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Comparative Genomics of Selected Species of Gram-Negative Bacteria

Ren, Chuan-Peng (2010)
Ph.D. thesis, University of Birmingham.

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Investigation of genomic diversity can provide insight into the evolutionary history of bacterial species. However, complete genome sequencing is not yet practical for large strain collections at the beginning of this project. In this project PCR-based methods to investigate the genomic diversity of non-sequenced strains were successfully developed. In \(Escherichia\) \(coli\), the distribution of two Type III secretion system, ETT2 (\(E.\) \(coli\) Type Three Secretion 2) and Flag-2 (\(E.\) \(coli\) Flagellar system 2), were surveyed among a collection of 79 strains. Remnants of both clusters were found to be present in most strains, suggesting that both have a long evolutionary history within \(E.\) \(coli\). The PCR-based methods were also developed for application as part of genome sequencing projects. They were used to explore the co-linear and variable regions between \(Campylobacter\) \(jejuni\) M1 and the genome sequenced strain \(C.\) \(jejuni\) strain 11168. The \(C.\) \(jejuni\) M1 genome was assembled into thirty-four genomic contigs relative to strain 11168, and the size and position of insertions/deletions were characterised. Similar methods were used to facilitate the finishing of the genome of \(Francisella\) \(tularensis\) strain FSC198, using sequence information from strain Schu S4. The completed genome sequence of FSC198 showed it to be almost identical to that of Schu S4. The two genomes differ at only 11 loci, eight SNPs (single nucleotide polymorphisms) and 3 VNTRs (variable number tandem repeats). This surprising finding suggested that the European isolate FSC198 may be derived from the US laboratory strain Schu S4. Two virulence factors, IglA and IglB, from a pathogenicity island of strain FSC198 were further investigated and found to interact at the protein level. These proteins are possibly involved in Type VI secretion, and may represent potential vaccine candidates.

Type of Work:Ph.D. thesis.
Supervisor(s):Pallen, Mark J.
School/Faculty:Colleges (2008 onwards) > College of Medical & Dental Sciences
Department:School of Medicine, Division of Immunity and Infection
Subjects:QR Microbiology
Institution:University of Birmingham
ID Code:489
This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder.
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