neutral basic …

Discovery And Functional Analyses Of Hessian Fly Effector-Encoding Genes, Lucio Navarro Escalante

Open Access Dissertations

The Hessian fly - wheat system is a well-known model of gene-for-gene interac- tion between host plants and parasitic insects. The Hessian fly uses secreted effector proteins to control susceptible host plant physiology, transforming the plant cells in a nutritive tissue to support the developing insect larva. HF-resistant wheat cultivars employ resistance (R) proteins to perceive the insect avirulence effectors (Avr) and display defensive immune responses. This study is focused in the discovery and functional analyses of insect effector-encoding genes. Chapter one of this thesis offers an introduction about the molecular basis of HF-wheat interactions. In Chapter two, I present …

The Impact Of The Foot And Mouth Disease Control Pathway On Milk Production In India, Benjamin Allen

Open Access Dissertations

India has decided to invest in eradicating foot and mouth disease (FMD). If

Role Of Deltac And Deltad In Zebrafish Retinal Development, Sylvia Imelda Bonilla

Open Access Dissertations

Classical studies have shown that Notch-Delta signaling is essential for the maintenance of retinal progenitor cells. However, the specific roles of different Delta ligands on retinal development are not well characterized. The focus of this study was to investigate the specific functions of the Delta ligands, deltaC (Dlc) and deltaD (Dld), in zebrafish retinal development by using dlcb663 and dldtg249 mutant embryos. The retinal expression pattern of dlc and dld, determined by whole-mount in situ hybridization, demonstrated that both ligands have similar and distinct expression patterns in WT retinas throughout retinal development. In mutant retinas where dlc and dld are …

The Role Of Plk1 In Hepatitis B Virus (Hbv) Infection Of The Liver, Ahmed Mohamed Abdel-B Diab

Open Access Dissertations

With 250 million reported chronic infections globally, Hepatitis B Virus (HBV) is a major human health issue, linked to increased risk for development of hepatocellular carcinoma (HCC). Current treatments to control chronic HBV infection remain ineffective. New and effective therapies that target the persisting viral molecules are needed in order to clear infection. My research aims to understand the role of hepatitis B virus (HBV) in inducing HCC and identify novel host molecules that are targeted by HBV. Understanding how HBV modifies and manipulates host cellular pathways is critical for the development of mechanism based therapeutics. Here, I provide a …

The Role Of Individual Variation In Auditory And Visual Processing: Implications For Mate Choice, Kelly Ronald

Open Access Dissertations

Intersexual interactions often include a dynamic exchange of courtship signals in different sensory modalities. My work focuses on understanding the factors that contribute to variation in male sexual signals and variation in female sensory perception and behavioral responses to these signals. I addressed several specific research questions using the brown headed cowbird (Molothrus ater) as a model species: (i) how does male signaling behavior differ with the sex of the receiver? (ii) how do components within a signal combine to generate a response by the female, (iii) how is female sensory capacity in one modality related to her sensory capacity …

Macronutrient-Flavonoid Interactions, Effects In Model Food Matrices, Jennifer Louise Allen

Open Access Dissertations

Macronutrient-flavonoid interactions have been well documented through the years. Chapter 1 of this document provides an introduction of the literature documenting the theoretical and mechanical framework of their importance in human health, biological interactions, macronutrient interaction, and general bioaccessibility and bioavailability. Though macronutrient interactions have been characterized, often the levels utilized are above those that may be seen in processed food products due to undesirable effects. This document covers the effects two commonly used plant extracts, green tea extract and grape seed, may have on the macronutrient functionality in model food matrices. In Chapter 2 the effects of crude extracts …

Understanding, Evaluating, And Diagnosing Undergraduate Student Difficulties With Graph Choice And Construction, Aakanksha Angra

Open Access Dissertations

Creating effective graphical representations of biological data is an essential component in the practices of science and involves engaging concepts and skills of quantitative literacy. With undergraduate biology students increasingly involved in scientific inquiry and experimentation, they are faced with the task of choosing and creating appropriate graphical representations of their data to communicate their findings. However, difficulties with graph choice and construction that were previously documented in literature, still exist today at both the K-12 and undergraduate levels. The purpose of this dissertation is to understand the reasoning involved behind choosing certain graph types and the process that occurs …

