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Development Of Computational Techniques For Regulatory Dna Motif Identification Based On Big Biological Data, Jinyu Yang
Development Of Computational Techniques For Regulatory Dna Motif Identification Based On Big Biological Data, Jinyu Yang
Electronic Theses and Dissertations
Accurate regulatory DNA motif (or motif) identification plays a fundamental role in the elucidation of transcriptional regulatory mechanisms in a cell and can strongly support the regulatory network construction for both prokaryotic and eukaryotic organisms. Next-generation sequencing techniques generate a huge amount of biological data for motif identification. Specifically, Chromatin Immunoprecipitation followed by high throughput DNA sequencing (ChIP-seq) enables researchers to identify motifs on a genome scale. Recently, technological improvements have allowed for DNA structural information to be obtained in a high-throughput manner, which can provide four DNA shape features. The DNA shape has been found as a complementary factor …
Screen Printed Carbon Electrode Based Microfluidic Biosensor For Sweat Cortisol Detection, Shailu Shree Poudyal
Screen Printed Carbon Electrode Based Microfluidic Biosensor For Sweat Cortisol Detection, Shailu Shree Poudyal
Electronic Theses and Dissertations
A simple, cost-effective, microfluidic, field-deployable biosensor with screen printed carbon electrode (SPCE) was developed for detection of sweat cortisol with point of care applications. Cortisol detection in artificial sweat is an important screening tool for diagnosis and monitoring of various health conditions like Addison’s disease, stress disorder, and Cushing’s syndrome. A self-assembled monolayer of graphene oxide (GO) is functionalized on SPCE electrode, onto which cortisol antibodies are immobilized for cortisol detection. Microfluidic system ensured precise and controlled flow of reagents and antibodies. Electrochemical measurement is done using cyclic voltammetry, as a function of cortisol concentrations. Cyclic voltammetry measurement gives current …
Impacts Of Integrated Crop-Livestock System On Soil Surface Greenhouse Gas Fluxes At A Farm Scale In South Dakota, Brant Douville
Impacts Of Integrated Crop-Livestock System On Soil Surface Greenhouse Gas Fluxes At A Farm Scale In South Dakota, Brant Douville
Electronic Theses and Dissertations
Grazing and cover crops (CC) can impact soil nutrient cycling but may increase the greenhouse gas (GHG) emissions from soils. However, little is known about their impacts on soil properties and soil surface GHG emissions in an integrated crop-livestock system (ICLS) in South Dakota, USA. The present study was conducted at a farm scale at the Research Farm of South Dakota State University, Brookings, South Dakota, to assess the impact of cover crops and grazing on soil pH, electrical conductivity (EC), and bulk density (BD), and soil surface carbon dioxide (CO2), methane (CH4), and nitrous oxide …
Biofilm Formation By Common Dairy Sporeformers On Native And Modified Stainless Steel Surfaces, Shivali Jindal
Biofilm Formation By Common Dairy Sporeformers On Native And Modified Stainless Steel Surfaces, Shivali Jindal
Electronic Theses and Dissertations
Aerobic sporeformers can be traced in a variety of dairy products such as milk powders, evaporated milk, and canned products, which demonstrates their capability of resisting high temperature treatments such as pasteurization and Ultra high temperatures. These bacilli also actively attach to the stainless steel surfaces, consequently resulting in the formation of biofilms. Product quality as well as its safety is undesirably affected by the growth of these sporeforming bacteria. Therefore, creating an ideal environment for the processing of dairy products is a critical challenge for the dairy industry. Hence, the objective of this research was to analyze various surface …
Senecavirus A: Epidemiology, Pathogenesis And Infection Dynamics, Lok Raj Joshi
Senecavirus A: Epidemiology, Pathogenesis And Infection Dynamics, Lok Raj Joshi
Electronic Theses and Dissertations
Senecavirus A (SVA) is a positive sense single-stranded virus that belongs to the genus Senecavirus within the family Picornaviridae. Senecavirus has been present in US swine population since 1988. However, there have been only a few reports of SVA associated with disease in last two decades. In late 2014 early 2015, a sudden increase in the number of cases of Senecavirus A associated with vesicular disease was observed in Brazil, the US and China. Affected pigs presented vesicles on snout, coronary band, and dewclaw. Additionaly, increased neonatal mortality has been reported in the field. Many aspects of SVA epidemiology, …
