Life Sciences Commons^™

Mechanistic Insight Into The Role Of Dietary Fibers And Short Chain Fatty Acids In The Regulation Of Metabolism And Inflammation In The Pig, Hui Yan

Open Access Dissertations

Dietary fiber is a diverse mixture of polysaccharides exerting multiple functions as it passes through the gastrointestinal tract (GIT). Besides the influence on nutrient digestibility, dietary fiber affects growth performance and host metabolism via modulation of gut microbial community structure and production of short chain fatty acids (SCFA). A series of in vivo experiments were conducted to determine the effects of dietary fiber on pig growth performance and gut microbial community as well as host metabolism. In the first study, a comparison between soluble and insoluble fibers was conducted in terms of pig growth, gut microbial structure and SCFA production …

Intestinal Cytoplasmic Lipid Droplets, Associated Proteins, And The Regulation Of Dietary Fat Absorption, Theresa M. D'Aquila

Open Access Dissertations

Dietary fat provides essential nutrients, contributes to energy balance, and regulates blood lipid concentrations. These functions are important to health, but can also become dysregulated and contribute to diseases such as obesity, diabetes, and cardiovascular disease. The small intestine absorbs dietary fat through an efficient multi step process of digestion, uptake, metabolism, and secretion or storage. When dietary fat is taken up by the absorptive cells of the small intestine, enterocytes, it can be secreted into circulation where it contributes to blood lipid levels or temporarily stored in cytoplasmic lipid droplets (CLDs). The objective of this dissertation is to investigate …

The Effects Of Including Almonds In An Energy-Restricted Diet On Weight, Body Composition, Visceral Adipose Tissue, Blood Pressure And Cognitive Function, Jaapna Dhillon

Open Access Dissertations

Inclusion of almonds in an energy restricted diet has been reported to enhance or have no effect on weight loss. Their effects specifically on visceral fat stores during energy restriction have not been widely examined. Additionally, almond consumption has been associated with reduced blood pressure, but whether this is linked to or is independent of changes of body composition has not been examined. Moreover, almond consumption during energy restriction may be an effective strategy for reversing the negative effects of dieting on cognitive performance. The unique nutrient profile of almonds also has the potential to influence cognitive function post-prandially. The …

Graphical Methods In Rna Structure Matching, Jiajie Huang

Open Access Dissertations

Eukaryotic genomes are pervasively transcribed; almost every base can be found in an RNA transcript. This is a surprising observation since most of the genome does not encode proteins. This RNA must serve an important regulatory function – important because producing non-coding RNA is an energy intensive process, and in the absence of strong selection one would expect it to disappear.

RNA families with common functions have specifically conserved structural motifs, which are directly related to the functional roles of RNA in catalysis and regulation. Because the conserved structures depend on base-pairing, similar RNA structures may have little or no …

Food Security Crop Price Transmission And Formation In Nigeria, Patrick L. Hatzenbuehler

Open Access Dissertations

The three studies in this dissertation explore the current conditions and operations of markets for seven key food security crops (cassava, cowpeas, maize, millet, rice, sorghum, and yams) in Nigeria.

Chapter 2 is an empirical analysis of the current agricultural statistics system in Nigeria. A number of sources gather and report agricultural statistics for the country. Since there has not been an agricultural census implemented there for multiple decades, however, there is no objective source for data verification. Therefore, this study uses two additional types of “on the ground information” to assess if agricultural production estimates reflect growing conditions: prices …

Evaluating The Two-Stage Ditch As A New Best Management Practice, Andi Hodaj

Open Access Dissertations

A two-stage ditch involves modifications of a traditional drainage ditch to resemble more the features of a natural stream. The idea is to create or simulate extended benches on both sides of the ditch that would develop naturally over a period of time in a stream because of geomorphological processes. Previous research in Indiana and Ohio has shown that two-stage ditches offer the potential to reduce sediment load and extend the interaction time between water and vegetation on the benches allowing larger uptake of nutrients from the vegetation on the extended benches, and increasing the denitrification rates in the bench …

Computational Labeling, Partitioning, And Balancing Of Molecular Networks, Biaobin Jiang