Dissecting The Multifaceted Relationship Between Maize And Cochliobolus Carbonum Race 1, Kevin Chu

Open Access Dissertations

The maize pathogen Cochliobolus carbonum race 1 (CCR1) utilizes HC-toxin, an inhibitor of histone deacetylases, as a key determinant of virulence. The maize Hm1 gene confers complete resistance to CCR1 at all stages of development by encoding for an NADPH-dependent reductase that inactivates HC-toxin. Hm1A, Hm1-SM1, and Hm1-SM2 are alleles of Hm1 that exhibit an adult plant resistance (APR) phenotype, being fairly susceptible during the seedling stage and gradually increasing in resistance with development. The HM1A protein differs from HM1 by five amino acid substitutions while HM1-SM1 and HM1-SM2 have a single amino acid substitution each in the predicted NADPH …

The Influence Of Carrier Water Quality, Coapplied Foliar Fertilizer, And Water Conditioning Adjuvant On Herbicide Efficacy, Pratap Devkota

Open Access Dissertations

Water is the primary carrier for herbicide applications; therefore, carrier water quality factors such as pH, hardness, temperature, or turbidity could be critical for influencing herbicide performance. Currently, there is no information on the effect of carrier water temperature on herbicides applied for weed control in agronomic crops. In previous research, carrier water pH or hardness was found to influence herbicide efficacy; however, the results were variable depending upon herbicides and weed species. The antagonism of coapplied agrochemicals on glyphosate efficacy were reported by previous researchers. In contrary, the enhancement of glyphosate efficacy was illustrated by water conditioning adjuvants such …

Laser Shock Imprinting Of Metallic Nanostructures And Shock Processing Of Low-Dimensional Materials, Yaowu Hu

Open Access Dissertations

Laser shock imprinting (LSI) is proposed and developed as a novel ultrafast room-temperature top-down technique for fabricating and tuning of plasmonic nanostructures, and processing of one-dimensional semiconductor nanowires and two-dimensional crystals. The technique utilizes a shock pressure generated by laser ablation of sacrificial materials. Compared with conventional technologies, LSI features ambient condition, good scalability, low cost and high efficiency.

Chd Chromatin Remodelers Promote Epigenetic Control Of Development In Arabidopsis Thaliana, Benjamin Carter

Open Access Dissertations

Chromatin remodeling is a vital biological process that facilitates activation and repression of gene expression as well as compaction of large eukaryotic genomes into compact nuclei. The CHD3 family of chromatin remodelers play key roles as epigenetic modifiers and transcriptional regulators in both plants and animals. PKL is a CHD3 remodeler that represses expression of seed genes during germination in Arabidopsis. Unlike animal CHD3 remodelers, PKL does not function as a member of a multi-subunit Mi-2 NuRD complex. Instead, PKL acts as a monomer in vivo and promotes the epigenetic modification H3K27me3, which is associated with transcriptional repression of tissue-specific …

The Influence Of Chirality On The Behavioral Responses Of Longhorned Beetles (Coleoptera: Cerambycidae) To Volatile And Contact Pheromones, Gabriel Patrick Hughes

Open Access Dissertations

In this dissertation, I present research I conducted to test the hypothesis that chirality influences the behavioral resposnses of longhorned beetles to volatile and contact pheromones. Structures of pheromones in the longhorned beetles generally fall along taxonomic lines, and various structural modifications such as functional groups and stereochemistry are used to grant species spcecificity to these signals. Effects of chirality on the bioactivity of volatile pheromones has been documented in the longhorned beetle subfamily Cerambycinae, but little is known about how stereochemistry affects behavioral responses of conspecifics to contact pheromones in this subfamily, and volatile pheromones in the Lamiinae.

Designer Collagen-Fibril Biograft Materials For Tunable Molecular Delivery, Rucha Joshi

Open Access Dissertations

One of the biggest challenges in tissue engineering currently is the formation of a functional microvascular network as part of an engineered tissue graft. Despite many advances in tissue engineering methods, the field still awaits biograft designs that enable neovascularization at clinically relevant size scales. Critical to the design of such materials are tissue-specific physico-mechanical properties and controlled local therapeutic molecular release.