Characterization Of Pyrenophora Tritici-Repentis In Wheat And Rye To Study Tan Spot Susceptibility And Insights Into Its Relationship With Stem Rust Resistance, Sidrat Abdullah
Electronic Theses and Dissertations
Tan spot, caused by the ascomycete fungus, Pyrenophora tritici-repentis (Ptr), is a major foliar fungal disease of wheat worldwide. To date, Ptr isolates have been grouped into eight races based on the production of three host selective effectors (toxins), Ptr ToxA, ToxB, and ToxC, which are associated with necrosis and chlorosis symptoms on wheat differential lines. In order to see the correlation between stem rust resistance and tan spot susceptibility in 1970’s, to know the pathogen virulence profile, and explore the sources of tan spot resistance, we recovered isolates from wheat and rye and evaluated wheat and rye lines with …
Silencing Seed Dormancy Genes To Mitigate Risk Of Transgene Flow To Weedy Rice, Alexander Wireko Kena
Silencing Seed Dormancy Genes To Mitigate Risk Of Transgene Flow To Weedy Rice, Alexander Wireko Kena
Electronic Theses and Dissertations
The flow of fitness-enhancing transgenes from genetically modified crops into wild/weed relatives may cause serious ecological and economic consequences. Seed dormancy (SD) is a key adaptive trait that distributes germination over time, resulting in weed persistence in agroecosystems. Thus, silencing major genes controlling SD would reduce the adaptive fitness of weeds. SD-enhancing genes cloned from weedy rice include SD7-1, SD7-2, SD12a, SD12b, and SD12c. The goal of this study was to develop a transgenic mitigation (TM) strategy using SD gene-silencing structures as mitigating factors to reduce the risk of transgene flow to wild/weed populations. TM vector constructs consisted of the …
Assessing The Near-Wall Hemodynamics In The Left Coronary Artery Using Cfd, John Junior Asiruwa
Assessing The Near-Wall Hemodynamics In The Left Coronary Artery Using Cfd, John Junior Asiruwa
Electronic Theses and Dissertations
The objective of this thesis is to computationally investigate the flow mechanics and the near-wall hemodynamics associated with the different take-off angles in the left coronary artery of the human heart. From this study, we will be able to evaluate if the increase in the take-off angles of the left coronary artery will significantly increases or decrease the likelihood of plaque (atherosclerosis) buildup in the left coronary artery bifurcations. This study quantifies the effects of the varying take-off angles on the branches along the left anterior descending (LAD) of the left coronary artery using computational fluid dynamics (CFD) simulations. The …
Interactive Effects Of Cover Crops, Invertebrate Communities And Soil Health In Corn Production Systems, Claire Lacanne
Interactive Effects Of Cover Crops, Invertebrate Communities And Soil Health In Corn Production Systems, Claire Lacanne
Electronic Theses and Dissertations
The adoption of regenerative farming practices is gaining traction, but the costs and benefits are not often considered on a systems level. Encouraging biodiversity and soil health is the goal of many agricultural practices used in regenerative farming; regenerative systems employ practices which abide by the two main principles of increasing biodiversity and decreasing disturbance, with the goal of encouraging ecosystem functioning to minimize inputs and maximize the productivity of a farm. I examined the management of corn (Zea mays) fields across four states in the Upper Midwest region of the United States. Regenerative systems in this study …
Phenotypic Plasticity Of Native And Invasive Cool-Season Grasses In Response To Frequency Of Moisture Availability, Ming-Yu Stephens
Phenotypic Plasticity Of Native And Invasive Cool-Season Grasses In Response To Frequency Of Moisture Availability, Ming-Yu Stephens
Electronic Theses and Dissertations
Phenotypic plasticity, the ability of an individual to alter its growth in response to environmental conditions, is an attribute that is considered a likely invader attribute, as it provides the opportunity to expand its ecological niche breadth. Adaptive phenotypic plasticity can affect not only the ability to establish in a new environment, but also the ability to outperform the existing vegetation over time. Bromus inermis (smooth brome) and Poa pratensis (Kentucky bluegrass) are invasive species in tall- and mixed-grass prairie ecosystems. The objectives of this two-part study were to quantify the adaptive plasticity of biomass accumulation and tiller production in …
Biotic Integrity In The Northwestern Great Plains And Mechanisms Regulating Stream Condition In South Dakota, Chad Kaiser
Biotic Integrity In The Northwestern Great Plains And Mechanisms Regulating Stream Condition In South Dakota, Chad Kaiser
Electronic Theses and Dissertations
