Life Sciences Commons^™

Structural And Functional Characterization Of The Endosome-Associated Deubiquitinating Enzyme Amsh, Christopher Williamson Davies

Open Access Dissertations

The endosomal sorting complexes required for transport (ESCRT) machinery is a ubiquitin-dependent molecular mechanism made of up of four individual complexes: ESCRT-0, -I, -II, III, that is necessary for regulating the degradation of cell surface receptors directed towards the lysosome. Not only are the ESCRTs implicated in endosomal sorting and trafficking of proteins, its members also have roles in other important biological processes such as: cytokinesis, HIV budding, transcriptional regulation, and autophagy. As a function of its involvement in several processes throughout the cell, the ESCRT machinery is implicated in a wide variety of diseases including cancer, neurological disease, bacterial …

Smooth Muscle-Specific Removal Of Brain-Derived Neurotrophic Factor Results In Increased Vagal Afferent Innervation To The Intestine And Increased Satiation In Mice, Jessica Erin Biddinger

Open Access Dissertations

Vagal afferents transmit signals regarding food-derived stimuli in the gastrointestinal (GI) tract to the brain. Vagal mechanoreceptors called intraganglionic laminar endings (IGLEs) innervate the smooth muscle wall of GI organs and detect stretch and tension to regulate GI reflexes and satiation. Brain-derived neurotrophic factor (BDNF) is expressed in the smooth muscle of developing GI organs when vagal afferents from the nodose ganglion begin to innervate the GI tract. Therefore, it was hypothesized BDNF is necessary for development of vagal afferents that innervate this tissue. Targeted smooth muscle-specific BDNF homozygous knockout (BDNF SM -/-) mice were generated and .vagal afferent innervation …

Environmental Tradeoffs In Bioenergy Production And Agricultural Practices, Alicia Lynn English

Open Access Dissertations

The focus of this dissertation is the environmental tradeoffs of stover removal within the Corn Belt. The environmental tradeoffs considered are mainly concerned with managing soil erosion and soil quality. The analysis layers soil characteristics, management strategies and per acre costs using an integrated RUSLE2/WEPS model and an economic optimization model to illuminate a lower bound supply response. Different assumptions were tested in regards to sustainability, prices, and market integration for five states and 18,760 soil types throughout the Corn Belt. Sustainability was defined to limit soil erosion from wind and water to 5 tons/acre/year and the soil organic matter …

Effects Of Hearing Aid Amplification On Robust Neural Coding Of Speech, Jonathan Daniel Boley

Open Access Dissertations

Hearing aids are able to restore some hearing abilities for people with auditory impairments, but background noise remains a significant problem. Unfortunately, we know very little about how speech is encoded in the auditory system, particularly in impaired systems with prosthetic amplifiers. There is growing evidence that relative timing in the neural signals (known as spatiotemporal coding) is important for speech perception, but there is little research that relates spatiotemporal coding and hearing aid amplification.

This research uses a combination of computational modeling and physiological experiments to characterize how hearing aids affect vowel coding in noise at the level of …

Brain Bioavailability Of Polyphenols: Implications For Delivery Of Brain Health Benefits, Tzu-Ying Chen

Open Access Dissertations

Consumption of fruits and vegetables has been associated with neuroprotection and cognitive benefits throughout the life span. These associations have sparked interest in plant-derived polyphenols as biologically active agents with potential for targeting brain benefits. However, little is known regarding the ability of the polyphenols or their metabolites from polyphenol-rich products to cross the blood-brain-barrier, and be available for biological action. Furthermore, additional insight is needed on factors affecting the absorption and brain distribution of polyphenol metabolites in vivo. To fill gap in current knowledge, this thesis will focus on the effects of diabetogenic diet and diabetic state which have …

Reasoning Across Language And Vision In Machines And Humans, Andrei Barbu

Open Access Dissertations

Humans not only outperform AI and computer-vision systems, but use an unknown computational mechanism to perform tasks for which no suitable approaches exist. I present work investigating both novel tasks and how humans approach them in the context of computer vision and linguistics. I demonstrate a system which, like children, acquires high-level linguistic knowledge about the world. Robots learn to play physically-instantiated board games and use that knowledge to engage in physical play. To further integrate language and vision I develop an approach which produces rich sentential descriptions of events depicted in videos. I then show how to simultaneously detect …

