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Decoding Heterogeneous Big Data In An Integrative Way, Xia Zhang Jan 2013

Decoding Heterogeneous Big Data In An Integrative Way, Xia Zhang

Graduate Theses and Dissertations

Biotechnologies in post-genomic era, especially those that generate data in high-throughput, bring opportunities and challenges that are never faced before. And one of them is how to decode big heterogeneous data for clues that are useful for biological questions. With the exponential growth of a variety of data, comes with more and more applications of systematic approaches that investigate biological questions in an integrative way. Systematic approaches inherently require integration of heterogeneous information, which is urgently calling for a lot more efforts.

In this thesis, the effort is mainly devoted to the development of methods and tools that help to ...


Phylogeography Of Eastern Leatherwood (Dirca Palustris L.) Resolved By Chloroplast Sequencing And Microsatellite Genotyping, Bryan James Peterson Jan 2013

Phylogeography Of Eastern Leatherwood (Dirca Palustris L.) Resolved By Chloroplast Sequencing And Microsatellite Genotyping, Bryan James Peterson

Graduate Theses and Dissertations

The broad distribution of eastern leatherwood (Dirca palustris L.), from Florida to Canada, contrasted with its patchy restriction to rich, mesic forests and the paucity of vectors for dispersal of its seeds, represents a classic example of Reid's paradox of plant migration. It long has been presumed that temperate forest species of eastern North America persisted in southern glacial refugia near the Gulf Coast, after which many dispersed nearly 2000 km to contemporary northern range limits. The rates of migration necessary to account for present distributions exceed those suggested by contemporary observations of seed dispersal. I used ecological niche ...


Inflorescence Branching In Maize: A Quantitative Genetics Approach To Identifying Key Players In The Inflorescence Development Pathway, Rebecca Lynne Weeks Jan 2013

Inflorescence Branching In Maize: A Quantitative Genetics Approach To Identifying Key Players In The Inflorescence Development Pathway, Rebecca Lynne Weeks

Graduate Theses and Dissertations

Inflorescence branch number in maize and other cereal crops has long been recognized as an important factor impacting grain yield. In maize, inflorescence architecture is determined by the collective actions of many genes. Among these, the ramosa mutants play an important role in regulating branch number by imposing short-branch identity on lateral meristems of the inflorescence. In addition, a number of QTL have been identified which alter the branching of male inflorescences, however few of these QTL co-localize with known inflorescence branching genes, indicating that some components of this pathway have yet to be discovered. We conducted a suppressor/enhancer ...


The Genetic Basis Of Host Response To Experimental Infection With The Porcine Reproductive And Respiratory Syndrome Virus In Pigs, Nicholas James Boddicker Jan 2013

The Genetic Basis Of Host Response To Experimental Infection With The Porcine Reproductive And Respiratory Syndrome Virus In Pigs, Nicholas James Boddicker

Graduate Theses and Dissertations

Porcine reproductive and respiratory syndrome (PRRS) is the most economically important disease in the swine industry. The effects of PRRS are two fold in that it causes reproductive problems in breeding females and respiratory problems in growing animals. Vaccination has generally not been effective in the prevention of PRRS, partially due to the rapid mutation rate and evolution of the virus. The overall objective of this thesis was to discover the genetic basis of host response to PRRS virus (PRRSV) using data from the PRRS Host Genetics Consortium PRRS-CAP project by conducting genome-wide association analyses and estimating genetic parameters. Eight ...


Investigation Of The Arabidopsis Nonhost Resistance Mechanism Against The Soybean Pathogen, Phytophthora Sojae, Rishi Sumit Jan 2013

Investigation Of The Arabidopsis Nonhost Resistance Mechanism Against The Soybean Pathogen, Phytophthora Sojae, Rishi Sumit

Graduate Theses and Dissertations

Nonhost resistance (NHR) provides immunity to all members of a plant species against all isolates of a microorganism that is pathogenic to other plant species. Three Arabidopsis thaliana PEN (penetration deficient) genes, PEN1, 2 and 3 have been shown to provide prehaustorial NHR against the barley pathogen Blumeria graminis f. sp. hordei. Arabidopsis pen1-1 mutant is penetrated by the hemibiotrophic oomycete pathogen, Phytophthora sojae that causes root and stem rot disease in soybean. The P. sojae susceptible (pss) 1 mutant is infected by both P. sojae and the hemibiotrophic fungal pathogen, Fusarium virguliforme that causes sudden death syndrome in soybean ...


