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A Bioinformatics Methodology For The Annotation And Analysis Of Sperm Chromatin Remodeling Proteins In Sequenced Drosophila Species, Zain A. Alvi

Seton Hall University Dissertations and Theses (ETDs)

Spermatogenesis is the process by which mature functional spermatozoa are formed, and is initiated in the stem cell niche of the testes. During the post-meiotic stage of spermatogenesis, spermiogenesis, transition proteins facilitate the transformation of chromatin from a histone-based nucleosome structure to a protamine-based nucleosome structure. This study is aimed at analyzing genomic, transcript, and protein sequences of transition proteins in 13 sequenced Drosophila species. The Drosophila melanogaster spermatid specific transition protein-like protein (Tpl^94D) was used as the reference sequence in this study. An extensive bioinformatics approach was employed in establishing the Tpl^94D orthologs. We identified …

Global Gene Expression Profiling Of Healthy Human Brain And Its Application In Studying Neurological Disorders, Simarjeet K. Negi

Theses & Dissertations

The human brain is the most complex structure known to mankind and one of the greatest challenges in modern biology is to understand how it is built and organized. The power of the brain arises from its variety of cells and structures, and ultimately where and when different genes are switched on and off throughout the brain tissue. In other words, brain function depends on the precise regulation of gene expression in its sub-anatomical structures. But, our understanding of the complexity and dynamics of the transcriptome of the human brain is still incomplete. To fill in the need, we designed …

Gene Expression Profiling Of Wood Decay Fungus Fibroporia Radiculosa Grown On Different Organic And Copper Based Preservatives, Ayfer Akgul

Theses and Dissertations

Copper tolerant brown rot fungi are able to depolymerize the structure of wood treated with copper or organic wood preservatives. This research used quantitative polymerase chain reaction (qRT-PCR) combined with RNA-seq to explore what genes of the brown-rot fungus, Fibroporia radiculosa, are expressed when the fungus is overcoming the wood preservatives and decaying the wood. The preliminary study of ACQ-treated wood indicated that the hydrogen peroxide needed for wood decay to proceed may come from AAOX (aryl alcohol oxidase), with oxalate regulation by ODC2 (oxalate decarboxylase), and copper regulation by COP (copper resistance P-type ATPase pump). The principal study measured …

Spatial Crowding And Confinement Effects On Bursty Gene Expression, Charles Wei-Shing Chin

Doctoral Dissertations

Synthetic biology and genetic engineering are valuable tools in the development of new, sustainable energy generation technologies. The characterization of stochastic gene expression is vital to the efficient application of genetic engineering techniques. Transcriptional bursting, in which periods of high expression are punctuated by periods of no expression, is extensively observed in gene expression. While various molecular mechanisms have been hypothesized to be responsible for transcriptional bursting, spatial considerations have largely been neglected. This work uses computational modeling to examine in detail the influence of spatial factors such as macromolecular crowding and confinement on gene expression.

In the first part …

Improving And Elucidating Factors Regulating Black Walnut (Juglans Nigra L.) Clonal Propagation, Micah E. Stevens

Open Access Dissertations

Black walnut (Juglans nigra L.) is a fine hardwood tree species native to the central hardwood region of the United States. High-quality black walnut timber is highly desirable. Traded in both regional and global markets, it has been used for veneer, and the manufacture of high-end products such as cabinets, furniture, and gunstocks. As a result of its high economic value, black walnut has been commercially cultivated for many years, and breeding programs have generated superior timber genotypes with improved marketable traits. Once elite genotypes were developed, it was quickly recognized that black walnut was recalcitrant to clonal propagation …

Role Of Lipid Mediators In P2x7 Signaling In Osteoblasts, Erin Eyer

Electronic Thesis and Dissertation Repository

P2X7 is a cell-surface nucleotide receptor that plays a critical role in skeletal mechanotransduction; however, the signaling pathways mediating these effects are poorly understood. Previous studies showed that the nucleotide analog benzoylbenzoyl-ATP induces anabolic gene expression in osteoblastic cells. Our first objective was to determine whether this effect was mediated by P2X7. Inhibition of anabolic gene expression by a P2X7-specific antagonist established involvement of this receptor. Our second objective was to investigate the role of lipid mediators, lysophosphatidic acid (LPA) and prostaglandin (PG), both of which are produced in response to P2X7 activation. The effect of P2X7 on expression of …