Characterization Of The Specificity And Functions Of The Protein Phosphatase Cdc14, Christie Eissler

Open Access Dissertations

Protein phosphorylation is perhaps the most ubiquitous posttranslational modification in eukaryotes and recent studies suggest that upwards of 75% of human proteins are phosphorylated. Many proteins are phosphorylated at multiple sites, often controlled by multiple kinases and phosphatases. Multisite phosphorylation can differentially affect the functional and regulatory cellular outcomes. For example, dephosphorylation of a protein at a particular site may inhibit nuclear localization of a protein while dephosphorylation of a different site may be necessary for enzymatic activation of a protein. Thus, multisite protein phosphorylation can complicate our understanding of the biological significance and the functional consequences of protein phosphorylation. …

Using X-Ray Imaging Techniques To Determine Density Of Foods, Shivangi Mohan Kelkar

Open Access Dissertations

Density depends on the experimental technique and structural properties of food. True, apparent and bulk are different types of densities. For porous foods such as baked food products and complex food systems, accurate measurement of density is challenging. Empirical correlations dependent on composition and temperature exist to calculate true density. Thus if composition and apparent density are known, porosity can be calculated, porosity = [1 - (apparent density/ true density)]. Various non-destructive diagnostic tools have been employed to study food microstructure. Among these, computed tomography (CT) and digital radiography (DR) utilizing x-ray imaging showed greater capability for evaluation of food …

Effects Of Dna Methylation Pattern On The Chromatin Structure, Isabel Cristina Jimenez Useche

Open Access Dissertations

DNA methylation plays an essential role in various biological processes such as stem cell differentiation, imprinting, X-chromosome inactivation, etc. Increased DNA methylation levels have been associated with chromatin compaction leading to gene silencing. For example, abnormal DNA methylation is associated with silencing of tumor suppressor genes and is observed in the onset of tumorigenesis. There is evidence suggesting that not all methylation events are relevant in chromatin compaction and the initiation of cancer. It seems that methylation at certain locations of the DNA might be key to start chromatin compaction and gene silencing, but the location of this methylation sites …

The Termite Digestome: Understanding The Digestive Physiology Involved In Lignocellulosic Biomass Degradation, Zachary John Karl

Open Access Dissertations

The purpose of this research was to advance the understanding of lower termite digestive physiology and discover potential biocatalysts that can aid in the degradation of lignocellulosic biomass. Various protein characterization and gene expression methods were used throughout this research in order to accomplish these objectives. The results of this dissertation indicate that: 1) termites and their symbionts act in a synergistic manner to degrade biomass in vitro, 2) the host fraction of the gut (i.e., foregut and midgut) is the likely site of glucose absorption, 3) the termite and its symbionts contribute specific enzymes to the digestive process, 4) …

The Role Of Resource Predictability In The Metapopulation Dynamics Of Insects, Byju Nambidiyattil Govindan

Open Access Dissertations

The metapopulation paradigm has emerged as an important tool to understand the dynamics of species living in fragmented landscapes. In this dissertation, I investigate the unpredictable nature of resource availability for species living in human-dominated heterogeneous and dynamic landscapes in the context of its consequences for long-term regional persistence of species. In particular, I test theoretical advancements in metapopulation ecology following a two-pronged approach - via experiments in the lab and observations in the field - using insects. In chapter 1, I introduce the concept of metapopulation ecology in the context of its relevance for dynamics of species living in …

Systems Evaluation Of Shallow Anhydrous Ammonia Placements, Rates, And Timing On Maize Plant Uniformity, Yield And N Use Efficiency, Péter Kovács

Open Access Dissertations

Farmers face increasing expectations from society to be more environmentally conscious and energy efficient with their fertilizer management practices during maize (Zea mays L.) production. With the advent of precision guidance systems, maize farmers in various tillage systems have more options in pre-plant nutrient banding relative to the intended crop rows or throughout the entire growing season. Field studies were conducted between 2010 and 2012 near West Lafayette, IN to identify best management practices to enhance maize plant uniformity, yield and nitrogen (N) efficiencies.

