Life Sciences Commons^™

Role Of Incompatibility Group 1 (Inci1) Plasmid-Encoded Factors On Salmonella Enterica Antimicrobial Resistance And Virulence, Pravin Raghunath Kaldhone

Graduate Theses and Dissertations

Foodborne illnesses are a leading cause of infectious diseases in the world. Among enteric organisms Salmonella is a key pathogen. It’s high prevalence in poultry and other food-animal sources make it imperative to study. Salmonella has the ability to modify its genetic content with help of mobile genetic elements such as plasmids. Incompatibiltiy group 1 (IncI1) plasmids are commonly reported in Salmonella. This study evaluates role on IncI1 plasmids in antimicrobial resistance and virulence in Salmonella. Genetic determinants of resistance and virulence are noted among our IncI1-containing Salmonella isolates. These genetic elements are also transferable and reported to carry respective …

Diversity In Grain Amaranths And Relatives Distinguished By Genotyping By Sequencing (Gbs), Xingbo Wu, Matthew W. Blair

Agricultural and Environmental Sciences Faculty Research

The genotyping by sequencing (GBS) method has become a molecular marker technology of choice for many crop plants because of its simultaneous discovery and evaluation of a large number of single nucleotide polymorphisms (SNPs) and utility for germplasm characterization. Genome representation and complexity reduction are the basis for GBS fingerprinting and can vary by species based on genome size and other sequence characteristics. Grain amaranths are a set of three species that were domesticated in the New World to be high protein, pseudo-cereal grain crops. The goal of this research was to employ the GBS technique for diversity evaluation in …

Detecting Large Deletions At Base Pair Level By Combining Split Read And Paired Read Data, Matthew Hayes, Jeremy S. Pearson

Computer Science Student Research

Background

Genomic structural variants (SV) play a significant role in the onset and progression of cancer. Genomic deletions can create oncogenic fusion genes or cause the loss of tumor suppressing gene function which can lead to tumorigenesis by downregulating these genes. Detecting these variants has clinical importance in the treatment of diseases. Furthermore, it is also clinically important to detect their breakpoint boundaries at high resolution. We have generalized the framework of a previously-published algorithm that located translocations, and we have applied that framework to develop a method to locate deletions at base pair level using next-generation sequencing data. Our …

Sequence Extension Of The Tryptophan And Shikimate Operons In Clostridium Scatologenes Atcc 25775, Shawn Johnston Smiley

Masters Theses & Specialist Projects

3-Methylindole and 4-methylphenol are cytotoxic and malodorant compounds derived from tryptophan and tyrosine, respectively. Each is present in swine waste lagoons and contributes to malodorous emissions from agricultural facilities. Clostridium scatologenes ATCC 25775 produces both compounds and serves as a model organism to study their metabolism and function. Through the repeated assembly and annotation of the Clostridium scatologenes genome, we propose a novel pathway for tryptophan degradation and 3-methylindole production by this organism. The genome of Clostridium scatologenes was sequenced, and re-assembled into contigs. Key elements of the tryptophan and shikimate pathways were identified. Contigs containing these elements were extracted …

Rna Sequencing In The Development Of Cancer-Cachexia, Thomas Allen Blackwell

Graduate Theses and Dissertations

Introduction: Cancer is a major public health problem in the U.S. and the world. In 2013 there were an estimated 1,660,290 new cases of cancer in the U.S. Cancer-Cachexia (CC) is a common effect of many cancers, and is directly responsible for 20-40% of cancer-related deaths. The mechanisms that control the development of CC are not well understood. Most investigations of CC focus on the post-cachectic state and do not examine the progression of the condition. The purpose of this study was to utilize RNA sequencing to analyze transcriptomic alterations throughout the progression of CC. Methods: Lewis Lung Carcinoma cells …

Dna Analysis Of Surfactant-Associated Bacteria In A Natural Sea Slick In The Gulf Of Mexico Observed By Terrasar-X, Kathryn Howe

