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  • Conserved properties in the metagenome of a large bacterioplankton population

    Creator:
    Wilhelm, Larry John
    Abstract:
    Candidatus Pelagibacter ubique is the first cultured representative of the SAR11 clade, a clade that is found throughout the oceans and accounts for approximately 25% of all bacterial cells [1]. It has a streamlined genome that is the smallest of any known free-living organism. In this study the complete genome...
    Resource Type:
    Masters Thesis
    Full Text:
    this study. I owe gratitude to Scott Givan and Daniel Smith for their expert technical

  • Algorithms for massive biological datasets

    Creator:
    Bryant, Douglas W. (Douglas Wesley)
    Abstract:
    Within the past several years the technology of high-throughput sequencing has transformed the study of biology by offering unprecedented access to life's fundamental building block, DNA. With this transformation's potential a host of brand-new challenges have emerged, many of which lend themselves to being solved through computational methods. From de...
    Resource Type:
    Dissertation

  • Genomic-assisted determination of the natural nutrient requirements of the cosmopolitan marine bacterium 'Candidatus Pelagibacter ubique'

    Creator:
    Tripp, H. James
    Abstract:
    To identify factors limiting 'Candidatus Pelagibacter ubique' maximum cell density and growth rate in pure culture on seawater, the genome sequence of 'Cand. P. ubique' was analyzed, culturing experiments with organic and inorganic nutrient additions were made, and radiotracer uptake experiments were performed. The genome was sequenced, custom data mining...
    Resource Type:
    Dissertation
    Full Text:
    experiments confirming bioinformatic predictions. Scott Givan provided copious bioinformatic support

  • Small RNA pathways in plants

    Creator:
    Montgomery, Taiowa A.
    Abstract:
    miRNA-guided cleavage initiates entry of primary transcripts into the trans-acting siRNA (tasiRNA) biogenesis pathway involving RNA-DEPENDENT RNA POLYMERASE6 (RDR6), DICER-LIKE 4 (DCL4), and SUPPRESSOR OF GENE SILENCING3 (SGS3). Arabidopsis thaliana TAS1 and TAS2 families yield tasiRNA that form through miR173- guided initiation cleavage on the 5’ side of the siRNA-generating...
    Resource Type:
    Dissertation
    Full Text:
    Babra for help with RNA blot assays, Kristin Kasschau for advice on microscopy, Scott Poethig for zip