Anhydrous ammonia (NH₃) placement during pre-plant application is of interest because of concerns …

Influence Of Cholesterol And Bilayer Asymmetry On Membrane Protein Distribution In Polymer-Tethered Raft-Mimicking Lipid Membranes, Noor Fueza Hussain

Open Access Dissertations

It is now widely recognized that lipid rafts, which are membrane domains enriched in cholesterol (CHOL) and sphingolipids (SL), play a significant functional role in the plasma membrane. Raft domains particularly affect membrane functionality by causing sequestering of membrane proteins. Underlying mechanisms of raft-associated membrane protein sequestration remain elusive, due to the complexity, transient nature, and small size of raft domains in cellular membranes. To address these challenges, this dissertation unveils the relationship between lipid raft composition and membrane protein sequestration and function using raft-mimicking model membrane mixtures comprised of coexisting liquid-ordered (lo) and liquid-disordered (ld) domains with reconstituted membrane …

Long-Term Disturbance Histories Of Managed And Natural Mixed-Hardwood Forests Of Central Indiana, Robert Charles Morrissey

Open Access Dissertations

Over the course of the last century, we have observed changes in forest composition and structure related to changes in disturbance regimes. Reduced frequency and severity of disturbance events has allowed for the ingrowth of shade-tolerant, mesophytic species into forest understories; the result is shifting species compositions and changes in forest structure. In some cases, the loss of masting species, such as oak (Quercus spp.) and hickory (Carya spp.), may also accompany a shift in forest function and further accommodate other species shifts among mammal, insect, and bird populations. Management efforts have been suggested as a possible means …

The Genetic Architecture Of Juvenile Migration In Rainbow Trout (Oncorhynchus Mykiss), Benjamin Charles Hecht

Open Access Dissertations

Animal migrations play a critical role in the health and balance of ecological systems and in the evolution and diversification of species, and this is perhaps best displayed amongst salmonid fishes (salmon, trout, and char) who exhibit variation in the propensity to migrate both within and among species. Rainbow and steelhead trout (Oncorhynchus mykiss), members of the salmonid family of fishes, capture this variation throughout their native range. Some populations and ecotypes will remain resident in freshwater habitats throughout their life history; while others have the ability to embark on tremendous marine migrations. Those that migrate undergo a suite of …

Management Of Potato Leafhopper And Maple Spider Mite On Nursery Grown Maples, Julia Prado Beltran

Open Access Dissertations

Potato leafhopper Empoasca fabae (Harris) (Homoptera: Cicadellidae) and maple spider mite Oligonychus aceris (Shimer) (Acarina: Tetranychidae) are important pests of maple trees. Investigations determined how insecticide use and fertilization impacted the abundance of E. fabae and O. aceris on `Red Sunset' red maple and `Autumn Blaze' Freeman maples. Bifenthrin applications directed against leafhoppers reduced damage to both cultivars, but increased O. aceris on Autumn Blaze. Using a threshold of one leafhopper per branch to trigger pesticide applications protected Red Sunset maples from leafhopper injury. It also prevented outbreaks of O. aceris on Autumn Blaze because few trees reached this density. …

Natural Genetic Variation Affecting Calcium Homeostasis, Rebecca Anna Replogle

Open Access Dissertations

Calcium (Ca) is essential for multiple functions within the body including skeletal health. The level of Ca in the serum is tightly regulated. During periods of habitual low Ca intake, the body senses a decrease in serum Ca and increases renal conversion of 25 hydroxyvitamin D (25(OH)D) to 1,25 dihydroxyvitamin D (1,25(OH)2D). 1,25(OH)2D acts through the vitamin D receptor (VDR) to increase intestinal Ca absorption, renal Ca reabsorption and skeletal Ca resorption. Efficient intestinal Ca absorption, especially during periods of low Ca intake, is critical for protecting bone mass. Ca absorption and its primary regulator, 1,25(OH)2D, are affected by both …

The Chemistry Of Flavonoids In Model Beverages And Human Milk, Brian Jay Song

Open Access Dissertations

Interest in the chemistry and stability of flavonoids in foods has been generated by countless epidemiological, in vitro, and in vivo studies that suggest a variety of potential health promoting effects of diets rich in flavonoids. Flavonoids have been shown to interact with multiple components in beverages including macromolecules, minerals, certain vitamins, and other flavonoids. Furthermore, environmental conditions including light exposure, elevated temperatures, and relative humidity have been shown to modify flavonoid stability. However, specific mechanisms, relative kinetics of degradation reactions and the impact of macromolecules in model beverages and biological fluids on flavonoid stability remain largely unknown.