Identification And Characterization Of Effectors Secreted From Sedentary Endoparasitic Phytonematodes, William Brock Rutter Jan 2013

Identification And Characterization Of Effectors Secreted From Sedentary Endoparasitic Phytonematodes, William Brock Rutter

Graduate Theses and Dissertations

Sedentary endoparasitic phytonematodes are a group of taxa comprised of cyst nematodes (Heterodera and Globodera spp.) and root-knot nematodes (Meloidogyne spp. ), which are some of the most economically important crop pathogens on earth. These pests infect plant roots by creating elaborate feeding sites around the vasculature, which diverts nutrients away from the plant to feed the nematode and causes yield reduction in the plant. The nematodes create their feeding sites by delivering effector proteins into plant tissues. Effectors interact with plant components to modify development, metabolism, and defense pathways within plant cells, ultimately forming and maintaining the feeding site within ...


Evolutionary Proteomics Of Cotton, Guanjing Hu Jan 2013

Evolutionary Proteomics Of Cotton, Guanjing Hu

Graduate Theses and Dissertations

Polyploidy has played a spectacular role in plant evolution. Through allopolyploidization, two or more divergent genomes are combined into a common nucleus, which is often followed by rapid as well as longer-term genomic and epigenetic responses. However, since mRNA abundance and protein amounts are poorly related, still little is known how the genomic changes associate with or affect the actual plant function and adaption. Within this context, this dissertation specifically explores the evolutionary history of cotton species on the proteomic level, involving natural polyploidization and human-mediated cotton fiber selection.

In the work presented here, cotton proteomes of mature seeds and ...


On Inferring And Interpreting Genetic Population Structure - Applications To Conservation, And The Estimation Of Pairwise Genetic Relatedness, Arun Sethuraman Jan 2013

On Inferring And Interpreting Genetic Population Structure - Applications To Conservation, And The Estimation Of Pairwise Genetic Relatedness, Arun Sethuraman

Graduate Theses and Dissertations

The presence of population structure is ubiquitous in most wild populations of species. Detecting genetic population structure and understanding its consequences for the evolutionary trajectories of species has shaped a lot of our understanding of the process of evolution. This delineation of subdivision within a population plays an important role in several allied fields, including conservation genetics, association studies, phylogeography, and quantitative genetics. This dissertation addresses methods to infer and interpret subpopulation structure. In this regards, I discuss the standing motivation for developing new analytic tools, a classic population

genetics study of the imperiled freshwater turtle, Emys blandingii, the development ...


The Effects Of Biotic And Abiotic Stressors On Gene Expression In Chickens, Derrick Jamaal Coble Jan 2013

The Effects Of Biotic And Abiotic Stressors On Gene Expression In Chickens, Derrick Jamaal Coble

Graduate Theses and Dissertations

Poultry provides the largest livestock source of protein for human consumption. Due to this widespread consumption of poultry products, biotic and abiotic stressors of chickens can have negative impacts on the nutrition of humans, as well as the health and productivity of chickens. Salmonella-infected poultry products present a food safety threat to human consumers, while the exposure of poultry to hot environments raises animal welfare issues. Understanding the effects of Salmonella infection and heat stress on immunological and metabolic networks in chickens may help to develop strategies to circumvent these problems. Therefore, gene expression profiles of Salmonella-infected and ...


Functional And Mutational Analysis Of Human Recq-Like Dna Helicases In Saccharomyces Cerevisiae, Hamed Mirzaei-Souderjani Jan 2013

Functional And Mutational Analysis Of Human Recq-Like Dna Helicases In Saccharomyces Cerevisiae, Hamed Mirzaei-Souderjani

Graduate Theses and Dissertations

RecQ-like proteins are a family of DNA helicases that are evolutionary conserved from prokaryotes to eukaryotes. A large amount of experimental evidence suggests these proteins have a major role in the maintenance of genome stability. In humans five RecQ like helicase have been identified (RecQL1, BLM, WRN, RecQL4, and RecQL5), three of which are associated with rare genetic disorders with sever chromosomal and developmental abnormalities, and an elevated predisposition to cancer. Among the disease associated RecQ-like helicases, BLM and WRN have been subject to extensive research, while our collective knowledge about the function of RecQL4 is still very limited. Similarly ...