Anthropogenic disturbance of streams can alter biotic integrity in various ways. Some degradation is easy to classify and monitor, others such as habitat impairment may be less easy to quantify. The Index of Biotic Integrity (IBI) is a unique method of assessing the aquatic health of an ecosystem. Beginning in 2010 the South Dakota Department of Environment and Natural Resources (SD DENR) began implementing biological monitoring on wadeable streams by developing an IBI for the Northern Glaciated Plains ecoregion in eastern SD (Krause et al. 2013). Prior to this survey the condition of the majority of SD’s streams was unknown. …
Heterogeneous Nitrogen Losses: Cost-Effectiveness Analysis Of Changes In Management Across South Dakota, Archibold Quaye
Heterogeneous Nitrogen Losses: Cost-Effectiveness Analysis Of Changes In Management Across South Dakota, Archibold Quaye
Electronic Theses and Dissertations
The loss of nitrogen fertilizer into the atmosphere and waterways is of increasing concern for citizens and policy makers. This is particularly relevant for hypoxia in rivers, lakes, and oceans, but also relevant for policy makers in reducing the increasing concentration of greenhouse gases (GHG) in the atmosphere. GHGs trap heat in the atmosphere and include: carbon dioxide, methane, nitrous oxide and fluorinated gases. Overall, the estimated contribution from the agricultural sector to GHG emissions was 9% in 2013 (EPA, 2013). Further, the addition of nitrogen to the soil through the use of synthetic fertilizers is a main contributor to …
Identification Of Physiological And Morphological Traits Governing High Water Use Efficiency In Alfalfa, Krishna Ghimire
Identification Of Physiological And Morphological Traits Governing High Water Use Efficiency In Alfalfa, Krishna Ghimire
Electronic Theses and Dissertations
Alfalfa is an important forage crop worldwide. Being deep-rooted, N2-fixing and high yielding, alfalfa has great economic, ecological and nutritional benefits. While alfalfa is a high yielding crop, its high productivity depends on irrigation water in many areas and consumes the greatest amount of water among all the major crops. With a growing demand for water resources due to an increase in human population and industrial water use, plus frequent drought due to climate change, irrigation water has become increasingly scarce and expensive. To sustain high production of alfalfa with limited water resource, alfalfa cultivars with improved water use efficiency …
Exploring The Relationship Between Immediacy Behaviors And Student Motivation In Engineering Classrooms: Immediacy As A Cause Of Motivation, Andrea N. Barahona Guerrero
Exploring The Relationship Between Immediacy Behaviors And Student Motivation In Engineering Classrooms: Immediacy As A Cause Of Motivation, Andrea N. Barahona Guerrero
Electronic Theses and Dissertations
Instructor immediacy is an essential characteristic of effective instructors. Although instructional communication has done extensive research on the impact of immediacy behaviors on students, there is little available research observing immediacy behaviors as predictors of motivation on engineering students. As a result, this study examined the impact of engineering instructors’ use of immediacy behaviors on engineering students’ motivation. The results indicated that verbal immediacy predicted engineering student motivation. The thematic analysis revealed that when students perceived their instructors as helpful, students’ motivation to learn and ask more questions increased. The thematic analysis also observed that when instructors seemed unapproachable, students …
The Synthetic Biology Of N2-Fixing Cyanobacteria For Photosynthetic Terpenoid Production, Charles T. Halfmann
The Synthetic Biology Of N2-Fixing Cyanobacteria For Photosynthetic Terpenoid Production, Charles T. Halfmann
Electronic Theses and Dissertations
In the last few decades, concerns over global climate change, energy security, and environmental pollution have been rising. To overcome these challenges, the concept of “-nth generation” biofuels has emerged as a strategy to convert solar radiation into fuels and bulk industrial chemicals for societal use, while decreasing our consumption of nonrenewable energy sources. Nitrogen-fixing cyanobacteria hold a distinct advantage in biofuel production over plants, given their ability to convert sunlight, air (CO2 and N2), and mineralized water to energy-dense carbon molecules, as well as fix atmospheric nitrogen gas into ammonia for metabolism. Engineered cyanobacteria with …
Evaluation Of Supplementing Brewer's Yeast To Lactating Dairy Cows, Taylor Christine Aubrey
Evaluation Of Supplementing Brewer's Yeast To Lactating Dairy Cows, Taylor Christine Aubrey
Electronic Theses and Dissertations
