M.S. - Microbiology

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    EVOLUTION OF SARS-CoV-2 VARIANTS IN GEOGRAPHIC LOCATIONS WITH VARYING CASE INCIDENCE
    ( 2022) Fraser, Claire Jisu ; Butler, Marguerite A. ; Microbiology
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    A Biogeographic Analysis of SARS-CoV-2 Variants of Concern in Hawai‘i
    ( 2022) Hill, Ethan ; Butler, Marguerite ; Microbiology
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    Utilization of phosphatidylcholine, a lung surfactant component, as a major nurient source during Pseudomonas aeruginosa lung infection
    ([Honolulu] : [University of Hawaii at Manoa], [December 2013], 2013-12) Sun, Zhenxin
    Pseudomonas aeruginosa can grow to high-cell-density (HCD) during infection of the cystic fibrosis (CF) lung. Phosphatidylcholine (PC), the major component of lung surfactant, has been hypothesized to support HCD growth of P. aeruginosa in vivo. Three different pathways, the betaine, glycerol and fatty acid degradation (Fad) pathways, are involved in the degradation of PC components including a phosphorylcholine headgroup, a glycerol molecule, and two long-chain fatty acids (FAs). The Fad pathway still remains largely uncharacterized in P. aeruginosa. During the course of this work, fadBA1,4,5 operons (3-hydroxyacyl-CoA dehydrogenase and acyl-CoA thiolase) were shown to be the most important operons involved in fatty acid degradation through mutational analysis. Various fad mutants and the triple pathway mutant were analyzed extensively by in vitro growth analysis, virulence characterization, and competition study. Defect of growth on PC as sole carbon source was most significant on the triple pathway mutants, as expected. This growth defect translated to in vivo competition disadvantage in BALB/c mice, suggesting the importance of PC as nutrient source in vivo.
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    Natural selection and the genetically encoded amino acid alphabet
    ([Honolulu] : [University of Hawaii at Manoa], [May 2013], 2013-05) Ilardo, Melissa Ann
    Current science has advanced far beyond Crick's 'frozen accident' interpretation of the origin of the standard genetic code. Codon assignments can and do change, and new amino acids can be added to the code. Combined with the simple observation that the complex molecular machinery responsible for the standard code is a product of considerable evolution, it becomes legitimate and important to ask what else explains how and why one particular genetic code emerged within LUCA that still dominates the staggering diversity of life on our planet. Put another way, once we recognize the code as an evolvable phenomenon, we can ask what evolutionary forces shaped the emergence of the particular codon assignments found within the standard genetic code. Biological thinking has coalesced around three major ideas: the Adaptive Hypothesis, the Stereochemical Hypothesis, and the Biosynthetic or Co-Evolutionary Hypothesis. Assessing the validity of all three theories (and any further estimation of their relative contributions) depends upon further investigations of two fundamental assumptions. These assumptions relate to the two previously mentioned chemical languages between which the genetic code acts as an interface: nucleotides and amino acids. A plethora of nucleotides and amino acids formed through biotic and abiotic processes were available in abundance during the earliest stages of life's evolution, as will be addressed in detail in Chapter 2. For the purpose of concluding this review of ideas regarding the evolution of the standard genetic code, what matters is to notice that any estimates made as to the relative importance of the theories described in this chapter build from the assumption of four nucleotides to encode twenty amino acids.
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    HetP and its three homologues : regions necessary for function of HetP and requirement of homologues for fixation of nitrogen in the filamentous cyanobacterium Anabaena sp. strain PCC 7120
    ([Honolulu] : [University of Hawaii at Manoa], [August 2013], 2013-08) Hurd, Kathryn Lynn
    The filamentous cyanobacterium Anabaena sp. strain PCC 7120 is a Gram-negative prokaryote that performs oxygenic photosynthesis. In addition to being an obligate phototroph, Anabaena is capable of differentiating specialized nitrogen-fixing cells called heterocysts. The development of terminally-differentiated heterocyst cells occurs in the absence of fixed nitrogen and forms a one-dimensional pattern along the filament of vegetative cells. The exchange of intercellular signals controls the regulated spacing of the heterocyst cells that on average arise every tenth cell along the filament (Figure 1). The formation of heterocyst cells effectively separates the oxygen-labile nitrogenase complex from oxygen-evolving photosynthesis that occurs in vegetative cells. Heterocysts and vegetative cells are mutually interdependent. Heterocyst cells lack photosystem II and the capacity to fix carbon and must rely on the vegetative cells for sources of reductant. In return, heterocysts supply the filament with fixed nitrogen (Cumino et al. 2007; Marcozzi et al 2009). The development of two distinct cell types in a simple one-dimensional pattern makes Anabaena a simple example of cellular differentiation and pattern formation.