Open Access Dissertations

Recent advances in high throughput techniques enable large-scale molecular quantification with high accuracy, including mRNAs, proteins and metabolites. Differential expression of these molecules in case and control samples provides a way to select phenotype-associated molecules with statistically significant changes. However, given the significance ranking list of molecular changes, how those molecules work together to drive phenotype formation is still unclear. In particular, the changes in molecular quantities are insufficient to interpret the changes in their functional behavior. My study is aimed at answering this question by integrating molecular network data to systematically model and estimate the changes of molecular functional …

Biochemical Changes In Animal Models Of Fetal Alcohol Spectrum Disorder, Christine E. M. Keller

Open Access Dissertations

Fetal alcohol spectrum disorder (FASD) is a completely preventable disease, that has profound effects on life-long health and function of the affected individual. Prevalence estimates of FASD in the United States indicate 33.5 per 1,000 live births are affected with this disorder (Roozen, 2016). FASD is caused by maternal ethanol intake during pregnancy. However, recommendations of the amounts of alcohol safe to drink during pregnancy are not established. Further, we lack a comprehensive understanding of the biochemical pathways modified in prenatal ethanol exposure. Biomarkers are also lacking. Our results demonstrate the vast array of biochemical pathways modified in the chronic …

Influence Of Dietary Polyphenols On Carbohydrate Intestinal Digestion And Absorption, Sydney E. Moser

Open Access Dissertations

Both epidemiological and clinical evidence support the notion that polyphenol rich foods and beverages may modify glycemic response, glucose homeostasis and subsequent risk of Type-2 diabetes. In vitro evidence typically derived from experiments with pure phenolics and phenolic rich extracts have pointed to this benefit being associated with two potential mechanisms: (1) the ability of specific polyphenolics to inhibit carbohydrate digestion (amylase and glucosidase) and (2) polyphenolic inhibition of intestinal glucose transport. While the high potential of these activities is evident, little is actually known regarding the extent to which these benefits are extendable to the actual food matrix these …

Understanding Plant Response To Stress Using Gene Model Quality Evaluation And Transcriptome Analysis, Karthik Ramaswamy Padmanabhan

Open Access Dissertations

The overall aim of the project was to understand how plants reacted to environmental stress and evolved to overcome it. The land plants that we see today evolved from a green algal ancestor around 510 million years ago. Plants had to make significant changes to their cellular, morphological, regulatory and physiological processes during their adaptation to the terrestrial environment from an aquatic environment. The first part of the project was to find out how these changes were reflected on the protein makeup of the early land plants. The gene model sequence data of two early land plants, Physcomitrella patens (moss) …

Intestinal Adaptation To Repeated Exposure Of Flavonoid-Rich Foods: In Vitro And Clinical Data, Bejamin W. Redan

Open Access Dissertations

Interest in application of flavonoids for chronic disease prevention has grown significantly, but the low oral bioavailability of these compounds from acute doses is commonly highlighted as a limitation when considering their biological significance. Still, the impact of broad dietary patterns such as repeated exposure on flavonoid’s absorption, metabolism, and eventual efficacy is critical to consider since evidence suggests that their bioavailability may be enhanced with repeated exposure. To fill this gap in knowledge, this dissertation will focus on three major areas including characterization of flavonoid metabolites, in addition to use of in vitro models and clinical work to test …

X-Ray Fluorescence For Quantification Of Lead And Strontium In Vivo, Aaron James Specht

Open Access Dissertations

Lead (Pb) is a toxicant well known for its effects on almost every organ system in the body. Pb use in industry has declined since removal of Pb from gasoline, but many developing countries still have significant use of Pb. Exposure to Pb has been linked with diseases causing neurodegeneration and thus have lasting effects long after the initial exposure. Another metal, strontium (Sr), has been linked with bone disease in particular situations and shown to have uses in treating osteoporosis as a supplement. However, there are no studies of the effects of Sr using a meaningful biomarker. The most …

Evolutionary Potential Of A Dispersal-Restricted Species In Response To Climate Change, Lorena Torres Martinez

Open Access Dissertations

Habitat replacement and fragmentation associated with projected climate change pose a critical threat to global biodiversity. Edaphically limited plant species with restricted dispersal abilities will be especially handicapped to track their optimal climate spatially. Instead, the persistence of these species will depend on their capacity to adapt in situ to novel climate regimes. Here I evaluated the evolutionary potential of Lasthenia fremontii, an annual plant species restricted to ephemeral wetlands called vernal pools in California to adapt to the projected patterns of climate change. Across L. fremontii distribution there is a latitudinal gradient in precipitation which, combined with reduced …

