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Extracellular Matrix Remodeling And The Inflammatory Response During Skeletal Muscle Regeneration In Sarcopenic Obese Mice, Lemuel Arthur Brown

Graduate Theses and Dissertations

AIM: Sarocpenic obesity is a national concern within the United States because this metabolic syndrome is tied with reduced mobility and quality of life. Both obesity and aging are associated with insulin-resistance, chronic low-grade inflammation and muscle weakness. Skeletal muscle regeneration is a process that involves the coordinated effort of myogenic regulatory factors (MRFs), inflammatory signaling, and extracellular matrix (ECM) remodeling for optimal regeneration. It has been demonstrated that obesity and aging have a reduction in muscle regeneration. It has not been examined if sarcopenic obesity will further reduce muscle mass and the regenerative process. The purpose of this study …

Nitrogen Biogeochemistry In Binghamton, Ny, A Medium-Sized Urban Ecosystem, Stephanie Craig

Graduate Dissertations and Theses

Humans have altered nitrogen (N) cycling on a global scale, and elevated nitrogen levels are characteristic of urban ecosystems. The major reasons that N is higher in cities include imports of food, fuel and fertilizer. High N export from both point- and nonpoint-sources is common in large cities. While N cycling has been studied in large urban areas, less is known about its cycling in medium-sized cities, such as Binghamton, N.Y. We found that point-source N exported from the Binghamton-Johnson City Wastewater Treatment Plant (B-JC WWTP) was greater than nonpoint-source N exported from eight urban streams to the Susquehanna River, …

Generalized Partial Directed Coherence And Centrality Measures In Brain Networks For Epileptogenic Focus Localization, Joshua Aaron Adkinson

Doctoral Dissertations

Accurate epileptogenic focus localization is required prior to surgical resection of brain tissue for treatment of patients with intractable temporal lobe epilepsy, a clinical need that is partially fulfilled to date through a subjective, and at times inconclusive, evaluation of the recorded electroencephalogram (EEG). Using brain connectivity analysis, patterns of causal interactions between brain regions were derived from multichannel EEG of 127 seizures in nine patients with focal, temporal lobe epilepsy (TLE). The statistically significant directed interactions in the reconstructed brain networks were estimated from three second intracranial multi-electrode EEG segments using the Generalized Partial Directed Coherence (GPDC) and validated …

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 …

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 …

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 …

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 …

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), …

The Role Of Mechanical Loading In Chondrocyte Signaling Pathways, Qiaoqiao Wan

Open Access Dissertations

Chondrocytes are a predominant cell type present in articular cartilage, whose integrity is jeopardized in joint degenerative diseases such as osteoarthritis (OA). In the chondrocytes of patients with OA, the elevated levels of inflammatory cytokines such as interleukin 1β (IL1β) and tumor necrosis factor α (TNFα) have been reported. These cytokines contribute to degradation of cartilage matrix by increasing activities of proteolytic enzymes. In addition to their contribution to proteolytic enzymes, these cytokines adversely affect anabolic activity of chondrocytes by inhibiting the production of proteoglycans and type II collagen. Therefore, blocking the action of these cytokines is a potential strategy …

Farmers' Use Of Mobile Phone Technology For Agricultural Information Services In Lilongwe District, Malawi, Benjamin F. Chisama

Open Access Theses

Mobile phone technology can be a useful tool to provide farmers with relevant and reliable agricultural information for critical farming decisions in developing countries such as Malawi. An increasing number of rural farmers have been faced with information asymmetry challenges due to some pitfalls in the extension systems. In addition, knowledge gaps on farmers’ use of mobile phone technology; their awareness and use of MAIS; and their preferred topics to be delivered using mobile platforms were identified. However, little was known on how farmers were using existing MAIS. This study’s aim was to explore the potential of providing mobile agricultural …

The Biology And Management Of Waterhemp In Indiana, Joseph M. Heneghan

Open Access Theses

Waterhemp is a dioecious weed species indigenous to the Midwestern United states yet it has only recently become problematic in agronomic crop production in Indiana. Waterhemp is a small-seeded broadleaf which has increased in prevalence in conjunction with an increase in conservation tillage practices. Waterhemp germinates and emerges from the top 3 cm of soil and is known to exhibit extended periods of continual emergence, longer than most other summer annual weed species that are typically present in agronomic production settings. As a C4 species, waterhemp then grows rapidly and is capable of producing thousands of seeds, while effectively competing …

Metabolomics Approach To Investigate Oxidation Stabilities In Different Bovine Muscles With Postmortem Aging, Danyi Ma

Open Access Theses

Postmortem aging has been extensively practiced in the meat industry for decades due to its beneficial impact on improving eating quality attributes. However, prolonged postmortem aging may adversely impact color and/or lipid oxidation stabilities of meat, leading to decreased display shelf-life and increased rancid off-flavor. As physical/biochemical changes occur during postmortem aging, metabolites that impart antioxidant or pro-oxidant activities are generated or consumed, which could be related to the oxidation stabilities of postmortem muscles with aging. However, the underlying mechanism of the aging-induced oxidation susceptibility has not been fully established. Therefore, the overall objective of this thesis was to understand …

Evaluating The Physical Welfare Of Dogs In Commercial Breeding Facilities In The United States, Moriah J. Hurt

Open Access Theses

Despite high levels of public concern, the state of commercial breeding (CB) dog welfare is largely unknown. Therefore, this study aimed to characterize the physical welfare of dogs in CB facilities and their environment in Indiana. This study specifically aimed 1) to characterize dog foot health in CB facilities as a function of the length of time dogs were housed on a given flooring substrate, 2) to characterize visual dog body cleanliness and visual kennel cleanliness as a function of the flooring substrate, 3) to determine the efficacy of kennel cleaning procedures and 4) to characterize the dog dental and …