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    Detection of discordant isolates of drug resistant mycobacterium tuberculosis
    ([Honolulu] : [University of Hawaii at Manoa], [May 2013], 2013-05) Hoshide, Matt Kaneo
    Early diagnosis of mycobacterium tuberculosis is critical for proper treatment. With a regimen of rifampin and isoniazid, a patient with active tuberculosis can become non-infectious within 2 weeks (5). However, as resistance to these two drugs develops, second line antibiotic treatment must be used which lasts an extra 6 to 18 months and patients remain infectious for a longer period of time, which can further propagate the spread of mycobacterium tuberculosis (6). Testing for antibiotic resistance in M. tuberculosis is a lengthy process due to its long generation time. The WHO standard guideline for the drug susceptibility test of M. tuberculosis is inoculating the bacteria through dilution on Löwenstein Jensen agar with a set concentration of test antibiotic and incubating it at 37 degrees Celsius. Colonies are then counted on the 28th day and a proportion is calculated by comparing the colony count of the test medium to a control. If the proportion exceeds a critical proportion or if no colonies appear in the lowest drug concentration medium with the highest inoculum, the isolate is determined to be resistant or sensitive, respectively. However, if neither criteria are matched, the incubation must continue until the 40th day where the final results are read through the same process (7). The development of drug resistance strains in mycobacterium tuberculosis ultimately relies on exposure to the resistant drug because the presence of drug resistance mutations does not confer any selective advantage over strains lacking those mutations until exposure occurs (15). Within each geographical region, strains of M. tuberculosis may be under unique and various selective pressures to develop specific types of polymorphisms. Therefore, it can be hypothesized that there are genetic differences in the drug resistant strains of M. tuberculosis found in different regions and that the proportion of polymorphisms in genes associated with drug resistance will be different between geographic locations. Study Objectives 1. To sequence the hot spot regions of nine genes (rpoB, inhA promoter, katG, ahpC promoter, gyrA, gyrB, rrs, eis promoter, and tlyA). 2. To identify discordant isolates through the comparison of drug susceptibility data and sequence data. 3. To further define the resistance patterns found in M. tuberculosis within and between different geographical regions represented by the widely dispersed study sites
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    Development of a non-enzyme based capillary dipstick assay for the detection and purification of environmental pathogens
    ([Honolulu] : [University of Hawaii at Manoa], [December 2010], 2010-12) Luu, Van Phi
    Novel mAbs were produced with a wide range of anti-Dickeya binding reactivities. A mAb line produced from the first fusion generated a BOX-PCR type B,C and D binding antibody (MAb Pine-1). A second mAb line had broad spectrum specificity that reacts to BOX-PCR type A through E and most of the Dickeya reference strains (MAb Pine-2). Phylogenetic analysis based on gyr-B gene expression and BOX-PCR types are consistent with the mAb reactivities. Also a field dipstick assay was developed for the detection of live environmental pathogens that is able concentrate the organism for further analysis and was able to detect S. enterica serotype Typhimurium at 105 CFU/ml, which is within the infective dose of most Salmonella species. The dipstick is able to isolate and purify S. enterica serotype Typhimurium from a mixed culture of 100:1 S. marcescens to S. enterica serotype Typhimurium, with a final purity of greater than 80% determined by colony counts, which is culturable to streak for identification.
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    Numerous fatty acyl-CoA synthetase homologues are involved in fatty acid degradation in pseudomonas aeruginosa
    ([Honolulu] : [University of Hawaii at Manoa], [May 2011], 2011-05) Zarzycki-Siek, Jan Bozydar
    The goal of this research is to characterize the newly identified fatty acyl-CoA synthetase homologue, PA3860 (fadD3), which is thought to take part in Fad though its exact contribution to fatty acid metabolism in P. aeruginosa is unknown. Deciphering the role of fadD3 in fatty acid degradation will broaden our knowledge of the β-oxidation pathway in this bacterium. This was achieved by completing the following specific aims: 1. Purification of FadD3 and performance of biochemical analysis of its acyl-CoA synthetase function 2. Genetical characterization of fadD3 (PA3860) of P. aeruginosa through mutational analysis and gene fusion studies During the course of this research additional discoveries about the β-oxidation pathway of P. aeruginosa were made: 1) additional acyl-CoA synthetase homologues were found, i.e. fadD4, fadD5, and fadD6 2) and their role in Fad was determined along with fadD3.