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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 …

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 …

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 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 …

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 …

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 …

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’ …

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 …

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 …

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 …

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 …