HCNSO Student Theses and Dissertations

Under low wind speed conditions, surfactants accumulate at the air-sea interface, dampen short-gravity capillary (Bragg) waves, and form natural sea slicks that are detectable visually and in synthetic aperture radar (SAR) imagery. Marine organisms, such as phytoplankton, zooplankton, seaweed, and bacteria, produce and degrade surfactants during various life processes. This study coordinates in situ sampling with TerraSAR-X satellite overpasses in order to help guide microbiological analysis of the sea surface microlayer (SML) and associated subsurface water (SSW). Samples were collected in the Gulf of Mexico during a research cruise (LASER) in February 2016 to determine abundance of surfactant associated bacteria …

Hepatic Drug Metabolism, Uremic Toxins And Bacterial Composition Over Chronic Kidney Disease Progression, Emily Dee Hartjes

Electronic Thesis and Dissertation Repository

Uremic toxin retention and an altered gut microbiota are suspected to influence cytochrome P450s (CYPs) contributing to the unpredictable pharmacokinetics in chronic kidney disease (CKD). We aim to characterize dysbiosis and uremia to elucidate associations between CYP expression and CKD progression. Rats fed control or CKD-inducing diet were subsequently sacrificed across five time points over 42 days. CYP expression and activity were compared to alterations in the 1) plasma and liver metabolome and 2) bacterial microbiota. CYP3A2 and CYP2C11, respectively, were downregulated in CKD by ≥76% (p<0.001) simultaneously or slightly premature to CKD onset defined by creatinine. Metabolite profiles were altered before the gut microbiota and gut-derived uremic toxins including indoxyl sulfate, phenyl sulfate and 4-ethylphenyl sulfate correlated with CYP3A2 or CYP2C11. Identified bacterial genera, Turicibacter and Parabacteroides, characterized CKD and require future study. In conclusion, CYP3A2 and CYP2C11 are downregulated prior to dysbiosis but correlate with select uremic toxins.

An Approach To Identify Mycobacteriophage Diversity Prior To Dna Sequencing, Charles Gregory

Mahurin Honors College Capstone Experience/Thesis Projects

Over 6,869 Mycobacteriophages have been isolated and purified. Of these, 1,367 genomes have been sequenced at the DNA level and more are added each year through the SEA-PHAGES program. Sequenced mycobacteriophages are grouped into clusters based on a 50% or greater nucleotide identity. The number and breadth of these clusters represents the diversity present in the environment. Each year, as new phages are discovered by students in the SEA-PHAGES program, the question arises, “Which isolates should we sequence?” In order to sequence phages that represent the greatest possible diversity, and thus broaden under-represented clusters and identify new singletons, we need …

Rosa Hybrid Gene Gapc Is Mutated In The Presence Of The Rose Rosette Virus, William A. Beams, Eva L. Burelos, Charles C. Hundley, Landon R. Dame, Laura G. Sims, Jacob J. Adler

Kentucky Journal of Undergraduate Scholarship

Rose Rosette Disease (RRD) harms the global rose supply by modification of the growth and development in rose cultivar. RRD spreads via a negative-sense RNA plant virus transmitted by eriophyid mites. Importantly, there is no pre-existing knowledge about the biochemistry by which this virus debilitates roses. Here we implicate glyceraldehyde-3-phosphate dehydrogenase (GAPDH), one of the major metabolic enzymes in plants, as a possible target of the virus. Genomic DNA of the cytosolic form of the protein encoded by GAPC was extracted from both virally-infected and non-infected samples of the Rosa hybrid cultivar Rosa Tropicana. The sequence results provided several distinct …

Comparative Transcriptome Analysis Of Wild Tomato Species During Fruit Development, Altynay Zhanayeva

Masters Theses

Fleshy fruits in different species can display large variation in color. A link between fruit color and seed dispersal success is suggested by previous studies showing that high intensity of fruit color increases the visitation rate in seed-dispersing birds. Wild tomato species (Solanum spp.) are excellent model organisms for research on genetic basis of differential fruit color development during the ripening process. Despite polymorphism in fruit color, all tomato species have yellow flowers due to accumulation of carotenoid pigments, which suggests that the carotenoid pathway is intact. Thus, regulatory changes controlling enzymes activity during fruit maturation are likely …

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp01 And Dp02 From May 2015 - August 2015, Cole Easson, Jose V. Lopez

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during two planned DEEPEND cruise expeditions to the GOM. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable region was generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Bioinformatics analyses in QIIME and R was used to quality filter and assess microbial community diversity and taxonomic composition. These baseline characterizations track alpha and beta diversity at different depths ranging from 0 – …