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Targeted Proteomics For The Characterization Of Enriched Microbial Protein Isolates And Protein Complexes, William Judson Hervey

Doctoral Dissertations

The field of proteomics encompasses the study of identities, interactions, and dynamics of all proteins expressed by a living system. Research in this dissertation blends biochemical and quantitative proteomics techniques to increase the latitude of biological applications for the bottom-up mass spectrometry proteomics approach. Together, isolation of selected protein “targets,” such as multiprotein complexes, and quantitative characterization yields information essential for more detailed understanding of microbial cell function.

Often, a challenging aspect of characterizing a variety of biochemically enriched samples is limited protein yield. This dissertation describes an enzymatic proteolysis protocol employing an organic/aqueous solvent that alleviates excessive handling steps …

Genetic Variation Within The Daphnia Pulex Genome, Abraham Eaton Tucker

Doctoral Dissertations

Genetic variation within the diploid Daphnia pulex genome was examined using a high quality de novo assembly and shotgun reads from two distinct D. pulex clones. Patterns of variation and divergence at single nucleotides were examined in physical and functional regions of the genome using comparative assembly output and available annotations. Additionally, mitochondrial genomes of the same D. pulex clones were assembled and compared for patterns of divergence, and substitutional biases. Intron presence/absence polymorphisms were identified computationally and verified experimentally. Finally, gene duplicate demographics were examined for patterns of divergence and estimates of gene birth rates.