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Sublethal Toxicity Of Microcystis And Microcystin-Lr In Fish, Emily Dawn Rogers

Doctoral Dissertations

The occurrence of blooms of toxic cyanobacteria in freshwater environments is a global ecological and public health concern. Species of Microcystis are of particular importance because blooms occur in many freshwater environments throughout the world and microcystin toxin concentrations can exceed World Health Organization advisory levels. While microcystin has been associated with fish kills, sublethal effects of chronic exposure at environmentally relevant concentrations are relatively unknown. The objective of this research was to evaluate toxicity of microcystin and Microcystis in fish during all life history stages. We evaluated global gene expression response in larval zebrafish (Danio rerio), and …

Assessment And Performance Of Vsn-Inv Normalization On The Nci-60 Microrna Expression Profiles., Martin T. Disibio

Electronic Theses and Dissertations

Multiple normalization methods have been proposed for the analysis of microRNA microarray expression profiles but there is no consensus method. One of the more robust methods, quantile normalization, is commonly used in transcript (mRNA) studies and was therefore used for normalizing the first microRNA expression profiles of the NCI-60 cell panel, published in 2007. In this study the appropriateness of VSN-Inv, a recently proposed alternative normalization method, to the NCI-60 dataset is verified. VSN-Inv normalization results in much increased inter-sample correlations among control groups, and significantly higher intra-chip correlations of duplicate probes, versus quantile and no normalization. Furthermore, VSN-Inv normalization …

Survival Analysis Of Microarray Data With Microarray Measurement Subject To Measurement Error, Juan Xiong

Electronic Thesis and Dissertation Repository

Microarray technology is essentially a measurement tool for measuring expressions of genes, and this measurement is subject to measurement error. Gene expressions could be employed as predictors for patient survival, and the measurement error involved in the gene expression is often ignored in the analysis of microarray data in the literature. Efforts are needed to establish statistical method for analyzing microarray data without ignoring the error in gene expression. A typical microarray data set has a large number of genes far exceeding the sample size. Proper selection of survival relevant genes contributes to an accurate prediction model. We study the …

Microarray Analysis Of Gene Expression Profiles Of Tetrahymena H2b Ubiquitylation Mutant Strains, Zhe Wang

Theses

Microarray analyses were performed to compare the gene expression profiles of wild-type and mutant strains of Tetrahymena thermophila. These studies suggest that, in Tetrahymena, ubiquitylation of histone H2B is not required for H3K4 methylation. Even though the E2 ubiquitin-conjugating enzyme Ubc2 and the E3 ubiquitin ligase Bre1 are required for H2B ubiquitylation, these two enzymes affect the expression of a much broader spectrum of genes than H2B ubiquitylation, suggesting that Ubc2 and Bre1 are involved in pathways other than H2B ubiquitylation in Tetrahymena.

An Analysis Of Global Gene Expression Resulting From Exposure To Energetic Materials, Vernon L. Mcintosh Jr.

Doctoral Dissertations

AN ANALYSIS OF GLOBAL GENE EXPRESSION RESULTING FROM EXPOSURE TO ENERGETIC MATERIALS

A Dissertation

Presented for the Doctor of Philosophy Degree

University of Tennessee, Knoxville

VERNON LASHAWN MCINTOSH JR.

August 2010

Dedication

This dissertation is dedicated to my family. My mother and father Debra and Vernon McIntosh instilled in me the respect for academic excellence and the drive maximize my potential. Early on, my younger brother Kyle started showing signs of a shared interest in biology thus my desire to be a positive role model for him kept me motivated. Last but certainly not least, my loving wife and best …

High-Throughput Genomic/Proteomic Studies : Finding Structure And Meaning By Similarity, George Sidney Davidson

Biology ETDs

The post-genomic challenge was to develop high-throughput technologies for measuring genome scale mRNA expression levels. Analyses of these data rely on computers in an unprecedented way to make the results accessible to researchers. My research in this area enabled the first compendium of microarray experiments for a multi-cellular eukaryote, Caenorhabditis elegans. Prior to this research approximately 6% of the C. elegans genome had been studied, and little was known about global expression patterns in this organism. Here I cluster data from 553 different microarray experiments and show that the results are stable, statistically significant and highly enriched for specific biological …

Comparison Of Rna Quality From Stressed And Unstressed Recombinant Escherichia Coli, Mary Alice Salazar