The Interactive Effects Of Pesticide Exposure And Infectious Disease On Amphibian Hosts, Katherine M. Pochini

Open Access Theses

Natural systems are home to a multitude of natural and anthropogenic stressors, which draw an array of effects on ecological communities. While these effects have been investigated individually, it is important, given the routine co-occurrence of these stressors, to understand their interactive effects. Pesticide exposure and infectious disease are two common, co-occurring stressors that each have documented detrimental effects on species and, as evidence suggests, may have interactive effects. Moreover, existing research suggests that these interactive effects are highly context dependent, eliciting different results based on species, disease agent, toxin, and environment. Given the variability with which species may experience …

An Assessment Of The Competitive Ability Of Oak Species In The Central Hardwood Region Using Both Pre-Harvest Treatment Data And Stem Analysis Techniques, Robert William Edward Quackenbush

Open Access Theses

The density of advance regeneration of oak species has been in decline across the Central Hardwood Region (CHR) for the past 50 years. This phenomenon has been accredited to many different factors, ranging from predation and browse by wildlife, to human induced changes in the environment which include massive clearcutting, land use change from forest to agriculture, and suppression of fires which played an intricate role in the development of oak systems across the CHR. The objectives of this research project were to compare densities of oak advance regeneration across two different environmental gradients within the CHR, in particular the …

High School Students' Motivations And Views Of Agriculture And Agricultural Careers Upon Completion Of A Pre-College Program, Andrea K. Scherer

Open Access Theses

Pre-college summer residential experiences hosted by a College of Agriculture have the potential to expose high school students to new career opportunities and fields of study that they may not have considered, and may influence agricultural literacy, perceptions of agriculture, and interest in agriculture. Engaging these students is important for meeting the demand for more students graduating with agriculture degrees prepared to solve 21st century challenges. The purpose of this study was to explore and describe the outcomes of two separate pre-college experiences, the Molecular Agriculture Summer Institute (MASI) and the Purdue Agribusiness Science Academy (PASA), and participating high school …

Mapping And Analyzing Energy Use And Efficiency In A Modified Hydroponic Shipping Container, Rachel E. Sparks

Open Access Theses

In urban centers today, vertical farming is becoming a popular alternative to conventional agriculture in an effort to increase local food production and improve urban food security by growing crops using hydroponic methods in controlled environment spaces. More specifically, one vertical method involves growing crops inside refurbished shipping containers, or a “farm-in-a-box” concept, which offers a flexible, mobile, and scalable means of year-round food production in a variety of climates. Despite benefits of producing food locally, some of the concerns associated with these vertical farming systems include high energy consumption from climate control and electric lighting systems as well as …

Nutrient Runoff And Leachate After Land-Application Of Digestate In A Laboratory Study Using Rainfall Simulations, Min Xiao

Open Access Theses

There has been an increasing number of anaerobic digesters on livestock farms in the United States during the past two decades. Anaerobic digestion of manure allows production of renewable energy and generation of stabilized and nutrient-rich digestate that can be used as organic fertilizer. However, the majority of the existed studies using liquid digestate as fertilizer only focused on the effectiveness for crop yield, nutrient content and microorganism in soil. There is insufficient understanding in the environmental impact of digestate land-application. This laboratory study used six treatments including four different liquid digestate treatments, a chemical fertilizer treatment, and an unfertilized …

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 …

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 …

Evaluating The Prevalence And Effectiveness Of Breed-Specific Legislation, Felicia E. Trembath

Open Access Dissertations

Dog bites pose a persistent public health problem, which some jurisdictions pass breed-specific legislation (BSL) to address. However, very little non-anecdotal evidence regarding the efficacy of BSL has been presented. Currently, BSL research is hampered by the absence of standard terminology, an established prevalence, or a scientific consensus on its effectiveness. The purpose of this study is to propose standardized terminology for BSL, establish the prevalence of each type of BSL in the USA, and conduct a systematic review of the effectiveness of BSL.

After review of terminology currently in use, as well as review of the regulatory actions of …

Manipulating Air And Root-Zone Temperature For Energy-Efficient Floriculture Crop Production, Madeline W. Olberg

Open Access Theses

Given the high energy costs for greenhouse floriculture production, growers are constantly searching for more energy-efficient methods of production. For example, some growers will lower greenhouse air temperature set points or grow crops in unheated high tunnels (HTs) or outdoors in order to minimize or eliminate heating costs. Unfortunately, development can be delayed and morphology can be altered if the mean daily air temperature (MDT) is reduced. We proposed that reducing MDT in combination with root-zone heating (RZH) could be an energy-efficient method for producing high-quality floriculture crops without significant delays. Unheated HT and unprotected outdoor production are very low-cost …

The Impact Of Climate Change In Bangladesh On The Rice Market And Farm Households, Mst Ashrafun Nahar

Graduate Theses and Dissertations

Bangladesh is trying to achieve self-sufficiency in domestic rice production but climate change effects on agricultural production makes it challenging to attain the goal. The country is highly vulnerable to the effects of climate change since it is the major cause to rise in sea level, more warm summer, and happening food and cyclone in the country.

This study develops an Aggregate Farm Household Model to analyze the impact of potential land loss and yield reduction from climate change on production, consumption, prices, welfare, and the ability of government to achieve self-sufficiency in rice production. The model is calibrated to …