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Item Investigating the regulation of virulence by Sae in Staphylococcus aureus(Montana State University - Bozeman, College of Agriculture, 2020) Collins, Madison Paige Martin; Chairperson, Graduate Committee: Jovanka Voyich-Kane; Ranjan K. Behera, Kyler B. Pallister, Tyler J. Evans, Owen Burroughs, Caralyn Flack, Fermin E. Guerra, Willis Pullman, Brock Cone, Jennifer G. Dankoff, Tyler K. Nygaard, Shaun R. Brinsmade and Jovanka M. Voyich were co-authors of the article, 'The accessory gene saeP of the saeR/S two-component gene regulatory system impacts Staphylococcus aureus virulence during neutrophil interaction' in the journal 'Frontiers in microbiology' which is contained within this dissertation.; Kyler Pallister and Jovanka M. Voyich were co-authors of the article, 'Differential analysis of host/pathogen RNA expression via next generation sequencing reveals Staphylococcus aureus utilizes saeR/S-mediated factors to inhibit human neutrophil functions following phagocytosis' which is contained within this dissertation.Staphylococcus aureus (S. aureus) is a common commensal bacterium known to colonize, at minimum, 30% of the human population. It is also capable of causing a range of diseases that span from minor skin- and soft-tissue infections to life-threatening diseases. The diversity of S. aureus infections is due to the ability of the bacteria to sense and respond to environmental change. Virulence regulation in S. aureus can be attributed to the use of two-component gene regulatory systems (TCS). TCS can sense a variety of encounters including: antibiotics, heat stress, or immune cell encounter. Neutrophils are a key leukocyte involved in bacterial clearance in the human host. It follows that S. aureus has evolved mechanisms to sense and respond to neutrophils. The Sae TCS, is immediately up-regulated after neutrophil phagocytosis and has been demonstrated to be critical in the success of S. aureus both in vitro and in vivo. SaeS, the histidine kinase, and the respective response regulator, SaeR, are established components of the Sae TCS and their importance during neutrophil evasion and pathogenesis is well established. However, little is known about two accessory genes, saeP and saeQ. Results described herein using human neutrophil and murine models of infection provide evidence that SaeP modulates the Sae-mediated response of S. aureus against human neutrophils and suggest that saeQ and saeP together impact pathogenesis in vivo. To identify additional host and pathogen factors important during neutrophil interaction, we used differential analysis of host/pathogen RNA expression via Next Generation Sequencing to define the influence of SaeR/S on the host-pathogen transcriptome following neutrophil phagocytosis. Results determined that in the early stages of S. aureus infection, SaeR/S-dependent factors significantly modulate neutrophil processes involved in several pathways including autophagy, TNF-alpha signaling, and NF-kappaB signaling. These results suggest S. aureus uses SaeR/S-regulated virulence factors to hijack human neutrophil function at the transcriptional level to inhibit proper killing by neutrophils and allow for S. aureus persistence within the host.Item Bacteriophage in host associated microbial communities examined with continuous culture systems(Montana State University - Bozeman, College of Letters & Science, 2018) Dills, Michael Stefan; Co-Chairs, Graduate Committee: Mark J. Young and Seth WalkMechanistic understanding of the role of extracellular and parasitic elements in host ecosystems is currently lacking. Extensive surveys have catalogued a large diversity of bacteriophage which associate differentially with definable host states. This work is an attempt to aid in the development of a coherent model for complex symbiosis within mammalian host ecosystems by investigating the role of bacteriophage in microbial community structure. It details an investigation of continuous culture systems as a platform to study bacteriophage within polymicrobial communities of the human GI tract. It then describes an experiment testing an extracellular community's ability to modulate bacterial community structure.Item Comparative genomic analyses of Yellowstone hot spring microbial mat Synechococcus spp.(Montana State University - Bozeman, College of Agriculture, 2015) Olsen, Millie Helen Thornton; Chairperson, Graduate Committee: David M. Ward; Shane Nowack, Jason M. Wood, Eric D. Becraft, Kurt LaButti, Anna Lipzen, Joel Martin, Wendy S. Schackwitz, Douglas B. Rusch, Frederick M. Cohan, Donald A. Bryant and David M. Ward were co-authors of the article, 'Comparative genomics of Synechococcus isolates with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat' submitted to the journal 'Frontiers in microbiology' which is contained within this thesis.The question of "What is a microbial species?" has been a highly debated issue in the field of microbiology. Many have accepted a molecular species demarcation approach, that any two organisms with a high enough 16S rRNA sequence similarity are members of the same species. However, the Ward lab has shown that there are many ecologically distinct Synechococcus spp. inhabiting hot springs of the Lower Geyser Basin in Yellowstone National Park, WY, that would be defined as members of the same species using the molecular demarcation approach. Using a theory-based species demarcation approach with a conserved photosystem gene (psaA), evidence of the existence of putative ecotypes, or predicted ecologically distinct species, has been found in the microbial mat, distributed along both temperature and light gradients. Isolates representative of these ecologically distinct populations have also been shown to have distinct temperature adaptations and light adaptations. I obtained the genomes of these isolates, which include representatives of populations with different temperature distributions and different vertical distributions, and replicate isolates within individual putative ecotypes. Using these genome sequences, I compared the psaA gene phylogeny and multi-locus sequence phylogenies with a phylogeny created using genes shared among the genomes to explore the effects of recombination on phylogenies of closely-related organisms. I then explored the underlying genetic mechanisms of the niche adaptations of these ecotypes by (i) comparing the isolate gene content, diel transcription patterns, and positive selection evidence of putative ecotypes with different vertical distributions in the mat and different light adaptations, (ii) comparing the gene content and evidence of positive selection among isolates representative of populations with different temperature distributions, and (iii) comparing the gene content and evidence of positive selection among replicate isolates within individual putative ecotypes. I found that, while recombination may have caused the inaccurate demarcation of genetically distinct isolates into a single PE, there is genomic evidence that species of Synechococcus that are ecologically distinct from one another exist, along both temperature and vertical gradients. Members of a species are ecologically homogenous, though there is evidence of some genetic heterogeneity within a species.Item Transformation of Gaeumannomyces graminis and the fate of transforming DNA(Montana State University - Bozeman, College of Agriculture, 1991) Pilgeram, Alice LaRayne; Co-chairs, Graduate Committee: Don E. Mathre and Joan HensonItem Chemotherapeutic elimination of genetic components(Montana State University - Bozeman, College of Agriculture, 1983) Miller, Roger Vincent