Sirt1 Regulation Of The Heat Shock Response In An Hsf1-Dependent Manner And The Impact Of Caloric Restriction, Rachel Rene Raynes Jan 2013

Sirt1 Regulation Of The Heat Shock Response In An Hsf1-Dependent Manner And The Impact Of Caloric Restriction, Rachel Rene Raynes

Graduate Theses and Dissertations

The heat shock response (HSR) is the cell's molecular reaction to protein damaging stress and is critical in the management of denatured proteins. Activation of HSF1, the master transcriptional regulator of the HSR, results in the induction of molecular chaperones called heat shock proteins (HSPs). Transcription of hsp genes is promoted by the hyperphosphorylation of HSF1, while the attenuation of the HSR is regulated by a dual mechanism involving negative feedback inhibition from HSPs and acetylation at a critical lysine residue within the DNA binding domain of HSF1, which results in a loss of affinity for DNA. SIRT1 is ...


The Effects Of Heat Stress In Redox Balance And Inflammatory Signaling In Porcine Skeletal Muscle, Sandra Isabel Rosado Montilla Jan 2013

The Effects Of Heat Stress In Redox Balance And Inflammatory Signaling In Porcine Skeletal Muscle, Sandra Isabel Rosado Montilla

Graduate Theses and Dissertations

Heat stress (HS) is a major concern for human health as well as for the swine industry. In 2012, HS resulted in the largest number of weather related human fatalities in the US. Animal production is also compromised as HS leads to poor sow performance, decreased carcass value and increased veterinary costs. However, the molecular effects of HS on skeletal muscle are still unclear. This study aimed to determine the extent to which HS disrupted redox balance and initiated an inflammatory response in oxidative and glycolytic porcine skeletal muscle. Moreover, we quantified the contribution of reduced feed intake to the ...


Determination And Quantification Of Surface Lipid Metabolites In Maize Silks: A Pathway Model For Surface Lipid Biosynthesis Based On Simultaneous Profiling Of Polar And Non-Polar Metabolites, Layton Andrew Peddicord Jan 2013

Determination And Quantification Of Surface Lipid Metabolites In Maize Silks: A Pathway Model For Surface Lipid Biosynthesis Based On Simultaneous Profiling Of Polar And Non-Polar Metabolites, Layton Andrew Peddicord

Graduate Theses and Dissertations

The elongated stigmas in maize (i.e. silks) are a vital organ for the reproductive success of a major U.S. agricultural crop. These silks possess an extractible coat of surface lipids that is predominantly composed of a complex array of hydrocarbons that function to protect the silks against abiotic and biotic stresses. While hydrocarbons are most likely produced from the conversion of fatty acids, the exact biochemical mechanisms for their synthesis remain unknown. Our team is leveraging genetic variation and morphological gradients during silk development to dissect the metabolic network responsible for surface lipid accumulation.

These metabolomic efforts require ...


Mammalian Orthoreovirus Localization To Stress Granules And Escape From Translation Shutoff, Kate Carroll Jan 2013

Mammalian Orthoreovirus Localization To Stress Granules And Escape From Translation Shutoff, Kate Carroll

Graduate Theses and Dissertations

A clinically benign member of the dsRNA virus family Reoviridae, Mammalian Orthoreovirus (MRV) serves as a model system to determine the nuances of replication within the family. MRV is composed of ten dsRNA gene segments that are contained in a double capsid structure and encode 12-13 viral proteins. It has previously been shown that at early times in MRV infection, granules form throughout the cytoplasm of the host cells that have been termed stress granules (SGs). MRV induces the formation of these SGs by activation of the kinase Protein Kinase R (PKR) which subsequently phosphorylates the initiation factor eIF2α to ...


Density Response Of Maize Canopy Architecture In Adapted And Unadapted Synthetic Populations, Naser Bader Alkhalifah Jan 2013

Density Response Of Maize Canopy Architecture In Adapted And Unadapted Synthetic Populations, Naser Bader Alkhalifah

Graduate Theses and Dissertations

ABSTRACT

Since the 1950's, the average maize grain yield, on a per unit area basis, has risen exponentially and without a pause. Associated with this increase have been changes in shoot morphology which permit more light penetration into the canopy. Changes in plant traits including plant height, leaf number, individual leaf area, vertical leaf angle, tassel size and weight, and leaf area density distribution along the main stem have been reported in the literature; however, the response of canopy components to changes in plant density has not been examined in closed populations and at today's densities. The objective ...


Hybrid Breeding In Perennial Grasses Based On Self-Incompatibility And Self-Fertility, Andrea Sofia Arias Aguirre Jan 2013

Hybrid Breeding In Perennial Grasses Based On Self-Incompatibility And Self-Fertility, Andrea Sofia Arias Aguirre

Graduate Theses and Dissertations

For a long time, petroleum-based fuels have been used to provide energy, but limited supplies along with environmental effects of fossil fuels created the need of alternative and clean energy sources. Grasses in general have a low lignin content compared to woody species which is desirable for ethanol production. Furthermore, other features such as: low water and nutrient requirements, and a high rate of carbon fixation that make grasses desirable for biomass production. Perennial grasses have also environmental advantages such as reduced soil organic matter and tillage requirements compared with annual species. Perennial ryegrass has been increasingly used in Europe ...