Role Of Hnrnp A1 In The Regulation Of Hdm2 Gene Expression, Heriberto Moran

Dissertations, Theses, and Capstone Projects

hnRNP A1 is one of the most abundant and ubiquitously expressed member of hnRNPs (Heterogenous Nuclear Ribonucleoproteins) family of proteins that play multiple roles in gene expression by participating in major steps in the processing of nascent RNA transcripts 1. It is involved in mRNA biogenesis mechanisms such as the transcription, splicing, stability, export and translation of cellular and viral transcripts. The functions of hnRNP A1 extend to the processing of microRNAs, telomere maintenance and DNA repair 1. Our previous studies have shown that hnRNPA1 had reduced protein level and increased cytoplasmic accumulation in senescent human diploid fibroblasts 2,10. Our …

Anthropogenic Pollution Effects On Mitochondrial Energy Metabolism, Gene Expression, And Genotypes Of Natural Fundulus Heteroclitus Populations, Xiao Du

Open Access Dissertations

Energy balance is a major concern for organisms developing stress tolerance, as combating pollutant toxicity is usually metabolically costly. Mitochondria, which are responsible for cellular energy production, are a potential target of pollutant toxicity. Thus, understanding mitochondrial energy metabolism will shed light on pollution adaptation. This research examines the oxidative phosphorylation (OxPhos) modulations due to chronic pollution exposure, how gene expression changes covary with OxPhos changes, and genotypic changes potentially underlying these phenotypic changes in response to pollution. Mitochondrial energy metabolism was investigated by quantifying hepatocyte OxPhos function in two independent, polluted F. heteroclitus populations from Elizabeth River, VA and …

Novirhabdovirus Infection In Wild-Type And Rag1 Mutant Zebrafish Suggests Roles Of Lymphocytes In Resistance, Du Ngoc Nguyen

Theses and Dissertations

Disease development of wild-type and Rag1 mutant zebrafish was evaluated after challenge with Snakehead Rhabdovirus (SHRV), a novirhabdovirus. Rag1 mutants lack T and B lymphocytes and thus lack lymphocyte-based acquired immunity. Wild-type zebrafish became more disease resistant as they aged (4 months and older) and at an elevated temperature (28°C) but mutants remained sensitive at all ages and temperatures tested. Quantitative reverse transcription polymerase chain reaction (RT qPCR) demonstrated that interferon gamma and MxA expression significantly increased in both types of fish at 2 days post-infection with subsequent dwindling of expression. The high interferon gamma expression suggests activation of natural …

Evaluation Of The Water Stress-Inducible Promoter Wsi18 In The Model Monocot Brachypodium Distachyon, Patrick D. Langille

Electronic Thesis and Dissertation Repository

Water deficit-inducible promoters that function in multiple species are valuable components for engineering stress-tolerant crops. Wsi18 is a water deficit-inducible promoter native to Oryza sativa. In this study, Brachypodium distachyon (B. distachyon) was used to determine if Wsi18 retained its water deficit-inducible characteristics in another monocot. Transgenic B. distachyon plants, in which the Wsi18 promoter drove the expression of the uidA reporter gene, were developed and exposed to osmotic stress generated by mannitol, salt stress conditions, and the water deficit-signaling phytohormone abscisic acid (ABA). GUS histochemical assays demonstrated increased uidA expression in the leaves and stem of …

Phenotypic And Gene Expression Analysis Of Diverse Rice Genotypes In Response To Drought, Miranti Rahmaningsih

Graduate Theses and Dissertations

Drought is one of the most limiting factors for rice (Oryza sativa L.) growth and development with vegetative and reproductive stages the most sensitive and distinct phases. During the vegetative stage, drought can cause reduction in growth and biomass accumulation. Moreover, water stress at reproductive stage can reduce yield significantly. Plants are protected against drought by three different mechanisms: drought avoidance, drought tolerance, and drought escape. An integrated approach combining physiology, breeding, and genomics could be an effective way to characterize and mitigate this problem. The objectives of this research were to (1) screen a diverse set of rice genotypes …

The Effects Of 4-Nonylphenol On The Immune Response Of The Pacific Oyster, Crassostrea Gigas, Following Bacterial Infection (Vibrio Campbellii), Courtney Hart

Master's Theses

Endocrine disrupting chemicals (EDCs) are compounds that can interfere with hormone signaling pathways and are now recognized as pervasive in estuarine and marine waters. One prevalent EDC in California’s coastal waters is the xenoestrogen 4-nonylphenol (4-NP), which has been shown to impair reproduction, development, growth, and in some cases immune function of marine invertebrates. To further investigate effects of 4-NP on marine invertebrate immune function we measured total hemocyte counts (THC), relative transcript abundance of immune-relevant genes, and lysozyme activity in Pacific oysters (Crassostrea gigas) following bacterial infection. To quantify these effects we exposed oysters to dissolved phase …