Probiotics have been used as effective, natural feed additives in the dairy industry to improve animal health and performance. Yeast product supplementation can be beneficial in the diet of lactating dairy cows by increasing feed efficiency, alleviating disease, and improving production performance under heat stress. Objectives of this study were to evaluate supplementing a concentrated brewer’s yeast in the ration of a lactating dairy cow by assessing milk yield and composition, blood metabolites, rumen fermentation, and feed intake and efficiency. We hypothesized that diets containing a concentrated brewer’s yeast supplement would increase milk and component yields, benefit rumen fermentation, and …
The Influence Of Chromium Supplementation On The Insulin Pathway, Carcass Traits, And Meat Quality Of Feedlot Steers, Heather Rode
The Influence Of Chromium Supplementation On The Insulin Pathway, Carcass Traits, And Meat Quality Of Feedlot Steers, Heather Rode
Electronic Theses and Dissertations
Chromium supplementation (Cr) can increase efficiency of growth in livestock by amplifying insulin signaling. Previous research showed Cr increases nutrient utilization and changes in muscle growth and fat deposition. Therefore, the objective of this research was to determine how Cr affects carcass traits, meat quality, and the insulin pathway in feedlot steers. Calf-fed steers were allotted to 0 ppb (CON) or 400 ppb Cr propionate (Cr400) for 210d in experiment 1. Two longissimus muscle (LM) biopsies were collected to examine protein abundance and gene expression after adaptation to a terminal implant and after adaption to ractopamine hydrochloride (RAC). A follow …
Development And Application Of A Fish-Based Index Of Biotic Integrity For Lakes In Eastern South Dakota, Daniel T. Nelson
Development And Application Of A Fish-Based Index Of Biotic Integrity For Lakes In Eastern South Dakota, Daniel T. Nelson
Electronic Theses and Dissertations
The Index of Biotic Integrity (IBI) was developed to summarize the impact of watershed and water quality degradation to biotic communities and help to provide a more complete picture of water quality changes that are not captured in traditional physical and chemical measurements. In 2014, nearly 15% of South Dakota lakes did not meet their designated beneficial uses based on water quality measures but the impacts to the fish communities are unknown. The goal of this study was to develop a fish-based IBI for eastern South Dakota lakes by addressing three specific objectives:
1) Determine whether an IBI could be …
Dissecting The Histone-Binding Mechanism Of A Phd Finger Subtype, Daniel Boamah
Dissecting The Histone-Binding Mechanism Of A Phd Finger Subtype, Daniel Boamah
Electronic Theses and Dissertations
Disordered tails of histones are critical information retrieval hub and thus, aberrations in the flow of information through these hubs are associated with a number of pathological consequences in human. Mechanism for retrieval of information from these hubs is achieved by protein-protein interaction, i.e. proteins dock onto histone tails to initiate chromatin signaling. Eukaryotes have a number of small peptide binding domains that have evolved to specifically interact with histone tails, and these domains called histone readers as they read the information encoded on histone tails. Plant homeodomain (hereafter PHD) finger, a binucleated zinc finger, family is one such histone …
Using Rna Seq To Define Genes And Pathways Affecting Salmonella Vaccine Response In Beef Cattle, Sara Awrahman
Using Rna Seq To Define Genes And Pathways Affecting Salmonella Vaccine Response In Beef Cattle, Sara Awrahman
Electronic Theses and Dissertations
A Salmonella siderophore receptor and porin (SRP) proteins vaccine is an intervention strategy to control Salmonella burden in cattle. The vaccine works by stimulating immunity to produce antibodies against bacterial SRPs as siderophore molecules play a major role in transporting iron to bacteria. Blocking iron uptake system by antibodies causes death of bacterial cells. The vaccine can also be useful to protect humans against salmonellosis, which causes high rates of illness and death annually, by reducing shedding of Salmonella in the feces of cattle. Though other researchers have evaluated efficacy and immune response of this Salmonella SRP vaccine, genes …
On The Relationship Between Meaning And Prejudice: Examining Self-Transcendence And Value-Behavior Consistency In A Sample Of College Students, Ivonne Andrea Florez
On The Relationship Between Meaning And Prejudice: Examining Self-Transcendence And Value-Behavior Consistency In A Sample Of College Students, Ivonne Andrea Florez
Electronic Theses and Dissertations