Wax Ester Biosynthetic Pathway, Daolin Cheng Jan 2013

Wax Ester Biosynthetic Pathway, Daolin Cheng

Graduate Theses and Dissertations

Wax esters occur widely among bacteria, plants and mammals. Due to their special properties, they have many applications such as lubricants, cosmetics, pharmaceutical products, ink, polishes and candles. They are also considered as potential biofuels and biolubricants in the future. Wax ester producing enzymes synthesize wax esters from alcohols and fatty acyl coenzyme A thioesters. There are three gene families encoding enzymes capable of synthesizing wax esters. Two of them exist in plans; the jojoba-like wax synthase (WS), and the bifunctional wax synthase/diacylglycerol acyl transferase (WS/DGAT). We investigated the phylogenetic relationships among and between WS and WS/DGAT ...


Candidate Gene Based Association Study For Nitrogen Use Efficiency And Associated Traits In Maize, Bharath Kumar Thamasandra Narayana Jan 2013

Candidate Gene Based Association Study For Nitrogen Use Efficiency And Associated Traits In Maize, Bharath Kumar Thamasandra Narayana

Graduate Theses and Dissertations

Nitrogen (N) is a major macronutrient used in cereal production that stimulates plant growth and development. Demand for N fertilizer has been growing steadily at an annual growth rate of 1.8 percent due to the continuous increase in the cereal growing areas (mainly maize), and N is needed to maximize yield potential of agricultural crops. It has been estimated that N fertilizer used by cereals is only 33%. The rest of the applied N fertilizer is lost in the combination of surface runoff, gaseous release from soil, leaching and de-nitrification processes. In the future, for a sustainable crop production ...


Molecular Evolution Of The P53 Network In Reptiles, Shikha Parsai Jan 2013

Molecular Evolution Of The P53 Network In Reptiles, Shikha Parsai

Graduate Theses and Dissertations

The p53 molecular network is a master regulator of how cells respond to DNA-damaging stresses. Its primary function is to respond to DNA-damage by several options: apoptosis, cellular senescence, and temporary arrest of cellular growth for DNA repair. The p53 network's tight regulation of cellular fate after damage has obvious beneficial effects of preventing tumorigenesis, and possible costly effects later in life such as the accumulation of damaged cells and other aging phenotypes. Because many reptile species have evolved unique organismal stress responses, we tested the related hypothesis that the evolutionary dynamics of, and mode of selection on, genes ...


Association Mapping Analysis For Brassinosteroid Candidate Genes And Plant Architecture In A Diverse Sorghum Bicolor Panel, Maria Betsabe Mantilla Perez Jan 2013

Association Mapping Analysis For Brassinosteroid Candidate Genes And Plant Architecture In A Diverse Sorghum Bicolor Panel, Maria Betsabe Mantilla Perez

Graduate Theses and Dissertations

Sorghum bicolor (L) Moench is a cultivated and self-pollinated species used traditionally for human consumption, livestock feed and forage production. Recently, sorghum has received attention as a bioenergy crop because of its high water use efficiency, yield biomass potential and biomass composition. To develop superior sorghum inbred lines for bioenergy production, it would be beneficial to understand the genetic mechanisms controlling plant architecture traits. Sorghum presents a remarkable diversity in the species bicolor that can be exploited to identify new genes associated with those traits of interest. Brassinosteroids (BR) are steroid hormones that control different aspects of plant growth and ...


Genomic And Genetic Studies Of Environmental Control Of Brachypodium Growth And Development, Ying Feng Jan 2013

Genomic And Genetic Studies Of Environmental Control Of Brachypodium Growth And Development, Ying Feng

Graduate Theses and Dissertations

Brachypodium distachyon has recently been established as a model for cereals and temperate grasses because of its sequenced small genome (~270M), a small stature, short life cycle, self-fertility, an efficient transformation system and particularly its diverse ecotypes. Determination of the function for each gene in the Brachypodium genome is urgently needed for utilization of this species. In this study we (1) analyze the expression of each gene involved in vernalization pathway in Brachypodium and the correlation of vernalization requirement with freezing tolerance, (2) develop a novel high-throughput RNAi method, Phi29-Amplified RNAi Construct (PARC), to construct a cold-specific RNA interference library ...


