Life Sciences Commons^™

Genetics And Morphology Of Invasive Tubastraea Species Within The Gulf Of Mexico: A Case Study Of Species Misidentification And Distribution, Amelia E. Mcclure

Theses and Dissertations

The invasive corals, Tubastraea coccinea and Tubastraea micrathus, are known to thrive in reefs within the Gulf of Mexico (GOM). Many studies have indicated that species within this genus are spreading throughout the western Atlantic due to their successful invasion on degraded and artificial reef systems. In the Northern GOM, artificial reefs have been created from decommissioned oil rigs and sunken vessels to provide a hard substrate for coral growth. Although, this method is demonstrating success, it is also facilitating, the dispersal of undesired species. The species, T. coccinea and T. micranthus, were thought to be the only …

Formulation Of Hybrid Knowledge-Based/Molecular Mechanics Potentials For Protein Structure Refinement And A Novel Graph Theoretical Protein Structure Comparison And Analysis Technique, Aaron Maus

University of New Orleans Theses and Dissertations

Proteins are the fundamental machinery that enables the functions of life. It is critical to understand them not just for basic biology, but also to enable medical advances. The field of protein structure prediction is concerned with developing computational techniques to predict protein structure and function from a protein’s amino acid sequence, encoded for directly in DNA, alone. Despite much progress since the first computational models in the late 1960’s, techniques for the prediction of protein structure still cannot reliably produce structures of high enough accuracy to enable desired applications such as rational drug design. Protein structure refinement is the …

Wavelet Analysis Of Short Globular Homologous Proteins In Mesophile And Thermophile Prokaryotes, John B. Linehan

College of Science and Health Theses and Dissertations

This study looked to identify features related to thermal stability and function in the amino acid chains of short globular proteins from mesophile and thermophile species, within the constraint that the protein fold to perform a speci_c function. To do so 540 homologous pairs of proteins were studied. The amino acid chains were con-verted to hydrophobicity signals by assigning a hydropathy score to each residue in the polypeptide. The hydrophobicity signals were passed through a wavelet packet transform and the resulting spectra analyzed. Bootstrapping was used to gener-ate a control data set to determine if the true ordering of amino …

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 …

Computational Genomic Models For Spatio-Temporal Investigation Of Early Lung Cancer Pathology, Smruthy Sivakumar

Dissertations & Theses (Open Access)

Lung cancer, of which non-small cell lung cancer (NSCLC) is the most common form, is the second most prevalent cancer and the leading cause of cancer-related deaths. NSCLCs primarily comprise adenocarcinomas (LUAD) and squamous cell carcinomas (LUSC). Advances in early detection and prevention have been limited by the lack of early-stage biomarkers and targets. A comprehensive molecular characterization of premalignant lesions and tumor-adjacent normal tissue can aid in better understanding NSCLC pathogenesis. However, these investigations are further challenged by limited tissue availability and low cellular fractions of detectable somatic mutations.

Therefore, there is a dearth of knowledge about the pathogenesis …

Contribution Of Retrotransposons To Breast Cancer Malignancy, Isaac D. Raplee

USF Tampa Graduate Theses and Dissertations

The components contributing to cancer progression, especially the transition from early to invasive are unknown. Consequently, the biological reasons are unclear as to why some patients diagnosed with atypia and ductal carcinoma in situ (DCIS) never progress into invasive breast cancer. The “one gene at a time” approach does not sufficiently predict progression. To elucidate the early stage progression to invasive ductal cancer, expression signature of transcripts and transposable elements in micropunched samples of formalin-fixed, paraffin embedded (FFPE) tissue was conducted. A bioinformatics pipeline to analyze poor quality, short reads (>36 nts) from RNA-Seq data was created to compare …

