Bioinformatics Commons^™

Modeling The Egyptian Goose (Alopochen Aegyptiaca) Invasion; And Future Concerns, Percival Matzinger Marshall

Graduate Theses and Dissertations

In an increasingly interconnected world, the ecological and financial cost of invasive species is expected to continue to climb through the movement of exotic biota. Understanding the driving forces behind how a species invades, what environments promote their establishment, and what impacts they are likely to have on the invaded environment are all critical for management. Waterfowl, order Anseriformes, are one such category of invasive species of concern due to their popularity of accidental introduction, ease of movement, and propensity to affect both terrestrial and aquatic ecosystems. The Egyptian Goose (Alopochen aegyptiaca) is a native to the African continent that …

Ecology, Evolution, And Gene Transfer Between Diatoms And Bacteria, Cory B. Gargas

Graduate Theses and Dissertations

Although photosynthetic macro-eukaryotes (i.e., plants) make up the majority of organic biomass on earth, bacteria are the second largest taxonomic group, by biomass. Bacteria are ubiquitous in our environment, living on, and within, man-made surfaces, natural environments, and eukaryotes themselves. The relationship between bacteria and eukaryotes has existed from the very beginning of eukaryotic life in the form of bacterial endosymbioses that resulted in mitochondria and plastids. Other eukaryote–bacteria relationships have evolved since then, ranging from the beneficial (e.g., mutualistic) to harmful (e.g., parasitic or pathogenic). Understanding these eukaryote–bacteria relationships is key to understanding both the evolution of important ecosystem …

The Antimicrobial Resistance Plasmid Mobilome Of Salmonella Enterica And Related Enteric Species And Factors That Influence The Transfer Efficiency., Suad Algarni

Graduate Theses and Dissertations

The dynamic distribution of antimicrobial resistance genes in Salmonella enterica is considered a public health risk. S. enterica is one of the most important etiological agents of foodborne illness and has a critical impact on global human health. In S. enterica and related species, mobile genetic elements (MGEs) serve as primary vehicles for the dissemination of antibiotic resistance genes in the bacterial evolution. This dissemination can be impacted by different selective pressures that leads to diverse antibiotic response phenotypes. This project focusses on the dynamics of antimicrobial resistance genes, particularly exploring the transfer efficiency of multidrug resistance plasmids in S. …

Characterization Of Iron-Sulfur Cluster Biogenesis In Methanogenic Archaea, Thomas Modlin Deere

Graduate Theses and Dissertations

Iron-sulfur (Fe-S) clusters are among the oldest cofactors on the planet, used by proteins in almost all forms of life on Earth to carry out processes ranging from energy transfer to DNA replication. Among the organisms believed to use these Fe-S proteins more extensively than almost any others are the methanogens, an ancient lineage of archaeal microbes that produce methane as a required product of their metabolism. Methane, the primary component of commercial natural gas, is both a potent greenhouse gas and an important fossil fuel. It can also be renewably produced as a biofuel. Biogenic methane is almost entirely …

Trunctrimmer: A First Step Towards Automating Standard Bioinformatic Analysis, Z. Gunner Lawless, Dana Dittoe, Dale R. Thompson, Steven C. Ricke

Computer Science and Computer Engineering Undergraduate Honors Theses

Bioinformatic analysis is a time-consuming process for labs performing research on various microbiomes. Researchers use tools like Qiime2 to help standardize the bioinformatic analysis methods, but even large, extensible platforms like Qiime2 have drawbacks due to the attention required by researchers. In this project, we propose to automate additional standard lab bioinformatic procedures by eliminating the existing manual process of determining the trim and truncate locations for paired end 2 sequences. We introduce a new Qiime2 plugin called TruncTrimmer to automate the process that usually requires the researcher to make a decision on where to trim and truncate manually after …

An Automated Method To Enrich And Expand Consumer Health Vocabularies Using Glove Word Embeddings, Mohammed Ibrahim

Graduate Theses and Dissertations

Clear language makes communication easier between any two parties. However, a layman may have difficulty communicating with a professional due to not understanding the specialized terms common to the domain. In healthcare, it is rare to find a layman knowledgeable in medical jargon, which can lead to poor understanding of their condition and/or treatment. To bridge this gap, several professional vocabularies and ontologies have been created to map laymen medical terms to professional medical terms and vice versa. Many of the presented vocabularies are built manually or semi-automatically requiring large investments of time and human effort and consequently the slow …