Molecular Response Of Spartina Alterniflora To The Deepwater Horizon Oil Spill, Mariano Alvarez

USF Tampa Graduate Theses and Dissertations

Although the “genome as a blueprint” metaphor has been pervasive in biology, recent advances in molecular biology have revealed a complex network of regulatory machinery that dynamically regulated molecular processes in response to environmental conditions. However, these patterns, as well as the evolutionary processes that underlie them, remain understudied in natural conditions. In 2010, the Deepwater Horizon oil spill released an estimated 4.9 million barrels of oil into the Gulf of Mexico, making landfall on salt marsh habitat dominated by the foundation species Spartina alterniflora. Despite the severe impacts to phenotype and fitness, S. alterniflora proved remarkably resilient in …

Genes Encoding Flower- And Root-Specific Functions Are More Resistant To Fractionation Than Globally Expressed Genes In Brassica Rapa, Naiyerah F. Kolkailah

Master's Theses

Like many angiosperms, Brassica rapa underwent several rounds of whole genome duplication during its evolutionary history. Brassica rapa is particularly valuable for studying genome evolution because it also experienced whole genome triplication shortly after it diverged from the common ancestor it shares with Arabidopsis thaliana about 17-20 million years ago. While many B. rapa genes appear resistant to paralog retention, close to 50% of B. rapa genes have retained multiple, paralogous loci for millions of years and appear to be multi-copy tolerant. Based on previous studies, gene function may contribute to the selective pressure driving certain genes back to singleton …

Investigating The Effects Of 17Α-Ethynylestradiol On Mitochondrial Genome Stability, Alicia M. Chivers

Dissertations and Theses

Environmental toxicants are ubiquitous throughout the environment as a result of human activity. Among these toxicants, environmental estrogens are a category of particular concern due to their environmental prevalence and potency in altering reproductive traits. While many studies have addressed the detrimental effects of environmental estrogens on both aquatic and terrestrial organisms, few have analyzed the potential for these compounds to alter mitochondrial function. Mitochondria are the primary energy-generating system for all eukaryotic life, supporting all aspects of development, metabolism, and growth. Each cell within the body contains many mitochondria which in turn contain multiple copies of their own DNA …

Methods For Differential Analysis Of Gene Expression And Metabolic Pathway Activity, Yvette Charly B. Temate Tiagueu

Computer Science Dissertations

RNA-Seq is an increasingly popular approach to transcriptome profiling that uses the capabilities of next generation sequencing technologies and provides better measurement of levels of transcripts and their isoforms. In this thesis, we apply RNA-Seq protocol and transcriptome quantification to estimate gene expression and pathway activity levels. We present a novel method, called IsoDE, for differential gene expression analysis based on bootstrapping. In the first version of IsoDE, we compared the tool against four existing methods: Fisher's exact test, GFOLD, edgeR and Cuffdiff on RNA-Seq datasets generated using three different sequencing technologies, both with and without replicates. We also introduce …

Spatiotemporal Control Of Staphylococcus Aureus Biofilm Development, Derek E. Moormeier

Theses & Dissertations

Chronic biofilm-related infections caused by the human pathogen Staphylococcus aureus often lead to significant increases in morbidity and mortality in both hospital- and community-associated settings. Typically, S. aureus biofilm development occurs in three stages: 1) attachment, 2) tower maturation, and 3) dispersal. Here, utilizing BioFlux1000 time-lapse microscopy we have expanded upon these fundamental stages of biofilm development and also unveiled and characterized two additional stages (multiplication and exodus).

The attachment and multiplication stages were shown to be protease sensitive but independent of most cell surface-associated proteins. Following multiplication, an exodus of the biofilm population that followed the transition of the …

Gene Expression And Physiological Analysis To Study Differences Between Oryza Sativa Cultivars Susceptible And Resistant To Chalky Grain Formation Subjected To High Nighttime Temperatures., Nicholas Lawson

Graduate Theses and Dissertations

Starch composition and grain quality of rice is greatly influenced by genotype and environmental factors. The detrimental effects of high nighttime temperatures on rice yield and quality has recently become apparent, with some of the warmest average nighttime temperatures being recorded in the past few years. One of the most notable effects of this stress, an increase in grain chalk formation, correlates with a decrease in quality. This effect varies greatly between cultivars as some show less temperature-sensitive quality reduction than others. The goal of this research is to elucidate fundamental changes that occur in developing plants and grains as …

