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, …

Rare Occurrences Of Free-Living Bacteria Belonging To Sedimenticola From Subtidal Seagrass Beds Associated With The Lucinid Clam, Stewartia Floridana, Aaron M. Goemann

Masters Theses

Lucinid clams and their sulfur-oxidizing endosymbionts comprise two compartments of a three-stage, biogeochemical relationship among the clams, seagrasses, and microbial communities in marine sediments. A population of the lucinid clam, Stewartia floridana, was sampled from a subtidal seagrass bed at Bokeelia Island Seaport in Florida to test the hypotheses: (1) S. floridana, like other lucinids, are more abundant in seagrass beds than bare sediments; (2) S. floridana gill microbiomes are dominated by one bacterial operational taxonomic unit (OTU) at a sequence similarity threshold level of 97% (a common cutoff for species level taxonomy) from 16S rRNA genes; …

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 …

Population Structure Of Late Blight (Phytophthora Infestans) In Colombia And Ecuador And Downy Mildew (Peronospora Farinosa F. Sp. Spinaciae) On Spinach In Arizona And California, Rebecca Marie Lyon

Masters Theses

In this study, Phytophthora infestans and Peronospora farinosa f. sp. spinaciae populations were analyzed using single nucleotide polymorphisms (SNPs). In Ecuador and Colombia, Phytophthora infestans causes significant damage to potato and tomato and the epidemiology is known to be highly clonal. Our objective was to measure population structure within the context of this clonal epidemiology using both synonymous and nonsynonymous markers. Candidate SNP sites were selected by comparing the draft genomes of the Ecuadorian isolates EC1-3527 and EC1-3626. Genotypes were assessed directly from infected tissue using a targeted sequencing approach. A total of 54 polymorphic sites were assessed in 93 …

Characterization Of Head Involution Defective (Hid) As A Pro-Apoptotic Gene In Megasalia Scalaris, Hakyong Kwak

Chancellor’s Honors Program Projects

No abstract provided.

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 …

Dominance Of Old End Growth Is Inherited In Fission Yeast, Julie Tia Rich

Chancellor’s Honors Program Projects

No abstract provided.

Distribution Of Abc Transporter Genes Across The Plant Kingdom, Thomas Scott Lane

Masters Theses

The ATP-binding cassette (ABC) transporter gene superfamily is ubiquitous among extant organisms. ABC transporters act to transport compounds across cellular membranes and are involved in a diverse range of biological processes and functions including cancer resistance in humans, drug resistance among vertebrates, and herbicide resistance in weeds. This superfamily of genes appears to be larger and more diverse in the plant kingdom—yet, we know relatively less about ABC transporter function in plants compared with mammals and bacteria. Therefore, we undertook a plant kingdom-wide transcriptomic survey of ABC transporters to better understand their diversity.

We utilized sequence similarity-based informatics techniques to …

Cloning Of Ribosomal Its Pcr Products Creates Frequent, Non-Random Chimeric Sequences – A Test Involving Heterozygotes Between Gymnopus Dichrous Taxa I And Ii., Karen Hughes, Samuel D. Morris, Ana L. Reboredo-Segovia

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Gymnopus dichrous exists in the southern Appalachians as two distinct entities with essentially identical nuclear ribosomal ITS1 sequences but differing ITS2 and LSU sequences (for convenience, called G. dichrous I and II). F₁ ITS heterozygotes between the two are routinely collected from nature. Cloning of ITS PCR products from F₁ heterozygotes produced sequences of both parental haplotypes but also numerous chimeric sequences (21.9%). The location of template switching was non-random leading to recovery of the same chimera several times and the chimeric region varied from 45bp to 300bp. By comparison, single-basidiospore isolates from heterozygote F₁ fruitbodies showed …