Recently, interest …

Design, Synthesis, And Evaluation Of Molecular Inhibitors For Biologically Relevant Enzymes, Sarah Emma St. John

Open Access Dissertations

The work in this thesis details the design, synthesis, and biological evaluation of molecular inhibitors for the inhibition of biologically relevant enzymes. The first three chapters of this thesis concern the polyphenol resveratrol and its inhibition of the quinone reductase 2 (QR2) enzyme. The work on this subject resulted in the complete design, synthesis, biological and structural evaluation of a second generation library of resveratrol analogues. From this work we identified a novel resveratrol analogue that inhibits QR2 in a previously unknown binding orientation. The fourth chapter of this thesis details the de novo design of molecules for the inhibition …

The Role Of Soil Microorganisms In The Resistance Of Giant Ragweed, Horseweed, And Common Lambsquarters To Glyphosate, Jessica Renee Schafer-Bugg

Open Access Dissertations

Continuous glyphosate use has contributed to an increasing number of problematic glyphosate-resistant (GR) weeds. The mechanism of resistance in many GR weeds is poorly understood, in part, due to a poor understanding of how exactly glyphosate kills a plant. In previous research, the efficacy of glyphosate was demonstrated to be strongly influenced by root invading soil-borne microorganisms. However, this interaction among plants, glyphosate, and soil microorganisms has only been studied in a number of crop plants, but not in weed species. This is surprising since the soil biotic environment has a strong impact on the activity of this important herbicide. …

Impacts And Feasibility Of The Us And The Eu Sustainability Criteria On Existing Land-Use Practices, Krissana Treesilvattanakul

Open Access Dissertations

Several studies have examined the land use and economic consequences of national and multi-national biofuel policies. They explored the impacts of biofuels mandates mainly based on the quantitative biofuel targets. However, the recently updated renewable policies of the United States and the European Union, which are the US Renewable Fuel Standard (RFS) and EU Directive 2009/28 of the Renewable Energy Directive (RED) both place restrictions on land that can be used to produce biofuel, and these restrictions are generally known as sustainability criteria. This research aims to determine to what extent sustainability criteria are actually binding; that is, would they …

Store-Operated Calcium Entry And Its Function During Fertilization In Porcine Eggs, Chunmin Wang

Open Access Dissertations

In a variety of mammalian cells, the depletion of intracellular Ca^{2+ stores leads to Ca2+ influx across the plasma membrane though a process known as store-operated Ca2+ entry. It not only plays a critical role in the replenishment of the Ca2+ stores but it is also responsible for the maintenance of long-lasting high intracellular Ca2+ levels and sustaining repetitive Ca2+ oscillations. During fertilization a Ca2+ signal, which can take the form of a single or multiple Ca2+ elevations (depending on the species) is the universal trigger for the egg-to-embryo transition. For sustaining …}

Genetic Engineering Of Black Cherry (Prunus Serotina) For Reproductive Sterility And Insect Pest Resistance, Ying Wang

Open Access Dissertations

Black cherry (Prunus serotina Ehrh.) is one of the most valuable hardwoods for high- end cabinetry, furniture, architectural millwork, paneling, and veneer. However, the damage caused by cambial-mining insect pests triggers gummosis in black cherry, a non-specific defense response in which resinous gum is deposited at the site of injury. The gum defects dramatically decrease the yield of high-quality black cherry lumber, and the value can be reduced by as much as 90%. The goal of this project was to optimize the transformation and in vitro rooting system, and to develop transgenic black cherry for reproductive sterility and insect pest …

Gas-Phase Covalent And Non-Covalent Ion/Ion Chemistry Of Biological Macromolecules, John Robert Stutzman

Open Access Dissertations

Gas-phase ion/ion chemistry involves the interaction of oppositely charged ions inside of the mass spectrometer. During this gas-phase chemistry, particle transfer (i.e., proton and electron) or synthesis can occur at rapid reaction rates. Particle transfer represents a mature area of ion/ion chemistry, while selective covalent modification represents a fairly new area of gas-phase chemistry. Gas-phase covalent chemistry is based on traditional solution phase organic chemistry.