Tobacco-Gene Activity Profile In Porphyromonas Gingivalis, Filifactor Alocis And Treponema Denticola., Neelima Chowdary Cherukumalli

Electronic Theses and Dissertations

Smoking is an established risk factor for periodontitis. Prior studies have shown that cigarette smoke extract (CSE) can induce profound phenotypic changes in Porphyromonas gingivalis and alters the virulence of this important periodontal pathogen. We hypothesized that CSE might also alter gene expression in established periodontal pathogens, Porphyromonas gingivalis and Treponema denticola, as well as in the emerging pathogen, Filifactor alocis. Oral bacteria were grown in CSE-conditioned medium (1000 ng/ml nicotine equivalents) or in unconditioned control medium. Total RNA was extracted and CSE-regulated genes were identified by comparison of the mRNA profiles of CSE with control cultures using RNA-Seq …

Some Distribution-Free Two-Sample Tests Applicable To High Dimension, Low Sample Size Data., Munmun Biswas Dr.

Doctoral Theses

The advancement of data acquisition technologies and computing resources have greatly facilitated the analysis of massive data sets in various fields of sciences. Researchers from different disciplines rigorously investigate these data sets to extract useful information for new scientific discoveries. Many of these data sets contain large number of features but small number of observations. For instance, in the fields of chemometrics (see e.g., Schoonover et al. (2003)), medical image analysis (see e.g., Yushkevich et al. (2001)) and microarray gene expression data analysis (see e.g., Eisen and Brown (1999), Alter et al. (2000)), we often deal with data of dimensions …

Calorie Restriction Effect On Circadian Clock Gene Expression, Sonal Arvind Patel

ETD Archive

Calorie Restriction (CR) is a powerful paradigm known to delay aging and thus increase longevity in several organisms, from yeast to non-human primates. Many molecular pathways have been proposed to mediate the beneficial effects of CR, however, the mechanism is still unknown. Circadian clock which is an internal time keeping system is regulated by feeding. Thus our aim was to study the effect of CR on the circadian clock. Here we show that CR significantly affects the expression of circadian clock genes in mice at the mRNA and protein levels, suggesting that CR reprograms the clocks at the transcriptional and …

What’S In A Gene: Undergraduates’ Ideas And Misconceptions About Gene Function, Justin M. Levaughn

Theses and Dissertations--Science, Technology, Engineering, and Mathematics (STEM) Education

The purpose of this study was to field test a two-tiered instrument including multiple-choice and short answer tasks to assess college students’ ideas and level of understanding in genetics. The instrument was constructed from previously tested assessment tasks and findings from the current research literature. Ninety-seven freshmen enrolled in a biology lab course were surveyed. Test validity and reliability were measured using Chronbach coefficients. Multiple-choice and short answer responses were analyzed using descriptive statistics to identify frequencies of answer selections. Written responses were independently evaluated using a five-point scoring rubric by three researchers to identify common misconceptions revealed in students’ …

The Role Of Microrna In Cardioprotection: Ischemic Preconditioning And Mesenchymal Stem Cell Paracrine Effects, Kristin Luther

Dissertations

Changes in gene expression and protein levels are an important aspect of cardioprotection in which short non-coding RNA known as miRNA may play a key regulatory role. We investigated the functions of several miRNAs in the context of two cardioprotective stimuli, ischemic preconditioning (IPC) and mesenchymal stem cell (MSC) paracrine effects. We hypothesized that downregulation of a set of miRNAs (miR-148a/b, miR-30b, and let-7a*) augments expression of protective heat shock proteins during IPC, and that MSC exosomes transfer miR-21 to cardiomyocytes, resulting in downregulation of pro-apoptotic genes and reduction of infarct size.

IPC increased the level of Hsp70, Hsp90, and …

Farnesol-Mediated Regulation Of Hepatic Lipid Metabolism In Heparg Cells, Asmita Pant

Wayne State University Dissertations

Non-alcoholic fatty liver disease is emerging as one of the most common liver disorders worldwide and is characterized by accumulation of triglycerides (TGs) in liver. The endogenous isoprenoid farnesol reduces hepatic TG levels in rodents, and this effect appears to involve at least two nuclear receptors, peroxisome proliferator-activated receptor α and farnesoid X receptor (FXR). However, farnesol’s effects on human hepatic lipid metabolism are currently unknown. The objective of this study is to evaluate how farnesol treatment would affect hepatic lipid accumulation and metabolism in a cellular model of human hepatic steatosis that was created by incubating the hepatocyte-like HepaRG …