Learning From Data: Plant Breeding Applications Of Machine Learning, Alencar Xavier

Open Access Dissertations

Increasingly, new sources of data are being incorporated into plant breeding pipelines. Enormous amounts of data from field phenomics and genotyping technologies places data mining and analysis into a completely different level that is challenging from practical and theoretical standpoints. Intelligent decision-making relies on our capability of extracting from data useful information that may help us to achieve our goals more efficiently. Many plant breeders, agronomists and geneticists perform analyses without knowing relevant underlying assumptions, strengths or pitfalls of the employed methods. The study endeavors to assess statistical learning properties and plant breeding applications of supervised and unsupervised machine learning …

Physiological Bases And A Novel Genetic Determinant Of Water-Use Efficiency (Wue), Jie Yin

Open Access Dissertations

Water-use efficiency (WUE), the ratio of biomass to water loss, is a heritable but complex trait, the genetic basis of which is largely unknown. We utilized diverse accessions of the halophyte Eutrema salsugineum to ultimately identify a novel genetic determinant of WUE. E. salsugineum accessions from locations with low water availability, temperature, and radiation have lower transpirational water loss and greater biomass, resulting in higher WUE. High-WUE accessions also have lower stomatal density and index and larger thinner leaves than low-WUE accessions. We identified 14,808 single nucleotide polymorphisms (SNPs) between two accessions of E. salsugineum,Shandong (SH) and Yukon (YK), …

Influence Of Dietary Component Manipulation And Feed Management Strategies On Growth And Rumen Development Of Weaned Dairy Heifers, Tana Shea Dennis

Open Access Dissertations

Well-developed replacement heifers provide a central foundation for the continued success of the dairy industry. Emphasis on improving pre-weaned calf nutrition has predominated in the industry, but opportunities exist to improve post-weaning heifer nutrition and management. We aimed to evaluate common feed management strategies seen in the industry and their effects on growth, feed efficiency (G:F), and rumen development of calves from birth to 8 mo of age using pen- and individually-fed animal trials. Little information exists regarding post-weaning performance and rumen development of calves fed conventional or high planes of nutrition pre-weaning; therefore, we evaluated two milk replacer feeding …

Investigation Of An Energetic Coupling Between Ligand Binding And Protein Folding, Nathan W. Gardner

Open Access Dissertations

The cellular environment presents a protein with many small molecules with which it may interact. Many novel interactions between proteins and non-substrate metabolites are being uncovered through proteome-wide screens. The homodimeric Escherichia coli cofactor-dependant phosphoglycerate mutase (dPGM) was identified as an ATP binding protein in a proteome-wide screen, but dPGM does not use ATP for catalysis. This dissertation elucidates the effect of ATP and other non-substrate metabolites on dPGM. Initial investigations revealed a partially unfolded, monomeric intermediate of dPGM that forms during equilibrium unfolding. ATP binding was found to occur at the active site of dPGM and to be energetically …

Mitigating Prevalence And Persistence Of L. Monocytogenes Using Novel Sanitation Strategies In Delis, Susan Rose Hammons

Open Access Dissertations

Ready-to-eat (RTE) deli meats sliced at retail are predicted to cause 83% of deli meat-associated listeriosis cases annually. While L. monocytogenes is commonly found in delis (55-90%), environmental prevalence varies by store (0-40%). Study 1 evaluated efficacy of 10 standardized SSOPs by testing 28 food and non-food contact surfaces for L. monocytogenes over 6 months in 30 retail delis. Intervention strategies employed in this study significantly decreased L. monocytogenesprevalence on FCS and NFCS in stores with moderate prevalence (0.5%, 0.8% reduction). However, we found that L. monocytogenes could persist despite implementation of SSOP control strategies. Study 2 assessed an …

Investigation Of Cellular Microenvironments And Heterogeneity With Biodynamic Imaging, Daniel Alexander Merrill

Open Access Dissertations

Imaging of biological tissue in a relevant environment is critical to accurately assessing the effectiveness of chemotherapeutic agents in combatting cancer. Though many three-dimensional (3D) culture models exist, conventional in vitro assays continue to use two-dimensional (2D) cultures because of the difficulty in imaging through deep tissue. 3D tomographic imaging techniques exist and are being used in the development of 3D efficacy assays. However, most of these assays look at therapy endpoint (dead or living cancer cell count) and do not capture the dynamics of tissue response.