Gene Set Testing By Distance Correlation, Sho-Hsien Su

Graduate Theses and Dissertations

Pathways are the functional building blocks of complex diseases such as cancers. Pathway-level studies may provide insights on some important biological processes. Gene set test is an important tool to study the differential expression of a gene set between two groups, e.g., cancer vs normal. The differential expression of a gene set could be due to the difference in mean, variability, or both. However, most existing gene set tests only target the mean difference but overlook other types of differential expression. In this thesis, we propose to use the recently developed distance correlation for gene set testing. To assess the …

Metatranscriptomics Analysis Of Ileum Microbial Communities In Necrotic Enteritis Chickens, Ruchita Uttarwar

Graduate Theses and Dissertations

Necrotic enteritis (NE) is a recognized multifactorial disease that causes an annual loss of $6 billion to the poultry industry. Thus, it has become essential to carry a comprehensive study of the composition of chicken gut which hosts this disease. The objective of this research is to measure the changes occurring in microbiome inside intestinal ilium of NE affected broilers which were treated with tributyrin supplement. This supplement is an anti-inflammatory metabolite that stabilizes intestinal integrity. The experimental design consisted of two challenge groups (No -Challenge, Clostridium Perfringens (CP) - Challenge) and one treatment group (tributyrin). To our knowledge, this …

The Effects Of Storage Temperature On The Bovine Nasal Microbiome, Hunter Usdrowski

Animal Science Undergraduate Honors Theses

Bovine respiratory disease (BRD) is one of the largest economic burdens facing United States beef producer’s modern day. The complexity in the onset and development of this multifactorial disease necessitates further insights into its functions to alleviate the tremendous consequences it generates for producers. The respiratory microbiome and their metabolomics play an important role to maintain health and predict BRD. However, due to low biomass, new technology is needed to increase the microbial concentration for omics (e.g. metatranscriptomics) research. In this study, a novel self-enrichment storage technique on the bovine nasal microbiome was performed and compared to a traditional nasal …

Evolutionary Inference From Admixed Genomes: Implications Of Hybridization For Biodiversity Dynamics And Conservation, Tyler Chafin

Graduate Theses and Dissertations

Hybridization as a macroevolutionary mechanism has been historically underappreciated among vertebrate biologists. Yet, the advent and subsequent proliferation of next-generation sequencing methods has increasingly shown hybridization to be a pervasive agent influencing evolution in many branches of the Tree of Life (to include ancestral hominids). Despite this, the dynamics of hybridization with regards to speciation and extinction remain poorly understood. To this end, I here examine the role of hybridization in the context of historical divergence and contemporary decline of several threatened and endangered North American taxa, with the goal to illuminate implications of hybridization for promoting—or impeding—population persistence in …

Massard Prairie Restoration And Soil Microbiome Succession, Jeffrey M. Shaver, Emily S. Bellis, Chizuko Iwaki, Jake Qualls, Jay Randolph, Jeremiah Smith

Journal of the Arkansas Academy of Science

We have initially sequenced soil microbial DNA from 4 restored and 4 virgin tallgrass prairie soil samples from Ben Geren Park and Massard Prairie (Fort Smith, AR), respectively. As expected, the soil microbiomes are distinct, with several lineages of nitrogen-fixing bacteria more common in virgin tall grass prairie. However, we predict that as restoration of tallgrass prairie in Ben Geren Park progresses, the soil microbiome of restored prairie will more closely mirror those of the virgin prairie.

Diversification Across A Dynamic Landscape: Phylogeography And Riverscape Genetics Of Speckled Dace (Rhinichthys Osculus) In Western North America, Steven Michael Mussmann

Graduate Theses and Dissertations

Evolution occurs at various spatial and temporal scales. For example, speciation may occur in historic time, whereas localized adaptation is more contemporary. Each is required to identify and manage biodiversity. However, the relative abundance of Speckled Dace (Rhinichthys osculus), a small cyprinid fish in western North America (WNA) and the study species for this dissertation, establishes it an atypical conservation target, particularly when contrasted with the profusion of narrowly endemic forms it displays. Yet, the juxtaposition of ubiquity versus endemism provides an ideal model against which to test hypotheses regarding the geomorphic evolution of WNA. More specifically, it also allows …

Genetic And Epigenetic Investigations On Pulmonary Hypertension Syndrome In Meat Type- Chickens, Khaloud Alzahrani