All Theses

High quality, intact RNA is required for DNA microarray studies, cloning, and reverse transcriptase polymerase chain reaction (rt-PCR) analysis. There are several analytical methods used to assess the RNA quality. The RNA Integrity Number (RIN) from the Agilent Bioanalyzer is one quality control assay used to evaluate RNA. For recombinant Escherichia coli cultured under stressful conditions the RNA profiles obtained using the Agilent Bioanalyzer indicate RNA degradation; however, RNA obtained and purified in parallel from unstressed recombinant cultures indicate acceptable RNA values without significant degradation. We proposed that for stressed E. coli the RIN value is not necessarily indicative of …

Towards An Understanding Of The Etiology Of Abdominal Aortic Aneurysms: Identification Of Genes Implicated In Aaa Risk And Development, John Hunt Lillvis

Wayne State University Dissertations

Abdominal aortic aneurysm (AAA) is a common disease for which mechanisms of formation are still not well understood. Despite a strong genetic component to AAA risk, specific risk alleles are still largely unidentified. AAA is also a localized disease with a majority occurring in the infrarenal abdominal aorta and is six times more common than aneurysms of the thoracic aorta. To determine whether risk alleles are present in functional positional candidate genes. we: 1. performed a genetic association study using DNA from AAA cases and controls in ten candidate genes and 2. performed exon sequencing on three genes with evidence …

The Role Of Pax6 In Lens Placode Formation, Jie Huang

All Theses and Dissertations (ETDs)

THE ROLE OF PAX6 IN LENS PLACODE FORMATION by Jie Huang Washington University in St. Louis, 2010 Professor David Beeebe, Chairperson Although placodes are ubiquitous precursors of tissue invagination, the mechanism of placode formation and its importance for invagination are unclear. We tested the "restricted expansion hypothesis" of lens placode formation by conditionally deleting the transcription factor, Pax6, or the matrix component, Fn1. Deletion of Pax6 from the lens-forming ectoderm prevented placode formation without altering cell proliferation or volume. Pax6CKO ectoderm expanded, rather than being constrained to a constant area, as normally occurs during lens placode formation, and expressed lower …

A Multiresolution Approach To The Detection Of Image Discrepancies For Improved Quality Control Of Oligonucleotide Microarray Images, Vetria L. Byrd

All ETDs from UAB

The impact of microarrays on biological research has been phenomenal. By enabling scientists to assess the expression levels of thousands of genes simultaneously this high-throughput technology significantly reduces the time spent per experiment and allows for more complicated experiments. The microarray process is a complex series of steps that yields enormous amounts of data in microarray images. The Affymetrix GeneChip® system pioneered microarray technology, creating an image file format that has become standard for microarray image processing. During a microarray experiment, a microarray chip is scanned using a confocal laser scanner that captures the raw data (.DAT). A summary of …

A Microarray Study On Gene Expression Of Drosophila Melanogaster 'M Response To Multiple Cold Exposures, Jian Zhang

Digitized Theses

In the field, insects suffer multiple cold exposures during winter. When exposed to repeated low temperatures, Drosophila melanogaster females show an increase in survival, but a reduction in reproduction. In this study, microarrays were used to analyze the gene expression of female D. melanogaster after multiple, single sustained (or single prolonged) and single short cold treatments, which exposed the flies at 0 °C for repeated 2 h, single 10 h and single 2 h respectively. Candidate genes involved in the 6 h recovery from different types of cold exposures were identified. After repeated cold exposures, candidate genes particularly included those …

Dna-Damage-Independent Mitochondrial Dysfunction Drives A Loss Of Retina Function Prior To Neuron Death In The Harlequin Mouse Model Of Aging, Alex Michael Laliberte

Digitized Theses

Although there are many aging-associated retinal diseases, the aging mechanisms which initiate retinal disease remain elusive. To investigate this problem, a model of premature aging, the harlequin mouse, was examined for deficits in retinal function, anatomy and histology, as well as changes in retinal oxidative stress, gene expression and mitochondrial DNA damage. Retinal function of the harlequin mouse, as assessed by electroretinography, was compromised in advance of change in retinal anatomy and histology. Functional deficits occurred in parallel with increased oxidative stress, assessed by in situ dihydroethidium staining. Furthermore, microarray transcriptome analysis of harlequin mice identified markers of mitochondrial stress, …