Transcriptome Analysis Of Vaccine Responses To Francisella Tularensis Or Venezuelan Equine Encephalitis Virus, Rebecca Ann Erwin-Cohen

Walden Dissertations and Doctoral Studies

The lack of vaccines for emerging and re-emerging diseases highlights technical gaps and indicates a need for innovative approaches to produce new vaccines. Vaccines may be improved by knowledge of host responses to vaccination, disease pathogenesis, and the effect of age and genetics on vaccine outcome. This study's purpose was to quantitatively assess the molecular epidemiology of Francisella tularensis (Ft) and Venezuelan Equine Encephalitis Virus (VEEV). Study results support the Epidemiology Nexus model which holds that association of changes in gene expression to vaccination facilitate understanding the mechanisms of immune development and link public health and disease epidemiology. My research …

Studies On Development Of End Rot In Sweetpotato, Ratchanee Pattaravayo

LSU Doctoral Dissertations

End rot development in sweetpotato is caused by several pathogens and exacerbated by unfavorable environments. A critical need exists to know what factors in the environment trigger end rot development and how to manage the crop to minimize the incidence of end rots which are the overall objectives of this study. This research was divided into three studies: 1) Effect of environmental factors on expression of end rot in sweetpotato roots. Factorial combinations consisted of flooding/non-flooding; skinned/non-skinned; cured/non-cured; recommended storage/ambient storage are environmental variables not tested previously together in a systematic way. Results showed that curing at 29oC and 85-90% …

Extraction And Biochemical Characterization Of Alligator Mississippiensis Glycosaminoglycans And An Ex-Vivo Murine Pilot Study To Test Their Potential Effect On A Selected Panel Of Genes Associated With Cystic Fibrosis, Jose Daniel Estrada Andino

LSU Doctoral Dissertations

Cystic fibrosis (CF) is a genetic disorder with a median survival age of 40.7 years. Chronic airway inflammation and dehydration are critical features of CF. The size and structure-dependent hydration and anti-inflammatory properties of glycosaminoglycans (GAGs) such as hyaluronic acid (HA) may help ameliorate these symptoms. The GAGs contained in farmed Alligator mississippiensis by-products offer a potential to improve waste management practices and increase revenue in the alligator industry, through their development for use in biomedical applications. This study aimed to efficiently extract and characterize GAGs from alligator carcasses (ACS), backstraps (ABS), feet (AFT) and eyeballs (AEB), to evaluate their …

Improving Species Reintroduction Through Conservation Genomics, Xiaoping He

Electronic Theses and Dissertations

Reintroduction is the release of a species collected from captive or wild sources into its historical habitat where it has been locally extirpated with the aim to re-establish a self-sustaining population. Increasing pressures on global biodiversity caused by human activities has led to an upsurge in reintroductions in the last decades, but the reintroduction success rate is generally low. Populations can differ in reintroduction performance because of their genetic background which may limit their scope for adapting to novel environments as well as narrow their tolerance ranges for environmental stressors likely to be encountered in the initial acclimation phase of …

Determination Of Cyclic-Di-Gmp- Controlled Gene Expression In A Pharmacologically Important Bacterium, Morgan A. Stark

Undergraduate Honors Thesis Projects

The second messenger molecule cyclic dimeric GMP (c-di-GMP) regulates a myriad of processes in gram-negative bacteria. However, less is known about the roles it plays in gram-positive bacteria. Differential gene expression in three strains of the gram-positive bacterium, Streptomyces coelicolor, is being studied using RNA sequencing and Real Time PCR to gain insight into c-di-GMP signaling. The rmdA rmdB (regulator of morphology and development) double mutant was compared to the wild type strain known as MT1110. The rmdA and rmdB genes are needed for the formation of aerial mycelium, an important step in the life cycle of Streptomyces coelicolor (Hull …

Role Of An Adenylyl Cyclase Isoform In Alcohol's Effect On Cyclic Amp Regulated Gene Expression In Mammalian Cells, Rebecca Ann Hill

LSU Doctoral Dissertations

Research suggests that the cyclic AMP (cAMP) signaling pathway including CREB-CRE regulated expression of various genes is implicated in the predisposition to and development of alcoholism in humans. Alcohol also induces changes in inflammatory and immune responses; these changes increase the incidence of pneumonias and other infections, which can negatively affect recovery from infections. Cyclic AMP (cAMP) is known for its immunosuppressive effects and is also required for proper development of the immune system. Previous work in our laboratory has demonstrated that ethanol enhances the activity of adenylyl cyclase (AC) in an isoform-specific manner; type 7 AC (AC7) is most …