Graduate Theses and Dissertations

This dissertation presents a collection of studies that investigate the genetic and epigenetic associations to ascites phenotype in broiler chickens. Ascites is a significant metabolic disease associated with fast-growing meat-type chickens (broilers) and is a terminal result of pulmonary hypertension syndrome PHS. It is a multi-factorial syndrome caused by interactions between genetic, physiological, environmental, and managemental factors. It was estimated that ascites accounts for losses of about US$1 billion annually worldwide and for over 25% of broilers mortality. Although traditional and molecular genetic methods in the selection and in performance improvements, has greatly reduced ascites frequency, yet it has not …

Genomic Approaches To Identify Important Traits In Avian Species, Bhuwan Khatri

Graduate Theses and Dissertations

This dissertation focusses on identifying different molecular markers that have impact on overall poultry production. Chapter one reviews microRNA (miRNA), copy number variation (CNV) and single nucleotide polymorphism (SNP) as markers suggested in different avian species by various studies. It reviews modern genomic approaches that are employed for next generation sequencing data analysis and verification.

Chapter two seeks to identify and validate the muscle specific miRNAs in the breast muscle of modern broilers and its foundational chicken line. Small RNA sequencing was performed to identify differentially expressed mature miRNAs in the breast muscles of these two chicken lines. Results showed …

Unravelling The Layers Of Cell Wall Synthesis And Function In Rice, Ritu Mihani

Graduate Theses and Dissertations

The plant cell wall is of critical importance to plant growth and survival, functioning in maintaining structural integrity, supporting cell expansion, and acting as the first line of defense in response to biotic and abiotic stresses. The major components of the cell wall are cellulose, hemicelluloses, lignin, and pectin. Recent focus on the transcriptional machinery regulating cell wall biosynthesis in plants has revealed many key transcription factors responsible for orchestrating cell wall deposition. However, many of these TFs act redundantly and work coherently with a suite of TFs to activate the cell wall biosynthetic machinery. Heterologous expression of TFs is …

Phylogeny And Evolutionary Genomics Of Non-Photosynthetic Diatoms, Anastasiia Onyshchenko

Graduate Theses and Dissertations

Diatoms are prolific photosynthesizers responsible for some 20% of global primary production. In real terms, the oxygen in one of every five breaths traces back to photosynthesis by marine diatoms. Among the tens of thousands of diatom species, a small handful of colorless diatom species in the genus Nitzschia have lost photosynthesis altogether and rely exclusively on extracellular organic carbon for growth. I used DNA sequence data to reconstruct the phylogeny of this group, and found that nonphotosynthetic diatoms are monophyletic, indicating that photosynthesis was lost just one time over the course of some 200 million years of diatom evolution. …

Bayesian Network Modeling And Inference Of Gwas Catalog, Qiuping Pan

Graduate Theses and Dissertations

Genome-wide association studies (GWASs) have received an increasing attention to understand genotype-phenotype relationships. The Bayesian network has been proposed as a powerful tool for modeling single-nucleotide polymorphism (SNP)-trait associations due to its advantage in addressing the high computational complex and high dimensional problems. Most current works learn the interactions among genotypes and phenotypes from the raw genotype data. However, due to the privacy issue, genotype information is sensitive and should be handled by complying with specific restrictions. In this work, we aim to build Bayesian networks from publicly released GWAS statistics to explicitly reveal the conditional dependency between SNPs and …

Transcriptome-Based Gene Networks For Systems-Level Analysis Of Plant Gene Functions, Chirag Gupta

Graduate Theses and Dissertations

Present day genomic technologies are evolving at an unprecedented rate, allowing interrogation of

cellular activities with increasing breadth and depth. However, we know very little about how the

genome functions and what the identified genes do. The lack of functional annotations of genes

greatly limits the post-analytical interpretation of new high throughput genomic datasets. For plant

biologists, the problem is much severe. Less than 50% of all the identified genes in the model plant

Arabidopsis thaliana, and only about 20% of all genes in the crop model Oryza sativa have some

aspects of their functions assigned. Therefore, there is an …

Genome Wide Association And Next Generation Sequencing Approaches To Map Determinants Of Ascites In Broiler Chickens, Shatovisha Dey

Graduate Theses and Dissertations

These studies have investigated different candidate genomic regions for their contributions to ascites in broilers. Ascites syndrome is a manifestation of idiopathic pulmonary arteriole hypertension that concerns the poultry industry worldwide. Investigations have demonstrated the disease to be genetically regulated and to exhibit moderate to high heritabilities. Although previous studies have indicated a few chromosomes to be involved with ascites, no genes have been identified to date with direct links to the disease. This dissertation presents a collection of studies that determine the genomic and genetic interactions for regions on chromosome 2 and 9 for ascites phenotypes in broiler chickens. …