The present study examined whether the value of self-transcendence and the degree to which individuals report behaving consistently with their values (value-behavior consistency) impact the association of meaning and racial prejudice against White and Black individuals. The study was conducted with a college population from a university located in the southern United States. The final sample was composed of 362 people, 281 females and 81 males, with a majority of participants self-identifying as White (73.8%). To assess meaning, the Purpose in Life test – Short Form (PIL-SF) and the Meaning in Life Questionnaire Presence subscale (MLQ-Presence) were administered. Social judgment …
Conditions Responsible For The Success Of Carnivorous Plants In Nutrient-Poor Wetlands, Matthew John Abbott
Conditions Responsible For The Success Of Carnivorous Plants In Nutrient-Poor Wetlands, Matthew John Abbott
Electronic Theses and Dissertations
Despite the vast array of past research focused on carnivorous plants, few studies have investigated the ecological interactions between carnivorous and non-carnivorous plant species. I addressed the following three questions: (1) does niche complementarity promote coexistence between fire-adapted carnivorous and non-carnivorous species? (2) do carnivorous plants rely on both leaf traps and arbuscular mycorrhizal fungi to access different nutrients that are in high demand after fire in nutrient poor bogs? (3) why are carnivorous plants largely absent from nutrient-rich wetlands? I addressed the first question by examining the three-way interacting effects of fire, prey-derived nutrient availability, and root competition from …
A Probabilistic Approach To Multiple-Instance Learning, Silu Zhang
A Probabilistic Approach To Multiple-Instance Learning, Silu Zhang
Electronic Theses and Dissertations
This study introduced a probabilistic approach to the multiple-instance learning (mil) problem. In particular, two bayes classication algorithms were proposed where posterior probabilities were estimated under dierent assumptions. The rst algorithm, named instance-vote, assumes that the probability of a bag being positive or negative depends upon the percentage of its instances being positive or negative. This probability is estimated using a k-nn classication of instances. In the second approach, embedded kernel density estimation (ekde), bags are represented in an instance induced (very high dimensional) space. A parametric stochastic neighbor embedding method is applied to learn a mapping that projects bags …
Co2 Adsorption On Volcanic Ash: Net Contribution Of Volcanic Eruptions To The Global Carbon Cycle, Lee New
Co2 Adsorption On Volcanic Ash: Net Contribution Of Volcanic Eruptions To The Global Carbon Cycle, Lee New
Electronic Theses and Dissertations
Adsorption of co2 on mineral surfaces accounts for a small percentage of the terrestrial co2 sink. Volcanic ash is virtually free of co2 when erupted and has a high surface area resulting in a high capacity for co2 adsorption. Volcanism is commonly assumed to be only a source of co2, but pyroclastic eruptions can also potentially serve as a sink. Adsorption was investigated for 6 volcanic ash samples of andesitic composition from four volcanoes: Okmok, Redoubt, Spurr, and Tungurahua. The eruption of volcano redoubt released 0.75 x 109 metric tons of co2 and 55 x 109 kg of ash throughout …
The Impact Of Simulated Microgravity On The Growth Of The Model Legume Plant Medicago Truncatula, Gemma Elizabeth Lionheart
The Impact Of Simulated Microgravity On The Growth Of The Model Legume Plant Medicago Truncatula, Gemma Elizabeth Lionheart
Electronic Theses and Dissertations
Simulated microgravity has been a useful tool to help understand plant development in altered gravity conditions. Thirty-one genotypes of the legume plant Medicago truncatula were grown in either simulated microgravity on a rotating clinostat, or a static, vertical environment. Twenty morphological features were measured and compared between these two gravity treatments. Within-species genotypic variation was a significant predictor of the phenotypic response to gravity treatment in 100% of the measured morphological and growth features. In addition, there was a genotype–environment interaction (G×E) for 45% of the response variables, including shoot relative growth rate (p < 0.0005), median number of roots (p ∼ 0.02), and root dry mass (p < 0.005). These findings are discussed in the context of improving future studies in plants space biology by controlling for genotypic differences, and by connecting traits to their underlying genetic causes by using genome-wide association (GWA) mapping. In the long-term, manipulation of genotype effects, in combination with M. truncatula’s symbiotic relationships with rhizobacteria and arbuscular mycorrhizal fungi, will be important for optimizing legumes for cultivation on long-term space missions.
