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  • 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:
    paper. Miya Howell, Joshua Cuperus, Dawei Li, Jesse Hansen, Amanda Alexander, Elisabeth Chapman, and

  • 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:
    DISSERTATION OF Samuel E. Fox for the degree of Doctor of Philosophy in Molecular and Cellular Biology

  • Genetic Structure in Populations of the Douglas-fir Swiss Needle Cast Fungus Nothophaeocryptopus gaeumannii

    Creator:
    Bennett, Patrick I.
    Abstract:
    The fungus Nothophaeocryptopus gaeumannii is the causative agent of Swiss needle cast (SNC), a foliar disease of Douglas-fir. Disease is characterized by premature loss of foliage and reduced growth resulting from the inhibition of photosynthesis due to the occlusion of stomata by the ascocarps of N. gaeumannii. Although the disease...
    Resource Type:
    Dissertation
    Full Text:
    , Dr. Jeff Stone, for his kind patience and great wisdom to which I owe a great deal of my success

  • 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:
    Poisson log-linear mixed-e↵ect model to the count data, and decomposed the total variance into between

  • Photoacclimation in Marine Phytoplankton Under Various Light and Nutrient Regimes and the Resulting Effect on Photosynthetic Electron Flow and Chlorophyll Fluorescence Transients

    Creator:
    Brown, Matthew B.
    Abstract:
    Photoacclimation is the process by which plants and phytoplankton adjust the concentration and composition of their photosynthetic machinery (i.e. their photoacclimation state) in response to changes in their light or nutrient environment. The purpose of photoacclimation is to balance the rate at which light energy is absorbed with the energetic...
    Resource Type:
    Dissertation
    Full Text:
    parameters as determined from 20 minutes carbon uptake measurements………………………………………. 115 P a g e

  • 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

  • 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:
    understanding of the subject. I would like thank my committee members: Dr. Jeff Chang, Dr. Walt Ream, Dr

  • 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:
    in chapter 3, chapter 4 and chapter 5. Jeff Morré and Dr. Samuel Bennett assisted with the

  • A G-type Lectin Receptor-like Kinase Associated with Septoria Canker Resistance and Susceptibility Described using Multi-omics and Biotechnology

    Creator:
    Lenz, Ryan R.
    Abstract:
    Managers of forest and plantation ecosystems are encountering growing problems involving plant pathogens and the expanding geographic ranges of these pathogens. Historically unexposed stands are exceptionally vulnerable when a non-native pathogen is introduced because these pathogens can cause devastating disease in a host population that lacks co-evolved resistance mechanisms. One...
    Resource Type:
    Dissertation
    Full Text:
    advisor. I also want to give a sincere thank you to my committee members, Drs. Tom Wolpert, Jeff

  • 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:
    pJHlasR5, pJHpsdR1, and pJHabcB1. The plasmids were transformed into E. coli DH5α Max Efficiency cells