Molecular Biology Commons^™

Validation Of Whole Genome Resequencing For Mapping The Genetics Of Ascites In Broilers And Viral Susceptibility In Layers, Katherine Pepper Lee

Graduate Theses and Dissertations

This dissertation focused on the efficacy and validity of whole genome resequencing (WGR) for fine mapping genetic determinants of particular traits in a given organism. Previously, our research group used WGR to identify haplotype blocks of single nucleotide polymorphisms associated with ascites resistance with some as strong candidates for use in marker-assisted selection (MAS). Chapter 2 discusses the completion of a MAS project through evaluation of ascites incidence as well as production traits of economic value to poultry producers. Thus, the MAS project also covered viability of this methodology in the industry. The MAS significantly reduced ascites incidence in broilers …

Development Of Indicators For Human Fecal Pollution Using Deep-Sequencing Of Microbial Communities, Shuchen Feng

Theses and Dissertations

The gut microbiome is shaped by both host physiology and environmental factors, which results in unique communities that contain certain members specific to a host. Microbial source tracking (MST) methods that rely on host-specific fecal microorganisms have been applied to detect human fecal pollution over the past two decades. The most common approach uses quantitative polymerase chain reaction (qPCR) to amplify certain sequences of these microorganisms, or human fecal markers. To date, most bacterial human fecal markers have focused on the HF183 cluster within the genus Bacteroides. However, cross-reactions with animals or variable Bacteroides abundance in humans have been found. …

Characterizing The Human Vaginal Microbiome Using High-Throughput Sequencing, Jean Megan E. Macklaim

Electronic Thesis and Dissertation Repository

The human vaginal microbiome undoubtedly has a significant role in reproductive health and for protection from infectious organisms. Recent efforts to characterize the bacterial species of the vagina using molecular techniques have uncovered an unexpected diversity. Using high-throughput sequencing I sought to describe the structure and function of the vaginal microbiome under different physiological states including healthy, bacterial vaginosis (BV), post-menopausal vaginal atrophy, and acute vulvovaginal candidiasis (VVC).

Partial 16S rRNA gene sequencing revealed that healthy, asymptomatic women most often have vaginal biotas dominated by Lactobacillus iners or L. crispatus. In contrast, BV is a heterogeneous, highly diversified condition …

Functional Genomic Investigation Of Aromatic Aminotransferases Involved In Ephedrine Alkaloid Biosynthesis In Ephedra Sinica (Stapf), Korey G. Kilpatrick

Electronic Thesis and Dissertation Repository

Ephedra sinica (Ephedraceae) is a broom-like shrub cultivated in arid regions of China, Korea and Japan. This medicinal plant accumulates large amounts of the ephedrine alkaloids, including (S)-cathinone, (1R,2S)-norephedrine, (1R,2S)-ephedrine and (1S,2S)-pseudoephedrine in its aerial tissues. These analogues of amphetamine mimic adrenaline and stimulate the sympathetic nervous system. While much is known about their pharmacological properties, the biological mechanisms by which they are synthesized remains largely unknown. A functional genomics platform was established in order to investigate alkaloid biosynthesis. RNA was extracted from Ephedra sinica stems …

Genome-Wide Identification Of Conditionally Essential Genes In Salmonella Typhimurium Using Tn-Seq Method, Anita Khatiwara

Graduate Theses and Dissertations

ABSTRACT

As more whole genome sequences become available, there is an increasing need for high-throughput methods that link genes to phenotypes and facilitate discovery of new gene functions. The objective of this study was to develop a high-throughput method to study gene functions in bacteria and use this method to study gene functions of S. enterica serotype Typhimurium (S. Typhimurium) under various environmental conditions encountered during its life cycle. Chapter I of this dissertation reviews the history and evolution of functional genomics in bacteria with focus on Salmonella, along with the recent techniques available. Chapter II, deals with the development …