Life Sciences Commons^™

Multipartite Graph Algorithms For The Analysis Of Heterogeneous Data, Charles Alexander Phillips

Doctoral Dissertations

The explosive growth in the rate of data generation in recent years threatens to outpace the growth in computer power, motivating the need for new, scalable algorithms and big data analytic techniques. No field may be more emblematic of this data deluge than the life sciences, where technologies such as high-throughput mRNA arrays and next generation genome sequencing are routinely used to generate datasets of extreme scale. Data from experiments in genomics, transcriptomics, metabolomics and proteomics are continuously being added to existing repositories. A goal of exploratory analysis of such omics data is to illuminate the functions and relationships of …

Application Of Hidden Markov Model Based Methods For Gaining Insights Into Protein Domain Evolution And Function, Amit Anil Upadhyay

Doctoral Dissertations

With the explosion in the amount of available sequence data, computational methods have become indispensable for studying proteins. Domains are the fundamental structural, functional and evolutionary units that make up proteins. Studying protein domains is an important part of understanding protein function and evolution. Hidden Markov Models (HMM) are one of the most successful methods that have been applied for protein sequence and structure analysis. In this study, HMM based methods were applied to study the evolution of sensory domains in microbial signal transduction systems as well as functional characterization and identification of cellulases in metagenomics datasets. Use of HMM …

Applications Of Evolutionary Bioinformatics In Basic And Biomedical Research, Ogun Adebali

Doctoral Dissertations

With the revolutionary progress in sequencing technologies, computational biology emerged as a game-changing field which is applied in understanding molecular events of life for not only complementary but also exploratory purposes. Bioinformatics resources and tools significantly help in data generation, organization and analysis. However, there is still a need for developing new approaches built based on a biologist’s point of view. In protein bioinformatics, there are several fundamental problems such as (i) determining protein function; (ii) identifying protein-protein interactions; (iii) predicting the effect of amino acid variants. Here, I present three chapters addressing these problems from an evolutionary perspective. Firstly, …

Utilizing In Silico And/Or Native Esi Approaches To Provide New Insights On Haptoglobin/Globin And Haptoglobin/Receptor Interactions, Ololade Fatunmbi

Doctoral Dissertations

Haptoglobin (Hp), an acute phase protein, binds free hemoglobin (Hb) dimers in one of the strongest non-covalent interactions known in biology. This interaction protects Hb from causing potentially severe oxidative damage and limiting nitric oxide bioavailability. Once Hb/Hp complexes are formed, they proceed to bind CD163, a cell surface receptor on macrophages leading to complex internalization and catabolism. Myoglobin, (Mb) a monomeric protein, that is normally found in the muscle but can be released into the blood in high concentrations during myocardial injury, is homologous to Hb and shares many conserved Hb/Hp interface residues. Both monomeric Hb and Mb species …

Genetic Modification Of Switchgrass (Panicum Virgatum L.) For Improvement Of Plant Architecture, Biomass Productivity And Sugar Release Efficiency For Biofuel, Wegi Aberra Wuddineh

Doctoral Dissertations

Switchgrass (Panicum virgatum L.) is a leading candidate bioenergy crop for sustainable biofuel production. To ensure its economic viability, tremendous improvements in switchgrass biomass productivity and recalcitrance to enzymatic saccharification are needed. Genetic manipulation of lignin biosynthesis by targeting transcriptional regulators of higher level domains of lignin biosynthesis and other complex traits could alter several bioenergy-desirable traits at once. A three-pronged approach was made in the dissertation research to target one plant growth regulator and transcription factors to alter plant architecture and cell wall biosynthesis.

Gibberellin (GA) catabolic enzymes, GA 2-oxidases (GA2oxs), were utilized to alternatively modify the lignin …

Evolution And Phylogeny Of The Parasitoid Subfamily Phasiinae (Diptera: Tachinidae), Jeremy Daniel Blaschke

Doctoral Dissertations

The first molecular phylogenetic analysis of the agriculturally important parasitoid subfamily Phasiinae (Diptera: Tachinidae) is presented, estimated from 128 worldwide taxa (80 genera) and approximately 7.6 kilobases of nuclear data. Special emphasis is placed on taxa with controversial taxonomic placement. The resultant phylogenetic tree is used to reconstruct ancestral character states, trace the evolution of significant adaptive traits within the Tachinidae, and test hypotheses about the classification of Phasiinae. Subfamily placements of the taxa Eutherini, Epigrimyiini, Litophasia, Strongygastrini, and Parerigonini are confidently resolved, the former three within Dexiinae and the latter two within Phasiinae. Due to sparse molecular evidence, …

Calmodulin-Like Protein 38: A Component Of Ribonucleoprotein Particles During Hypoxic Stress Responses In Arabidopsis, Ansul Lokdarshi

Doctoral Dissertations

Waterlogging stress leads to a crisis in energy metabolism and the accumulation of toxic metabolites due to the hypoxic and/or anoxic environment associated with this condition. To respond and adapt to this situation, higher plants employ an integrated genetic program that leads to the induction of anaerobic response polypeptide genes that encode metabolic and signaling proteins involved in altering metabolic flow and other adaptive responses. The study presented here shows that the Arabidopsis thaliana calmodulin-like protein CML38 is calcium sensor protein that serves as a member of the core anaerobic response gene family and is involved in modulating the survival …

Characterization Of The Role Of Alpha-Arylphorin In The Heliothis Virescens Midgut Response To Cry1ac Toxin From Bacillus Thuringiensis, Jerreme Jamael Jackson

Doctoral Dissertations

Homeostasis of the intestinal epithelium in Heliothis virescens is mediated by the proliferation and differentiation of multipotent intestinal stem cells (ISCs) that lie adjacent to the basal lamina. In response to extrinsic and intrinsic signals, ISC proliferation and differentiation promotes epithelial growth and regeneration following the loss of integrity. We tested the in vivo effects of the ISC mitogen, a [alpha]-arylphorin, on ISC proliferation and the morphological changes of the midgut during larval development. Additionally, we examined how these changes affected the intestinal epithelium response to Cry1Ac toxin from Bacillus thuringiensis. Histological and in vitro evidence supported two distinct …