Genetics and Genomics Commons^™

Computational Analysis Of Papionini Evolution Using Alu Insertions, Vallmer Edward Jordan Ii

LSU Doctoral Dissertations

Alu elements are primate specific retrotransposons that have remained active throughout the course of primate evolution. As a result of this sustained mobilization. Alu elements are present in greater copy number in primate genomes than any other transposable element. An average of over one million Alu elements has been identified in every sequenced haplorrhine genome to date. These characteristics qualify Alu elements as ideal characters for studying evolutionary relationship among primates.

The increasing availability of whole genome sequencing data presents novel challenges and opportunities for comparative genomic analyses. Genomic data is now publicly available for most primate species. Such an …

Analysis Of Chromatin Interactions Of Beaf-Associated Promoters Using 4c, Shraddha Shrestha

LSU Doctoral Dissertations

A high degree of chromosome compaction is needed to fit nearly 2 meters of DNA inside a human nucleus of around 10 µm diameter. Correct chromatin folding is crucial to facilitate important nuclear functions such as transcription, DNA replication and DNA repair. Nuclei contain a variety of proteins, many of which help regulate chromatin structure and function. The mechanisms by which these proteins work are diverse and complicated. Here, we study the chromatin interactions of Boundary Element Associated Factor (BEAF) associated sites to gain insight into eukaryotic genome organization. We used circular chromosome conformation capture (4C) technology to detect genome-wide …

R1 Retrotransposons In Drosophila Melanogaster Are Transcribed By Rna Polymerase I Upon Heat Shock, Himanshu Shekhar Raje

LSU Doctoral Dissertations

The ribosomal RNA genes of Drosophila melanogaster reside within centromere-proximal nucleolar organizers on both the X and Y chromosomes. Each locus contains between 200-300 tandem repeat rDNA units that encode 18S, 5.8S, and 28S ribosomal RNAs (rRNAs) for ribosome biogenesis. In arthropods like Drosophila, about 60% of rDNA genes are inserted with R1 and/or R2 retrotransposons at specific sites within the 28S regions; these units likely fail to produce functional 28S rRNA. We showed previously that R2 expression increases upon nucleolar stress caused by the loss of a ribosome assembly factor, the Nucleolar Phosphoprotein of 140 kDa (Nopp140). Here …

An Analysis Of Alu Elements In Baboons, Cody James Steely

LSU Doctoral Dissertations

Transposable elements compose a large portion of mammalian genomes and are estimated to make up anywhere from ~45% - ~70% of the human genome. Alu elements are primate-specific retrotransposons that are found in high copy number (> 1 million copies) and are spread throughout the genome. These elements are the most commonly repeated sequence in the human genome and have contributed to a number of disease states in humans. Alu elements are useful markers for population genetics and phylogenetics and have proven valuable in understanding difficult to determine relationships between species and within populations.

Baboons (genus Papio) are spread throughout …

The Determinants Of Nucleosome Patterns And The Impact Of Phosphate Starvation On Nucleosome Patterns And Gene Expression In Rice, Qi Zhang

LSU Doctoral Dissertations

In eukaryotic cells, DNA is a large molecule that must be greatly condensed to fit within the nucleus. DNA is wrapped around histone proteins to form nucleosomes, which facilitate DNA condensation, but on the other hand, may limit DNA processes. Organisms must respond to environmental stress in order to survive, and one strategy is by remodeling nucleosomes to promote changes in DNA accessibility to alter gene expression. Studies have demonstrated a clear correlation between nucleosome dynamics and transcriptional change in some eukaryotes, however factors that affect nucleosome positioning in plants are largely unknown, and the correlation between nucleosome dynamics and …

The Role Of Histone H2a.Z Abundance In Modulating Responses To Phosphorus Deficiency In Rice, Sara Zahraeifard

LSU Doctoral Dissertations

Histone variants contribute to chromatin complexity by creating specialized nucleosomes. Here, to investigate the pattern of H2A.Z histone variant distribution and its role in modulating gene expression in rice (Oryza sativa L.), we performed genome-wide profiling of ARP6-dependent H2A.Z deposition in rice seedlings. We demonstrated that under controlled conditions, the majority of H2A.Z deposition is within protein-coding genes (PCG), and the most highly expressed genes are enriched with H2A.Z at their 5’ ends near the transcription start site (TSS), whereas the medium- to low-expressed genes contain H2A.Z across the entire gene. Based on H2A.Z deposition, we categorized genes into …

Virulence Phenotypes Of Rotylenchulus Reniformis: Evaluation Of Host Status Of Cotton And Utility Of Single Nucleotide Polymorphisms (Snps) For Identification, Churamani Khanal

LSU Doctoral Dissertations

Comparative reproduction and pathogenicity of reniform nematode (Rotylenchulus reniformis) populations derived from single-egg masses and collected form West Carroll (WC), Rapides (RAP), Morehouse (MOR), and Tensas (TEN) parishes in Louisiana were evaluated in microplot and greenhouse trials. Data from microplot trials showed significant differences among isolates of reniform nematode in both reproduction and pathogenicity on upland cotton (Gossypium hirsutum) cultivars Phytogen 499 WRF, Deltapine 1133 B2RF, and Phytogen 333 WRF. Across all cotton cultivars, MOR and RAP isolates had the greatest and the least reproduction values of 331.8 and 230.2, respectively. Reduction in plant dry weight, …