No description available.

No description available.

The genome of B. phytofirmans OLGA172 has been sequenced by Next Generation sequencing methods. Over 42 kbp of its genome surrounding its 3CBA degradative genes, tfdCIDIEIFI, was assembled and annotated. The most important method used was the synteny method, which implies homology between the genes, and descent from a common ancestor (Guttman, 2008). The conserved gene order between B. phytofirmans PsJN, B. xenovorans LB400, and OLGA172 was used as a confirmation of annotation through BLASTn, enabled closing of the gaps in the sequencing data, and allowed prediction of genes further downstream. Though the whole genome is not yet assembled, a very significant region carrying a concentrated area of mobile genetic elements (MGE) has been found to surround the degradative genes in OLGA172. This thesis details the sequence evidence that, upon examination of closely related strains, OLGA172 and its related strain from pristine soils may be the ancestral chlorobenzoate degraders.

Vibrio vulnificus is an opportunistic human and animal pathogen with the highest death rate of any foodborne disease agent. The capsular polysaccharide (CPS) is essential for virulence. Over 100 CPS types (carbotypes) have been identified among natural isolates, yet little is known about the genetic mechanisms that drive such diversity. Chitin, the second most abundant polysaccharide in nature, induces competence in Vibrio species. We found that transformation frequency varies by strain and (GlcNAc)2 was the shortest chitin-derived polymer capable of inducing competence. We confirmed that V. vulnificus can undergo chitin-dependent carbotype conversion following the uptake and recombination of complete cps loci from exogenous genomic DNA. The acquisition of a partial locus was also demonstrated when internal regions of homology between the endogenous and exogenous loci existed. Thus, the same mechanism governing the transfer of complete cps loci also contributes to their evolution by generating novel combinations of CPS biosynthesis genes.

The genome of B. phytofirmans OLGA172 has been sequenced by Next Generation sequencing methods. Over 42 kbp of its genome surrounding its 3CBA degradative genes, tfdCIDIEIFI, was assembled and annotated. The most important method used was the synteny method, which implies homology between the genes, and descent from a common ancestor (Guttman, 2008). The conserved gene order between B. phytofirmans PsJN, B. xenovorans LB400, and OLGA172 was used as a confirmation of annotation through BLASTn, enabled closing of the gaps in the sequencing data, and allowed prediction of genes further downstream. Though the whole genome is not yet assembled, a very significant region carrying a concentrated area of mobile genetic elements (MGE) has been found to surround the degradative genes in OLGA172. This thesis details the sequence evidence that, upon examination of closely related strains, OLGA172 and its related strain from pristine soils may be the ancestral chlorobenzoate degraders.

Vibrio vulnificus is an opportunistic human and animal pathogen with the highest death rate of any foodborne disease agent. The capsular polysaccharide (CPS) is essential for virulence. Over 100 CPS types (carbotypes) have been identified among natural isolates, yet little is known about the genetic mechanisms that drive such diversity. Chitin, the second most abundant polysaccharide in nature, induces competence in Vibrio species. We found that transformation frequency varies by strain and (GlcNAc)2 was the shortest chitin-derived polymer capable of inducing competence. We confirmed that V. vulnificus can undergo chitin-dependent carbotype conversion following the uptake and recombination of complete cps loci from exogenous genomic DNA. The acquisition of a partial locus was also demonstrated when internal regions of homology between the endogenous and exogenous loci existed. Thus, the same mechanism governing the transfer of complete cps loci also contributes to their evolution by generating novel combinations of CPS biosynthesis genes.

No description available.

No description available.

Conjugation is a fundamentally important mechanism of horizontal DNA transfer between bacteria, bacteria x archea, and bacteria x eukaryotes. This work has concentrated on conjugation between bacteria x eukaryotes, specifically Escherichia coli x Saccharomyces cerevisiae. Four hypotheses were tested, investigating the barriers to this particular form of DNA transfer. The first investigated if a mutation that altered the cell-surface of the recipient S. cerevisiae could inhibit DNA transfer. The final three utilised a recombination-dependent-conjugation assay to investigate the barrier to DNA transmission through recombination. The hypotheses tested if the frequency of recombination, in this recombination-dependent-conjugation assay, differed when using similar or diverged DNA substrates, if a mismatch repair mutation within the recipient could affect the frequencies of recombination observed, and if the position on the plasmid of the gene of interest affected the frequency of transmission. Transmission of the Ura3 DNA sequence in the recipient S. cerevisiae was used to test all four hypotheses. The cell wall mutants mnn9, knr4, fks1 and kre6 were utilised to investigate if the cell-surface of the recipient could affect the frequency of transmission. The similar and diverged substrates utilised in the investigation of the affect of sequence similarity on recombination were the DNA sequences of ura3 from S. cerevisiae and Saccharomyces carlsbergensis, respectively and the MMR mutants utilised were msh2, pms1 and pol30-52. Cell wall mutants were not found to limit the frequency of transfer once donor-recipient contact was induced through the solid surface mating procedure. Sequence similarity, MMR and the relative position of the ura3 DNA sequence on the conjugative plasmids were shown to have little effect on the frequency of transmission in S. cerevisiae. This suggests that any DNA that enters the nucleus of S. cerevisiae (eukaryotes) can recombine with the chromosome and alter it to the same extent. However, trends within the data also suggest that DNA is transferred into the recipient and then transported to the nucleus to recombine with the chromosome as a single-stranded DNA molecule.

Thesis (Ph. D.)--Cornell University, March, 2008. / Vita. Includes bibliographical references (leaves 376-419).