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 …

Practical Bioinformatics Applications In Microbes, Sarah Anne Entwistle

Graduate Research Theses & Dissertations

This thesis examines three methodologies for applying bioinformatics techniques to microbial data. A computational analysis of RNA sequencing data showed that hbx1 is a global regulator in Aspergillus flavus. A particular focus of this analysis is the characterization of hbx1 in regard to regulation of secondary metabolite gene clusters and their production of aflatoxins. An analysis of bacterial genomes identified ORFans in both pathogenic and non-pathogenic genomes, along with their presence in sequence features. This investigation demonstrated that ORFan genes shared by pathogenic genomes were more related to bacterial pathogenicity. Evaluation of multiple types of recombination events in RNA sequencing …

Exploring Strategies To Integrate Disparate Bioinformatics Datasets, Charbel Bader Fakhry

Walden Dissertations and Doctoral Studies

Distinct bioinformatics datasets make it challenging for bioinformatics specialists to locate the required datasets and unify their format for result extraction. The purpose of this single case study was to explore strategies to integrate distinct bioinformatics datasets. The technology acceptance model was used as the conceptual framework to understand the perceived usefulness and ease of use of integrating bioinformatics datasets. The population of this study included bioinformatics specialists of a research institution in Lebanon that has strategies to integrate distinct bioinformatics datasets. The data collection process included interviews with 6 bioinformatics specialists and reviewing 27 organizational documents relating to integrating …

Examination Of Bovine Rumen Fluid And Milk Fat Globule Membrane Proteome Dynamics, Mallory Cate Honan

Graduate College Dissertations and Theses

Proteomic technology has been increasingly incorporated into agricultural research, as characterization of proteomes can provide valuable information for potential biomarkers of health and physiological status of an animal. As dairy cattle are a dominant production animal in the USA, their biofluids such as milk, blood, urine, and rumen fluid have been examined by proteomic analysis. The research outlined herein was performed to further characterize the dynamics of specific proteomes and relate them to dairy cattle physiology.

The first experiment evaluated the diurnal dynamicity of the rumen metaproteome in Holstein dairy cattle. Rumen fluid was collected from three mid to late …

Evaluating Predixcan’S Ability To Predict Differential Expression Between Alcoholics And Non-Alcoholics, John E. Drake Jr

Theses and Dissertations

PrediXcan is a recent software for the imputation of gene expression from genotype data alone. Using an overlapping set of transcriptome datasets from postmortem brain tissues of donors with alcohol use disorder and neurotypical controls, which were generated by two different platforms (e.g., Arraystar and Affymetrix), and an additional unrelated transcriptome dataset from lung tissue, we sought to evaluate PrediXcan’s ability to impute gene expression and identify differentially expressed genes. From the Arraystar platform, 1.3% of matched genes between the measured and imputed expression had a Pearson correlation ≥ 0.5. Our attempt to replicate this finding using the expression data …

Of Donuts And Promo : In Silico Approaches To Identification Of Transcriptional Regulators Of Salivary Acinar Differentiation, Connor Cillian Duffy

Legacy Theses & Dissertations (2009 - 2024)

The salivary gland is an organ often taken for granted by most people. However, its proper function is essential for several everyday activities, such as speaking, swallowing, and tasting. As such, impaired salivary gland function, such as that caused by Sjögren’s Syndrome or radiotherapy for head and neck cancers, can lead to a significantly reduced quality of life. The cells that produce saliva in salivary glands are known as acinar cells, which arise from proacinar cells generated during embryonic development. As such, in studying the promoter regions of proacinar and acinar genes, it may be possible to identify common transcription …

Dna Methylation And Genetic Divergence Associated With An Inducible Defensive Response In Mimulus Guttatus, David Farr

All Master's Theses

Phenotypic plasticity allows many organisms to respond to their environment by changing their phenotype, but the mechanisms to do so are not well understood. Yellow Monkeyflower (formerly Mimulus guttatus; now Erythranthe guttata) is one such organism that can serve as a model to promote our understanding of these mechanisms due to its striking response to insect herbivory. Monkeyflower responds to leaf damage by increasing the number of hair-like glandular trichomes, a putative defensive trait that reduces the magnitude of damage by insects. This plastic response is transgenerationally inherited in a way that is sensitive to genome-wide demethylation when …