The Bovine Rumen Microbiome Revealed By Different Fractions Of Rumen Contents, Ashlee L. Breakstone

Animal Science Undergraduate Honors Theses

The bovine rumen microbiota is very important in terms of animal functionality and digestion. The fermentative capability of the rumen provides means for the digestion of complex plant material that is indigestible by humans. The rumen is the working ground for millions of microorganisms, primarily bacteria, to digest and ferment feed into volatile fatty acids and bacterial protein for the animal’s energy and protein needs, respectively. Of significant importance is the rumen microbiomes ability to conform to certain factors such as genetics, feed, or geographic location. These changes can have a direct measure on animal growth, health, and performance. The …

Phylogeography And Vicariant Separation Of Two River Darters, Percina Uranidea And Percina Vigil, From Rivers That Drain The North American Interior Highlands, T. Yamashita, J. M. Rigsby, J. Stoeckel

Journal of the Arkansas Academy of Science

The phylogeography and separation of two river darters, Percina uranidea and P. vigil were investigated through sequencing of the mitochondrial Cytochrome B and Cytochrome Oxidase genes. These molecular markers revealed the darters exhibit moderate genetic divergence between two large river drainage systems within the Mississippi River basin associated with the Interior Highlands of midwestern North America. An additional haplotype network analysis also supported these trends. Phylogenetic divergence dating indicated that population separation between the river systems occurred after recent Pleistocene glacial events rather than an early Pleistocene separation.

Genetic Determinants Of Salmonella And Campylobacter Required For In Vitro Fitness, Rabindra Kumar Mandal

Graduate Theses and Dissertations

Non-typhoidal Salmonella (NTS) and Campylobacter play a major role in foodborne illness caused by the consumption of food contaminated by pathogens worldwide. A comprehensive understanding of the genetic factors that increase the survival fitness of these foodborne pathogens will effectively help us formulate mitigation strategies without affecting the nutrition ecology. The objective of this study was to identify the genetic determinants of Salmonella and Campylobacter that are required for fitness under various in vitro conditions. For the purpose, we used a high throughput Transposon sequencing (Tn-seq) that utilizes next generation sequencing (NGS) to screen hundreds of thousands of mutants simultaneously. …

Bio-Separation Process Improvement Via Genomic Manipulation: Development Of Novel Strains For Use In Immobilized Metal Affinity Chromatography (Imac), Ryan Curtis Haley

Graduate Theses and Dissertations

The dissertation is comprised of three parts. Part I describes proteomic analysis of native bacterial proteins from Escherichia coli (E.coli) that bind during Immobilized Metal Affinity Chromatography (IMAC). Part II describes the value in exploiting proteome based data as a tool toward the design an E. coli expression strain that is particularly useful when Immobilized Metal Affinity Chromatography is employed as the initial capture step of a homologous protein purification process. Part III describes a methodology of chromosomal mapping of all contaminant gene products.

The objective of Part I was to identify all E. coli proteins that bind to Co(II), …

Applications Of Variable Number Tandem Repeat Genotyping In The Validation Of An Animal Medical Model And Gene Flow Studies In Threatened Populations Of Reptiles, Candace D. Smith

Graduate Theses and Dissertations

We used variable number tandem repeats (VNTR) to validate the chicken as a human medical model for Pulmonary Arterial Hypertension. We identified seven regions on four chromosomes and interrogated for VNTR markers that significantly associate with Pulmonary Hypertension Syndrome/ascites. In those regions, we identified 7 candidate genes; AGTR1, ACE, p38MAPK, SST, 5HT2B, NET1, and CALM3 for further analysis as significantly contributing QTL for ascites/PHS. We also used variable number tandem repeats to measure gene flow and gather evidence for multiple paternity in a population of Timber rattlesnakes, Crotalus horridus. We were able to verify 1 VNTR that can be used …

Fecundity Of Male White-Tailed Deer On Holla Bend National Wildlife Refuge, Thomas A. Nelson, Michael W. Johnson

Journal of the Arkansas Academy of Science

Male reproductive tracts were collected from 57 white-tailed deer (Odocoileus virginianus) harvested on Holla Bend National Wildlife Refuge during the 1988 and 1989 archery deer seasons. Organ weights and total numbers of spermatozoa present were determined for both testes and epididymides. Among yearling and adult males, the mean weights of testes and epididymides peaked during November and decreased through the end of the collection period in mid-December. Total number of spermatozoa in the tract increased through October, peaked during the last half of November, and decreased through mid- December. No significant difference was found between the mean number of spermatozoa …