Life Sciences Commons^™

The Expanding Marine Built Environment And Biofilm Formation Processes, Rachel Mugge

Dissertations

The marine built environment (i.e., places or things made or modified by humans) in the northern Gulf of Mexico is rapidly expanding and includes over 2,000 known historic shipwrecks, nearly 4,100 artificial reefs, and other built structures for natural resource extraction, marine aquaculture, renewable energy generation, munitions dumping areas, and commercial and recreational activities. While these structures have the potential to develop into artificial reefs, acting as biodiversity hotspots that provide food and shelter and facilitate organism transport, it is unclear how they affect biodiversity and ecosystem function in the marine environment. The success of artificial reefs to become ecosystems …

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 …

F Plasmids In Escherichia Coli Decrease Permissivity To Coliphage, Cesar Eber Montelongo Hernandez

Dissertations

The urinary tract contains a community of bacteria called the urinary microbiota (urobiota) thatmay be relevant to health; the genomic component of the urobiota is the urinary microbiome (urobiome). Urinary bacteria have been associated with both asymptomatic states and disease conditions, such as urinary tract infection (UTI), overactive bladder (OAB), and urge urinary incontinence (UUI). Some bacteria, such as E. coli, are considered urinary pathogens (uropathogens) but also can be commensals. Bacteriophage (phage) are ubiquitous in nature and likely shape bacterial populations in every niche; thus, phage may be one factor that modulates the urobiota. Phages have a specific host …

Model-Based Deep Autoencoders For Characterizing Discrete Data With Application To Genomic Data Analysis, Tian Tian

Dissertations

Deep learning techniques have achieved tremendous successes in a wide range of real applications in recent years. For dimension reduction, deep neural networks (DNNs) provide a natural choice to parameterize a non-linear transforming function that maps the original high dimensional data to a lower dimensional latent space. Autoencoder is a kind of DNNs used to learn efficient feature representation in an unsupervised manner. Deep autoencoder has been widely explored and applied to analysis of continuous data, while it is understudied for characterizing discrete data. This dissertation focuses on developing model-based deep autoencoders for modeling discrete data. A motivating example of …

Elucidation Of The Molecular Mechanisms Of Electrically-Induced Cardioprotection, Anne Elizabeth Roessler

Dissertations

Cardiovascular disease is the leading cause of death worldwide. A myocardial infarction (MI), commonly known as a heart attack, is a major event in cardiovascular disease characterized by reduced blood flow to the heart. The ischemia and reperfusion (I/R) injury associated with an MI results in a region of dead tissue in the heart called an infarct, the size of which influences patient prognosis. In the 1980s, it was discovered that short, non-lethal episodes of I/R, termed ischemic preconditioning (IPC), can protect the heart against a subsequent MI. Ischemic preconditioning demonstrated the phenomenon of endogenous cardioprotection. Cardioprotection has great potential …

Knowledge-Based Analysis Of Genomic Expression Data By Using Different Machine Learning Algorithms For The Purpose Of Diagnostic, Prognostic Or Therapeutic Application, Venkata Jagan Mohan Thodima

Dissertations

With more and more biological information generated, the most pressing task of bioinformatics has become to analyze and interpret various types of data, including nucleotide and amino acid sequences, protein structures, gene expression profiling and so on. In this dissertation, we apply the data mining techniques of feature generation, feature selection, and feature integration with learning algorithms to tackle the problems of disease phenotype classification, clinical outcome and patient survival prediction from gene expression profiles.

We analyzed the effect of batch noise in microarray data on the performance of classification. Batchmatch, a batch adjusting algorithm based on double scaling method …

Bioinformatics Study Of Mammalian Mrna Polydenylation, Haibo Zhang

Dissertations

Messenger RNA polyadenylation is one of the key post-transcriptional events in mammalian cells, which have influences on many aspects of mRNA metabolism. Several human diseases have been shown to associate with abnormal polyadenylation, highlighting the importance of this process. The availability of the complete sequence of human and mouse genomes, together with their gene expression data provides valuable resources to study mRNA polyadenylation on a system level. This dissertation addresses the following issues of mammalian mRNA polyadenylation through bioinformatics approaches: (1) the extensive documentation of several key aspects of polyadenylation sites in humans and mice on a genomic level; (2) …