Browsing by Subject "bacteriophage"

Now showing 1 - 3 of 3
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    Dictionary-based methods and their applications in biology and medicine
    (2021-05) Lenskaia, Tatiana
    This study proposes methods to explore genome organization and identify genome interactions that do not rely on annotations and aim to work on whole genome data. These methods use string matching between collections of dictionaries that depict genomes with different levels of resolution. Each dictionary represents a mapping of the complete genome data into a set of unique fixed-length segments. The methods are inspired by biological mechanisms including restriction-modification systems and CRISPR-Cas defenses that use exact matching. The use of this string-oriented approach might help researchers better understand biological mechanisms and avoid many of the drawbacks associated with annotations. These methods shift the computational paradigm from looking for specific instances such as genes and other elements within a genome to "full-search" analysis without preconceived targets. We hypothesize that the development of efficient dictionary-based screening methods will lead to a better understanding of genome organization and genome interactions. The results of this study indicate that these methods can capture many biologically significant relationships not easily captured by traditional approaches. The results of this study contribute to (a) changing a computational paradigm for processing genome data; (b) developing new methods for analyzing genome organization and relationships between genomes; and, (c) identifying and evaluating potential genome interactions at a broader scale for biological and medical applications.
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    Discovering Ecological and Evolutionary Principles Governing Microbial Community Responses to Bacteriophage Infection of a Cross-Feeding Synthetic Coculture and Implications for Phage-based Applications
    (2020-08) Fazzino, Lisa
    Bacterial viruses, called bacteriophage (phage), infect bacteria and alter microbial community structure. Phages are an untapped resource to manipulate agriculture and medically applicable microbial communities. Yet, we cannot predict how phage impact a microbial community. My research aims to uncover ecological and evolutionary principles governing responses of microbial communities that contain cross-feeding interactions, where one species provides nutrients to (‘feeds’) another, phage. I combine wet-lab experiments on an engineered microbial co-culture with mathematical modeling to explore aspects of phage infection that are difficult to manipulate experimentally. I use a cross-feeding bacterial co-culture with Escherichia coli (E. coli) and Salmonella enterica (S. enterica) bacterial strains. In this cross-feeding system, E. coli cannot produce methionine, but does produce acetate and galactose. E. coli is paired with S. enterica that over-produces methionine and consumes acetate and galactose that E. coli secretes. To this co-culture, I add phage that infect either species. I have asked how simple cross-feeding co-cultures respond to phage infection. In Chapter 2, I used mathematical modeling and wet-lab experiments to show that single phage infections can break the cross-feeding relationship by liberating nutrients previously sequestered in the infected bacterial cells, ultimately changing community composition, and that partial, not full, resistance was necessary for this effect. In Chapter 3, ‘cocktails’ made of two different phage suppressed community growth the longest in a novel formulation that targeted both the pathogenic bacterial species and the slowest growing cross-feeder. Mathematical modeling showed that this was a generalizable concept to all cross-feeding systems. In Chapter 4, despite impacting community structure, I found that long term co-evolution between phage and E. coli cross-feeding with S. enterica only had weak effects on rates of adaptation. Phage treatments tended to increase rates of adaptations, as predicted by the Red Queen hypothesis, and cross-feeding tended to decrease rates of adaptation, as predicted by the Red King hypothesis. Overall, this thesis helps set baseline expectations of how phage influence cross-feeding microbial communities.
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    ToxIN-mediated resistance to and cell-free production of Salmonella bacteriophages
    (2023-05) McFarlane, John
    Salmonella remains a leading cause of foodborne illnesses in the U.S. and worldwide. Though numerous strategies are implemented to control foodborne Salmonella, many come with limitations that reduce their efficacy or restrict which foods can be treated. An alternative control strategy that addresses these limitations is the application of bacteriophage cocktails, consisting of numerous bacterial viruses which kill the target pathogen. However, the use of phages also comes with two significant drawbacks: phage resistance and manufacturing hurdles. Resistance to phages may reduce the efficacy of phage cocktails, while concerns with at-scale phage production include handling of pathogenic host bacteria and optimization of numerous, complex biological variables. In the first part of this work, I show that ToxIN, a resistance system which aborts phage infection, is present in outbreak strains of Salmonella; confers resistance to the broad host range phage FelixO1 and other phage isolates; and is found in the whole-genome sequences of numerous Salmonella serovars and in other human pathogens. The second half of this work describes the in vitro synthesis of FelixO1 using an Escherichia coli-based cell-free expression system, demonstrating for the first time that a Salmonella phage can be produced in this manner. Taken together, this work illustrates that ToxIN may be of concern for food applications of phages while also establishing an important milestone in advancing Salmonella biocontrol using phages.