Biodynamic imaging (BDI) is a 3D tomographic imaging and assay technique that uses …

Reflexivity: A First Demonstration, Melissa Jane Swisher

Open Access Dissertations

Currently, the emergent relation of reflexivity after training a set of baseline relations has not been demonstrated with any animal—human or nonhuman. True reflexivity can only be demonstrated if no identity (i.e., physically matching stimulus) relations are trained. In six experiments, the emergence of reflexivity and its opposite, anti-reflexivity, were explored. Pigeons received concurrent successive matching training on two or three arbitrary tasks: AB hue-form and BC form-hue (and AC hue-hue) matching. Once they had acquired these tasks, they were tested for BB (form-form) reflexivity or BB’ (form-form) anti-reflexivity matching. Most (10 of 13) pigeons that received three arbitrary tasks …

Three Essays Analyzing The Role Of Social Capital On Individual And Firm Decision Making, Ariana P Torres Bravo

Open Access Dissertations

The following dissertation is comprised of three essays that focus on different mechanisms on which social capital influences firm and entrepreneur behavior. All three essays use different econometric techniques to account for endogenous variables.

Essay 1: Are Local Market Relationships Trumping Organic Certification? The Case of Small and Medium Fruit and Vegetable Farmers. This article investigates how an organic fruit and vegetable farmer’s choice to use direct-to-consumer market channels impacts his/her decision to be certified organic. First, we model the decision to be certified organic as a conditionally independent decision from the farmer’s chosen market channels. Second, we estimate …

The Application Of The Hadoop Software Framework In Bioinformatics Programs, Dan Wang

Open Access Dissertations

The project described in this dissertation proposal attempted to improve the efficiency and scalability performance as well as the usability and user experience of three Bioinformatics applications - DNA/peptide sequence similarity comparison, digital DNA library subtraction, and DNA/peptide sequence de-duplication - by 1) adopting the Hadoop MapReduce algorithms and distributed file system and 2) implementing the fully automated Hadoop programs into a user friendly graphical user interface (GUI). In addition, the researcher was also interested in investigating the advantages and limitations of applying the Hadoop software framework as a general methodology in parallelizing Bioinformatics programs.

After considering the original calculation …

Immune Modulating Functions By Soypeptide Lunasin In Cancer Immunotherapy, Chun-Yu Tung

Open Access Dissertations

Chemotherapy is currently the mainstay of treatment for most cancer patients. Despite its efficacy in eliminating cancer cells, a high percentage of chemotherapy patients eventually relapse or suffer progression of the disease. Immunosurveillance is capable of recognizing and eliminating continuously arising transformed mutant cells, and thus cancer immunotherapy is one of the emerging therapeutic strategies that harnesses the power of the immune system to eradicate chemotherapy-resistant cancerous cells. However, the adverse side effects of chemotherapy impede the therapeutic effects of immunotherapy. Our previous studies demonstrate that lymphoma patients are refractory to clinical immunotherapy because of chemotherapy-induced immune dysfunction. In addition, …

Affinity Cryo-Electron Microscopy: Methods Development And Applications, Guimei Yu

Open Access Dissertations

Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies. Although less concentrated and smaller amounts of samples are required for single particle cryo-EM compared to X-ray crystallography, it remains challenging to study specimens that are low-abundance, low-yield, or short-lived. The recent development of affinity grid techniques holds great promise to tackle these challenging samples by combining the sample purification and freezing on TEM grids steps in cryo-EM grid preparation into a single step, revolutionize the grid preparation of cryo-EM, and extend single particle cryo-EM to a routine structural biology tool to characterize structures …

Evaluation Of Negative Energy And Mineral Balance In Periparturient Holstein-Friesian Cattle, Ameer Ahmed Abdelhameed

Open Access Dissertations

Most cows experience a state of negative energy and mineral balance during the periparturient period. This imbalance is a major problem in the dairy industry and it is more frequently seen in multiparous cattle due to their high milk production. A large amount of fat and protein is mobilized in order to address the energy deficit during the periparturient period. The ability to accurately monitor energetics and electrolytes status using accurate, rapid, and low cost point-of-care instruments will assist in optimizing animal health and productivity.