The Reptile Gut Microbiome: Its Role In Host Evolution And Community Assembly, Timothy John Colston
The Reptile Gut Microbiome: Its Role In Host Evolution And Community Assembly, Timothy John Colston
Electronic Theses and Dissertations
I characterize the endogenous (gut) microbiome of Squamate reptiles, with a particular focus on the suborder Serpentes, and investigate the influence of the microbiome on host evolution and community assembly using samples I collected across three continents in the New and Old World. I developed novel methods for sampling the microbiomes of reptiles and summarized the current literature on non-mammalian gut microbiomes. In addition to establishing a standardized method of collecting and characterizing reptile microbiomes I made novel contributions to the future direction of the burgeoning field of host-associated microbiome research. Through persistent and rigorous fieldwork I amassed the largest …
Risk, Reward, And The Role Of Habitat Selection On Community Dynamics In Temporary Ponds, Matthew Robert Pintar
Risk, Reward, And The Role Of Habitat Selection On Community Dynamics In Temporary Ponds, Matthew Robert Pintar
Electronic Theses and Dissertations
The processes that generate patterns of species diversity within and among habitat patches are a fundamental topic of interest in ecology. Traditionally, there was a focus on post-colonization effects such as predation, however, pre-colonization processes, such as habitat selection, are equally important determinants of community structure. In freshwater systems, the lethal effects of dominant predators (particularly fish) are well established, while the transition from permanent to temporary ponds is a defining characteristic. This transition produces distinct communities characterized by organisms with complex life cycles and plastic developmental strategies. This means that many organisms occupying habitat patches arrive there by the …
Exploring The Relationship Among Minority Stress, Internalized Homophobia, Mental Health Concerns, Social Support, And Relationship Satisfaction In Female Same-Sex Couples, Kassie Rose Terrell
Exploring The Relationship Among Minority Stress, Internalized Homophobia, Mental Health Concerns, Social Support, And Relationship Satisfaction In Female Same-Sex Couples, Kassie Rose Terrell
Electronic Theses and Dissertations
No abstract provided.
The Relationship Of Principal Gender And Teacher Perceptions Of School Climate On Suspension And Expulsion Rates Of High School Students, Roderick Lydell Payne
The Relationship Of Principal Gender And Teacher Perceptions Of School Climate On Suspension And Expulsion Rates Of High School Students, Roderick Lydell Payne
Electronic Theses and Dissertations
The purpose of this explanatory quantitative study was to determine if relationships exist between principal gender, teachers’ perceptions of the school climate, and the suspension rates of high school students in a large consolidated district in the mid-South. The research analyzed a single academic year, 2015–16, within the subject district. The study sample consisted of 20 high schools with similar characteristics. Ten of the high schools have a female principal and 10 of the high schools have a male principal. The independent variables of the study were principal gender and teachers’ perceptions of the school climate; dependent variables were the …
Southern Discomfort: Performing Femininity In The Deep South, Rachel Whitney Turnipseed
Southern Discomfort: Performing Femininity In The Deep South, Rachel Whitney Turnipseed
Electronic Theses and Dissertations
The “performance” of gender is variable and multifarious, fabricated in reaction to audience, mood, and previous experiences. Starting in childhood, people “police” our gender performances, and profoundly shape our self-presentation and sense of personal identity. We gradually learn to self-edit our performances of gender, after countless critiques by others, which often negatively impact our body image as they preserve “norms,” marginalizing anyone who does not conform. The mixed-media installation, Southern Discomfort: Performing Femininity in the Deep South, examines this process and its impact on young girls. The young, blonde, female figure who appears multiple times in my installation reveal girls …