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  • Advances in Freshwater Cyanobacterial Genomics

    Creator:
    Brown, Nathaniel M.
    Abstract:
    Limnology is undergoing a transition to high-throughput -omic analysis of freshwater bacterial communities. An important first step in making the transition is to characterize several genomes that can be used as references to guide metagenome assembly and analysis. Here I characterize four new freshwater cyanobacterial genomes, a pair of lake...
    Resource Type:
    Dissertation
    Full Text:
    lake community metagenomes, and a temperate phage. • The Anabaena sp. WA102 genome is sequenced with

  • Genome-enabled investigation of the minimal growth requirements andphosphate metabolism for Pelagibacter marine bacteria

    Creator:
    Carini, Paul J.
    Abstract:
    Members of the SAR11 clade of heterotrophic α-proteobacteria are ubiquitous and abundant in the world's oceans where they are thought to play a pivotal role in the global carbon cycle. The first SAR11 bacterium cultivated in vitro, 'Candidatus Pelagibacter ubique' HTCC1062 (Ca. P. ubique), was isolated by dilution into sterile...
    Resource Type:
    Dissertation
    Full Text:
    presented on May 23, 2013. Title: Genome-Enabled Investigation of the Minimal Growth Requirements and

  • Evolution of a streamlined cooperator in Pseudomonas aeruginosa quorum sensing

    Creator:
    Huie, Jessica L.
    Abstract:
    Social behavior leading to the production of common goods is prone to exploitation. One such behavior in Pseudomonas aeruginosa is quorum sensing (QS), by which the bacteria produce signals to regulate extracellular common goods. Exploitation comes in the form of cheaters which have a mutation in the central quorum sensing...
    Resource Type:
    Masters Thesis
    Full Text:
    Genome Research and Biocomputing (CGRB). Numerous genes were Table 2. Plasmids used in this study

  • Recombination, resistance, and drug discovery in Chlamydia

    Creator:
    Sandoz, Kelsi
    Abstract:
    The intracellular life cycle of Chlamydia has been difficult to study due to the inability to genetically manipulate the bacteria. As a result, indirect methods have been employed to study the pathogen and the aspects that contribute to its unique intracellular life cycle. A wide variety of laboratory adapted strains,...
    Resource Type:
    Dissertation
    Full Text:
    genome characterization to identify regions targeted by recombination. Through these studies, we show

  • Transcriptomic analysis using high-throughput sequencing and DNA microarrays

    Creator:
    Fox, Samuel E.
    Abstract:
    Transcriptomics and gene expression profiling enables the elucidation of the genetic response of an organism to various environmental cues. Transcriptomics enables the deciphering of differences between two closely related organisms to the same environment and in contrast, enables the elucidation of genetic responses of the same organism to different environmental...
    Resource Type:
    Dissertation
    Full Text:
    transcriptomic sequence resources must be available. As a basic research necessity, a quality genome or at

  • Processing and functional diversity of plant microRNA

    Creator:
    Cuperus, Josh
    Abstract:
    RNA interference pathways can involve amplification of secondary siRNAs by RNA-dependent RNA polymerases. In plants, RDR6-dependent secondary siRNAs, including transacting siRNAs (tasiRNAs), arise from transcripts targeted by some microRNAs (miRNAs). In the case of TAS3 tasiRNA formation, ARGONAUTE7 (AGO7)-miR390 complexes interact with primary transcripts at two sites, resulting in recruitment...
    Resource Type:
    Dissertation
    Full Text:
    direct genome sequencing-based approach to both map and rapidly identify one of the latter mutant

  • Quorum sensing gene regulation in Pseudomonas aeruginosa

    Creator:
    Gupta, Rashmi
    Abstract:
    Pseudomonas aeruginosa is an opportunistic human pathogen that infects immunocompromised individuals such as those suffering from burns or the genetic disorder cystic fibrosis. This organism utilizes a cell-cell communication mechanism known as quorum sensing (QS) to coordinate virulence gene expression and biofilm formation. It has three interconnected QS systems, namely...
    Resource Type:
    Dissertation
    Full Text:
    equipments and chemicals. I am also thankful to Centre for Genome Research and Biocomputing for their help

  • Cooperation and conflict in Pseudomonas aeruginosa quorum sensing

    Creator:
    Wilder, Cara N.
    Abstract:
    Pseudomonas aeruginosa is an environmental bacterium as well as an opportunistic pathogen that primarily infects immunocompromised individuals, including those suffering from cystic fibrosis. The density-dependent regulation of gene expression via cell-to-cell communication, also termed quorum sensing (QS), is an important virulence determinant in this organism. Generally, P. aeruginosa uses three...
    Resource Type:
    Dissertation
    Full Text:
    , colleagues, and members of the Microbiology Department who assisted, advised, and encouraged my research

  • Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes

    Creator:
    Zhuo, Bin
    Abstract:
    Differential expression (DE) analysis is a key task in gene expression study, because it uncovers the association between expression levels of a gene and the covariates of interest. This dissertation pertains to two particular aspects of DE analysis—identifying stably expressed genes for count normalization and accounting for correlation between DE...
    Resource Type:
    Dissertation
    Full Text:
    genome-wide data. Most conventional enrichment testing methods ignore or do not properly account for the

  • Genomic Resource Development and Studies of Thermal Tolerance in Symbiotic Cnidarians

    Creator:
    Elder, Holland L.
    Abstract:
    Reef building corals are the foundation of an entire ecosystem, but they are threatened primarily by rising ocean temperatures due to climate change. Corals depend on a thermally sensitive symbiosis with intracellular dinoflagellates. As oceans warm, this symbiosis is disrupted and results in coral mortality, declining populations and degraded reefs....
    Resource Type:
    Dissertation
    Full Text:
    Genome Research and Biocomputing (CGRB), Oregon State University (OSU). 12 The raw reads