This dissertation contains three studies that evaluated point-of-care instruments for measuring blood and plasma glucose, …

Is Metabolism Goal-Directed? Investigating The Validity Of Modeling Biological Systems With Cybernetic Control Via Omic Data, Frank T. Devilbiss

Open Access Dissertations

Cybernetic models are uniquely juxtaposed to other metabolic modeling frameworks in that they describe the time-dependent regulation of cellular reactions in terms of dynamic "metabolic goals." This approach contrasts starkly with purely mechanistic descriptions of metabolic regulation which seek to explain metabolic processes in high resolution — a clearly daunting undertaking. Over a span of three decades, cybernetic models have been used to predict metabolic phenomena ranging from resource consumption in mixed-substrate environments to intracellular reaction fluxes of intricate metabolic networks. While the cybernetic approach has been validated in its utility for the prediction of metabolic phenomena, its central feature, …

The Effect Of Voluntary Binge Caffeine And Ethanol Coexposure On Neurobehavioral Sensitivity To Cocaine In Male C57bl/6j Mice, Brandon M. Fritz

Open Access Dissertations

Recently, the co-consumption of highly caffeinated energy drinks and alcohol has become a public health concern. Consumption of these beverages has been linked to a wide variety negative consequences including alcohol poisoning, driving under the influence, physical harm, and sexual violence. The more protracted consequences of caffeinated alcohol consumption have received very little attention, however. Some evidence suggests that individuals that frequently consume energy drinks mixed with alcohol are more likely to develop an alcohol use disorder. Interestingly, both caffeine and alcohol use alone have been linked to polydrug abuse. It is therefore of interest whether combined caffeine and alcohol …

Biophysical Studies Of The Allosteric Regulatory Mechanism Of Syk Tandem Sh2 Domains Interacting With Immunoreceptor Tyrosine-Based Activation Motifs, Chao Feng

Open Access Dissertations

The non-receptor spleen tyrosine kinase (Syk) is an important player in signal transduction from immunoreceptors to various downstream targets. It is widely expressed in both haematopoietic and epithelial cells. Syk disorder is closely related with many inflammatory and autoimmune diseases, as well as cancers.

Syk associates with immunoreceptors through its tandem SH2 domains (tSH2), which contain two SH2 domains connected by interdomain A. The association of Syk with immunoreceptors is regulated by Y130 phosphorylation in interdomain A. The unphosphorylated tSH2 can bind with the doubly phosphorylated immunoreceptor tyrosine-based activation motif (dp-ITAM) of the cytoplasmic domains of immunoreceptors with very high …

Investigating The Role Of The Basic Helix-Loop-Helix Transcription Factor Mist1 In Pancreatic Diseases, Anju Karki

Open Access Dissertations

Acinar cells of the exocrine pancreas are dedicated to synthesize, package and secrete immense quantities of pro-digestive enzymes to maintain proper metabolic homeostasis for the organism. Dysregulation of enzyme secretion in acinar cells can give rise to exocrine diseases including acute pancreatitis (AP), a disease that targets acinar cells, leading to acinar-ductal metaplasia (ADM), inflammation and fibrosis—events that can transition into the earliest stages of pancreatic ductal adenocarcinoma (PDAC). The focus of this thesis is to interrogate transcriptional regulatory networks that are susceptible to AP and the role that these networks play in acinar cell and exocrine pancreas responses. The …

Crop Modeling For Assessing And Mitigating The Impacts Of Extreme Climatic Events On The Us Agriculture System, Zhenong Jin

Open Access Dissertations

The US agriculture system is the world’s largest producer of maize and soybean, and typically supplies more than one-third of their global trading. Nearly 90% of the US maize and soybean production is rainfed, thus is susceptible to climate change stressors such as heat waves and droughts. Process-based crop and cropping system models are important tools for climate change impact assessments and risk management. As data- science is becoming a new frontier for agriculture growth, the incoming decade calls for operational platforms that use hyper-local growth monitoring, high-resolution real-time weather and satellite data assimilation and cropping system modeling to help …