Protein Function, Diveristy And Functional Interplay, Ishita Kamal Khan

Open Access Dissertations

Functional annotations of novel or unknown proteins is one of the central problems in post-genomics bioinformatics research. With the vast expansion of genomic and proteomic data and technologies over the last decade, development of automated function prediction (AFP) methods for large-scale identification of protein function has be-come imperative in many aspects. In this research, we address two important divergences from the “one protein – one function” concept on which all existing AFP methods are developed:

Relationships Between Dietary Fiber Structural Features And Growth And Utilization Patterns Of Human Gut Bacteria, Xin Nie

Open Access Dissertations

Intake of dietary fiber is considered an essential strategy to influence gut microbiota, which is associated with many diet-related chronic diseases such as obesity, diabetes, and inflammatory bowel diseases. In order to make a better choice of dietary fiber for a desired microbiota shift related to a health outcome, knowledge of fiber degradation and utilization by gut bacteria is critical. However, it is still unclear how specific dietary fiber structures may influence the growth of target bacteria.

Underwater Bonding With Polymer Mimics Of Mussel Adhesive Proteins, Michael A. North

Open Access Dissertations

When it comes to underwater adhesion, shellfish are the true experts. Mussels, barnacles, and oysters attach to rocks with apparent ease. Yet our man-made glues often fail miserably when trying to stick in wet environments. Results described herein focus on poly[(3,4-dihydroxystyrene)-co-styrene], a polymer mimic of mussel adhesive proteins. Underwater bonding was examined as a function of several parameters including polymer molecular weight and composition. In doing so, several surprising results emerged. Poly[(3,4-dihydroxystyrene)-co-styrene] may be the strongest underwater adhesive found to date. Bonding even exceeded that of the reference biological system, live mussels. Adhesion was also found to be stronger under …

Towards Single-Chip Nano-Systems, Hossein Pajouhi

Open Access Dissertations

Important scientific discoveries are being propelled by the advent of nano-scale sensors that capture weak signals from their environment and pass them to complex instrumentation interface circuits for signal detection and processing. The highlight of this research is to investigate fabrication technologies to integrate such precision equipment with nano-sensors on a single complementary metal oxide semiconductor (CMOS) chip. In this context, several demonstration vehicles are proposed. First, an integration technology suitable for a fully integrated flexible microelectrode array has been proposed. A microelectrode array containing a single temperature sensor has been characterized and the versatility under dry/wet, and relaxed/strained conditions …

Regulation Of T Cells And Tissue Inflammation By Short Chain Fatty Acids, Jeong Ho Park

Open Access Dissertations

Intestinal microbiota regulate various biological processes in the host. Intestinal microbiota produce short chain fatty acids (SCFAs) via dietary fiber fermentation. SCFAs have profound effects on the immune system. We investigated the roles of SCFAs in regulating T cell differentiation and tissue inflammation. We found that SCFAs regulate T cell differentiation and T cell-mediated immunity. SCFAs enhanced both IL-10+ T cell and Th1/Th17 effector T cell differentiation. SCFAs inhibited histone deacetylase (HDAC) activity and upregulated acetylation of p70 S6 kinase and mTOR activation in T cells. We also found that prolonged exposure to high concentration of SCFA cause ureteral obstruction …

The Interpersonal Psychological Theory Of Suicide: Suicidal Ideation And Behaviors Of Lesbian, Gay, And Bisexual College Students And Their Heterosexual Peers, Rachel Ann Ploskonka

Open Access Dissertations

Lesbian, gay, and bisexual (LGB) college students are among the most vulnerable to suicidal ideation and behaviors when compared to both heterosexual college students and other, generally older, members of the LGB community (Oswalt & Wyatt, 2011). Joiner’s (2005) interpersonal psychological theory of suicide seems to be a possible framework for conceptualizing suicidal ideation and behaviors for LGB college students. Joiner (2005) posited that perceived burdensomeness and thwarted belongingness are associated with suicidal ideation and that acquired capability is related to suicidal behaviors. With respect to thwarted belongingness, researchers have posited that LGB college students have four primary interpersonal connections, …

An Ecology Of Place In Composition Studies, Jonathan Scott Wallin

Open Access Dissertations

Wallin, Jonathan Scott, Ph.D, Purdue University, December 2016. An Ecology of Place in Composition Studies. Major Professor: Patricia Sullivan.