Novel Mechanisms Involved With Lipid Metabolism In Adipose Tissue Of Dairy Cows, Dawn Koltes Jan 2013

Novel Mechanisms Involved With Lipid Metabolism In Adipose Tissue Of Dairy Cows, Dawn Koltes

Graduate Theses and Dissertations

Proper lipid metabolism is essential to the maintenance of milk production and fitness in the modern dairy cow. Little is known about the regulation of lipid metabolism in adipose tissue in dairy cattle, including the roles of adipokines and lipid droplet associated proteins. Therefore, the objectives of this study were to characterized changes in transcript abundances of adipokines during three different energy altering models, and lipid droplet associated proteins throughout the transition period and with leptin induced lipolysis. Transcript abundances of leptin decreased during feed restriction, while angiopoietin like protein 4 (ANGPTL4) increased during early lactation, feed restriction, and following ...


Controlling Biomass Properties For Optimizing Fast Pyrolysis Products, Brandon Jeffrey Jan 2013

Controlling Biomass Properties For Optimizing Fast Pyrolysis Products, Brandon Jeffrey

Graduate Theses and Dissertations

The energy future of the United States is likely to include a large number of traditional and alternative energy sources and technologies. Fast pyrolysis has been identified as one of the alternative energy conversion processes that could play a role in this energy future. Fast pyrolysis produces solid (biochar), liquid (bio-oil), and gaseous products (syngas). Bio-oil is the main component (up to 80%) and has a number of potentially useful applications. Bio-oil composition is complex and is related to cell wall composition, as compounds in the bio-oil derive from the individual cell wall components cellulose, hemicelluloses, and lignin.

While a ...


The Turnip Mosaic Virus And Its Effects On Arabidopsis Thaliana Gene Expression, Brian Anthony Campbell Jan 2013

The Turnip Mosaic Virus And Its Effects On Arabidopsis Thaliana Gene Expression, Brian Anthony Campbell

Graduate Theses and Dissertations

Utilizing natural and engineered viruses is an accepted approach to studying plant-virus interactions as it relates to symptomology. The majority of the research topics were generated by deciphering where short-comings in the literature existed. Specifically, how Turnip mosaic virus (TuMV) helper component protease (HC-Pro) small RNA (sRNA) binding affinity affects expression of genes correlated with disease phenotypes and studying debilitated viruses in a variety of RNA silencing deficient Arabidopsis thaliana plants. Taken as a whole, the research presented addressed the susceptibility of A. thaliana to TuMV.

The first study was conducted to monitor genes implicated in symptomology in various RNA ...


Gilt Growth, Compositional, And Structural Soundness Associations With Sow Productive Lifetime, Marja Tellervo Nikkilae Jan 2013

Gilt Growth, Compositional, And Structural Soundness Associations With Sow Productive Lifetime, Marja Tellervo Nikkilae

Graduate Theses and Dissertations

High sow removal rates pose a global problem and have a negative impact on herd productivity, producer profitability, and consumer acceptability. Worldwide, the main reasons for early culling are reproductive failure and leg/locomotion problems. Hence, this dissertation aimed to identify gilt composition and conformation traits associated with good sow lifetime performance. The specific objectives were: 1) to estimate genetic parameters for gilt growth, compositional, and structural soundness traits in commercial maternal lines, 2) to estimate genetic associations for growth, compositional, and structural soundness traits with sow longevity and lifetime reproduction, and 3) to investigate growth, compositional, and structural soundness ...


Effects Of Diets Containing Digestion-Resistant Starch On Wnt Pathway Control Of Proliferation And Differentiation Of The Colorectal Mucosa, Nicole Cray Jan 2013

Effects Of Diets Containing Digestion-Resistant Starch On Wnt Pathway Control Of Proliferation And Differentiation Of The Colorectal Mucosa, Nicole Cray

Graduate Theses and Dissertations

Resistant starch (RS) is not digested in the small intestine and is available for fermentation by the colonic microbiota, producing metabolites including short chain fatty acids (SCFAs). We hypothesized that diets containing resistant starch, serving as a prebiotic, will have inhibitory effects, mediated through the products of microbial fermentation, on the canonical Wnt signaling pathway. To test this hypothesis, we examined the molecular and morphologic effects of diets containing resistant starches on the early stage of colorectal carcinogenesis in azoxymethane-induced rat and mouse models. The first study examined the effects of diets containing naturally occurring resistant starch from Latin American ...