Thesis (M.App.Sc.) - Carleton University, 2007. / Includes bibliographical references (p. 115-120). Also available in electronic format on the Internet.

Thesis (M.S.)--Montana State University--Bozeman, 2007. / Typescript. Chairperson, Graduate Committee: John C. Priscu. Includes bibliographical references (leaves 100-111).

No description available.

Typescript (photocopy). / Digitized by Kansas Correctional Industries

Pseudomonas fluorescens NCIMB 11764 (Pf11764) is uniquely able to grow on the poison cyanide as its sole nitrogen source. It does so by converting cyanide oxidatively to carbon dioxide and ammonia, the latter being assimilated into cellular molecules. This requires a complex enzymatic machinery that includes nitrilase and oxygenase enzymes the nature of which are not well understood. In the course of a proteomics analysis aimed at achieving a better understanding of the proteins that may be required for cyanide degradation by Pf11764, an unknown protein of 17.8 kDa was detected in cells exposed to cyanide. Analysis of this protein by ESI-coupled mass spectrometry and bioinformatics searches gave evidence of strong homology with a protein (Hyp1) of unknown function (hypothetical) present in the bacterium Photorhabdus luminescens subsp. laumondii TTO1 (locus plu_1232). A search of available microbial genomes revealed a number of Hyp1 orthologs the genes of which are found in a conserved gene cluster known as Nit1C. Independent studies revealed that in addition to Hyp1, Pf11764 possesses a gene (nit) specifying a nitrilase enzyme whose closest homologue is a nitrilase found in Nit1C gene clusters (77% amino acid identity). DNA sequence analysis has further revealed that indeed, hyp1Pf11764 and nitPf11764 are contained in a cluster that includes also a gene specifying an oxygenase. Given the possible connection of Nit1C-endoded nitrilase and oxygenase enzymes to enzymatic cyanide degradation, there is strong reason for thinking that the genes specifying these enzymes contribute to bacterial growth on cyanide in those bacteria containing the Nit1C cluster. Because the biological function of the Hyp1 protein is currently unknown, it was cloned and the protein expressed in E. coli so that its properties could further be explored. Unfortunately, the expression of the protein in an insoluble form complicated these analyses. However, at least two lines of evidence suggest a possible role as a regulator of gene expression. First, over-expression of the protein was accompanied by the parallel elevation of the putative vector-encoded b-lactamase, implying that Hyp1Pf11764 can affect the expression of other genes. Second, a comparison of the amino acid sequence of select peptide fragments of Hyp1Pf11764, by conducting searches for homology with proteins in the existing nonredundant protein database, consistently revealed motifs in common with those present in bacterial response regulators that are part of two-component signal transduction systems widely distributed in bacteria.

Thesis (Ph. D.)--Ohio State University, 2008. / Title from first page of PDF file. Includes bibliographical references (p. 105-112).

No description available.

No description available.

Probiotics are live microorganisms that are similar to beneficial microorganisms found in the human gut. They are often known as lactic acid bacteria and are normally consumed in the form of yogurt. Most often the bacteria will come from two groups, Lactobacillus and Bifidobacterium. Vancomycin is a bactericidal antibiotic used in the treatment of antibiotic-associated colitis and endocarditis. In this study we will be examining the effects of vancomycin on the induced growth of lactobacilli in the Lewis male rat. The Lewis male rat was used because in the animal model of rheumatoid arthritis, vancomycin was shown to reduce the disease scores of adjuvant-induced arthritis and one research group also noted an increase in lactobacilli growth in the digestive tract with administration. As a control for this research project, to ensure induction of lactobacilli was achieved, Bene-Bac Pet powder was used. Bene-Bac Pet powder contains live, naturally occurring microorganisms and is recommended anytime an animal experiences changing nutritional or environmental conditions, one of them being antibiotic treatment. The rats were placed in four groups, two being control and the others being experimental. According to each group, rats were fed dextrose/maltodextrin substrate, Bene-Bac Pet powder, vancomycin and one group being fed both Bene-Bac powder and vancomycin. Fecal samples were obtained from the rat prior to initial treatment and then once every three days during the experimental period and two days after the conclusion of the experimental procedure (n=5 samples per rat). Samples were diluted and plated and the colony growth was noted. Vancomycin was expected to decrease the growth of lactobacilli in the Lewis rat following the treatments. There were significant changes (p = 0.02) among most groups by day 6 of the study. In contrast, there was an increase in the growth of lactobacilli in experimental groups. Vancomycin increases and maintains the growth of lactobacilli in the Lewis rat. / Department of Physiology and Health Science

The rate and accuracy of protein production is the main determinant of bacterial growth. Elongation Factor Tu (EF-Tu) provides the ribosome with aminoacylated tRNAs, and is central for its activity. In Salmonella enterica serovar Typhimurium, EF-Tu is encoded by the genes tufA and tufB. A bacterial cell depending on tufA499-encoded EF-Tu mutant Gln125Arg grows extremely slowly. We found evidence that this is caused by excessive degradation of mRNA, which is suggested to be the result of transcription-translation decoupling because the leading ribosome is ‘starved’ for amino acids and stalls on the nascent mRNA, which is thus exposed to Riboendonuclease RNase E. The slow-growth phenotype can be reversed by mutations in RNase E that reduce the activity of this enzyme. We found that the EF-Tu mutant has increased levels of ppGpp during exponential growth in rich medium. ppGpp is usually produced during starvation, and we propose that Salmonella, depending on mutant EF-Tu, incorrectly senses the resulting situation with ribosomes ‘starving’ for amino acids as a real starvation condition. Thus, RelA produces ppGpp which redirects gene expression from synthesis of ribosomes and favours synthesis of building blocks such as amino acids. When ppGpp levels are reduced, either by over-expression of SpoT or by inactivation of relA, growth of the mutant is improved. We suggest this is because the cell stays in a fast-growth mode. RNase E mutants with a conditionally lethal temperature-sensitive (ts) phenotype were used to address the long-debated question of the essential role of RNase E. Suppressor mutations of the ts phenotype were selected and identified, both in RNase E as well as in extragenic loci. The internal mutations restore the wild-type RNase E function to various degrees, but no single defect was identified that alone could account for the ts phenotype. In contrast, identifying three different classes of extragenic suppressors lead us to suggest that the essential role of RNaseIE is to degrade mRNA. One possibility to explain the importance of this function is that in the absence of mRNA degradation by RNase E, the ribosomes become trapped on defective mRNAs, with detrimental consequences for continued cell growth.