Genetics and Genomics Commons^™

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Pirna Expression In Regenerative Tissue Of Octopus Bimaculoides, Bailey Ervin

Honors Theses

Tissue regeneration is present in varying capacities across the animal kingdom. Animals such as Hydra and planarians have the capacity to regenerate entire bodies from extremely small sections of amputated tissue. Others, such as humans, have restricted capacities of regeneration, especially in terms of full appendages and specialized tissues such as cardiac and nervous tissue. One of the primary goals of studying regeneration in other organisms is to achieve the development of regenerative medicine. Interaction of P-element induced WImpy testis (PIWI) proteins and PIWI-interacting RNAs (piRNAs) have been implicated in germline genome maintenance, as well as transposable element silencing. Research …

Pirna Expression In The Tube Feet Of Lytechinus Variegatus, Reagan Milliet

Honors Theses

Tissue regeneration is an area of research with implications for medicine and animal health. While nearly all living multi-cellular organisms are capable of regeneration, there are major differences in the animal kingdom. Some organisms are capable of regenerating virtually every cell in their bodies. In hopes of engineering tissue regeneration for medical applications, the mechanisms by which organisms regenerate are being widely investigated. To better understand regeneration, the role of P-element Induced WImpy testis (PIWI) proteins are being evaluated. In collaboration with PIWIinteracting RNAs (piRNAs), PIWI proteins have been proven instrumental to transposon silencing and maintenance of the genome in …

A Genomic Investigation Of Divergence Between Tuna Species, Pavel V. Dimens

Dissertations

Effective management and conservation of marine pelagic fishes is heavily dependent on a robust understanding of their population structure, their evolutionary history, and the delineation of appropriate management units. The Yellowfin tuna (Thunnus albacares) and the Blackfin tuna (Thunnus atlanticus) are two exploited epipelagic marine species with overlapping ranges in the tropical and sub-tropical Atlantic Ocean. This work analyzed genome-wide genetic variation of both species in the Atlantic basin to investigate the occurrence of population subdivision and adaptive variation. A de novo assembly of the Blackfin tuna genome was generated using Illumina paired-end sequencing data and …

Characterizing Endogenous Dicer Products To Unravel Novel Rnai Biogenesis Pathways, Jacob Oche Peter

Dissertations

ABSTRACT

RNA interference (RNAi) is a pervasive gene regulatory mechanism in eukaryotes based on the action of multiple classes of small RNA (sRNA). Exploiting RNAi pathways in non-model systems have great potential for creating potent RNAi technologies. Here, we accessed RNAi-mediated control of gene expression in the two-spotted spider mite, Tetranychus urticae (T. urticae) using engineered dsRNA designed to modulate the host RNAi pathway and increase RNAi efficacy. Analysis of Dicer (Dcr) generated fragments revealed how exogenous RNAs access the host RNAi pathway in this animal, opening avenues for designing RNAi technology for their control. Further, some organisms …

Human 5’-Tailed Mirtrons Are Processed By Rnasep, Mohammad Farid Zia

Dissertations

Approximately a thousand microRNAs (miRNAs) are documented from human cells. A third appear to transit non-canonical pathways that typically bypass processing by Drosha, the dedicated nuclear miRNA producing enzyme. The largest class of non-canonical miRNAs are mirtrons which eschew Drosha to mature through spliceosome activity. While mirtrons are found in several configurations, the vast majority of human mirtron species are 5’-tailed. For these mirtrons, a 3’ splice site defines the 3’ end of their hairpin precursor while a “tail” of variable length separates the 5’ base of the hairpin from the nearest splice site. How this tail is removed is …

Development, Evaluation, And Application Of A Novel Error Correction Method For Next Generation Sequencing Data, Isaac Akogwu

Dissertations

Tremendous evolvement in sequencing technologies and the vast availability of data due to decreasing cost of Next-Generation-Sequencing (NGS) has availed scientists the opportunity to address a wide variety of evolutionary and biological issues. NGS uses massively parallel technology to accelerate the process at the expense of accuracy and read length in comparison to earlier Sanger methods. Therefore, computational limitations exist in how much analysis and information can be gleaned from the data without performing some form of error correction.

Error correction process is laborious and consumes a lot of computational resources. Despite the existence of many NGS data error correction …