The work demonstrated in this dissertation greatly involves gas-phase covalent and non-covalent Schiff base chemistry on peptide and protein ions. The reagent dianion, 4-formyl 1,3-benzene disulfonic acid, has been used to covalently modify unprotonated primary …

Measuring And Modeling The Response Characteristics Of The Environmental Phosphate Transducer In Escherichia Coli, Chetan Sood

Open Access Dissertations

The PhoR/PhoB two-component system in Escherichia coli is a biological transducer that senses the limitation of environmental inorganic orthophosphate, the bacteria's preferred source of the essential nutrient phosphate, and transmits that information to the interior of the cell initiating a response that mitigates phosphate starvation. In the first part of this study, we present and apply a fluorescence microscopy technique to measure, in vivo, the dynamic response characteristics of the transducer with single-cell resolution. We report that the transience in the PhoR/PhoB TCS response is consistent with the transducer having a threshold sensitivity to the concentration of environmental phosphate, …

Estimation Of Variation For High-Throughput Molecular Biological Experiments With Small Sample Size, Danni Yu

Open Access Dissertations

Motivation: In the quantification of molecular components, a large variation can affect and even potentially mislead the biological conclusions. Meanwhile, the high-throughput experiments often involve a small number of samples due to the limitation of cost and time. In such cases, the stochastic information may dominate the outcome of an experiment because there may not be enough samples to present the true biological information. It is challenging to distinguish the changes in phenotype from the stochastic variation.

Methods: Since the biological molecules have been quantified with different technologies, different statistical methods are required. Focusing on three types of important high-throughput …

Genes With Physiological Roles In Callipyge Muscle Hypertrophy, Hui Yu

Open Access Dissertations

Callipyge sheep is an excellent model to study genes regulation in muscle growth since the up-regulation of DLK1 and/or RTL1 results in extreme postnatal muscle hypertrophy in loin and hindquarters. DLK1 and/or RTL1 are the primary inducers of muscle hypertrophy due to the inheritance model for the callipyge phenotype. The overall aim of this dissertation is to study the physiological pathways responding to the up-regulation of DLK1 and / or RTL1 in the hypertrophied muscles. Microarray analysis of gene expression identified 375 genes that were differentially expressed in callipyge semimembranosus. Twenty-five transcripts were further verified by quantitative PCR in two …

Functional Characterization Of Metallothioneins In Arabidopsis And Barley, Nimnara Yookongkaew

Open Access Dissertations

Metalothioneins (MTs) are metal binding proteins that can bind metals such as Cu, Zn, and Cd but the functions of MTs in plants are largely unknown. To understand the function of MTs in Arabidopsis, T-DNA insertion mutants lacking 4 MT genes including MT1a, MT2a, MT2b and MT3 were developed. The quadruple mutant (mt1a/mt2a/mt2b/mt3) showed no visible phenotype under standard growth conditions. However, it accumulated higher Cu in leaves compared to wild type but lower Cu in seeds. Further analysis showed that triple mutants lacking both MT1a and MT2b, which are highly expressed in vascular tissues, had similar …

The City In Mind: Environmental Literacy And Adaptation In Nineteenth-Century British Literature, Adam Edward Watkins

Open Access Dissertations

This dissertation argues that a new paradigm of selfhood emerged in nineteenth-century British literature, one that recognized the individual will and environmental influence not as antithetical but as dialectical forces in the formation of the self. The concept of an externally negotiated subject challenges both the inward and socially determined conceptions of self that have dominated the relevant criticism. Informed by empiricist, associationist, and evolutionary theories of the mind, the portrayals of subject-formation in this study highlight the radical changes occurring in the human environment in nineteenth-century, which catalyzed the conception of a malleable yet self-forming subject. Along with the …

Statistical Models For Gene And Transcripts Quantification And Identification Using Rna-Seq Technology, Han Wu

Open Access Dissertations

RNA-Seq has emerged as a powerful technique for transcriptome study. As much as the improved sensitivity and coverage, RNA-Seq also brings challenges for data analysis. The massive amount of sequence reads data, excessive variability, uncertainties, and bias and noises stemming from multiple sources all make the analysis of RAN-Seq data difficult. Despite much progress, RNA-Seq data analysis still has much room for improvement, especially on the quantification of gene and transcript expression levels. The quantification of gene expression level is a direct inference problem, whereas the quantification of the transcript expression level is an indirect problem, because the label of …