Full Text Available
Note: Clicking the button above will open the full text document at the original institutional repository in a new window.
Development of novel computational tools to infer the distribution patterns of bacterial accessory genomic elements and the implications of microevolution towards pathogenicity
Thesis (PhD)--University of Pretoria, 2013.
Saved in:
| Other Authors: | |
|---|---|
| Format: | Thesis |
| Language: | English |
| Published: |
University of Pretoria
2014
|
| Subjects: | |
| Tags: |
No Tags, Be the first to tag this record!
|
| _version_ | 1867613498871119872 |
|---|---|
| access_status_str | Open Access |
| author2 | Reva, Oleg N. |
| author_browse | Reva, Oleg N. |
| author_facet | Reva, Oleg N. |
| collection | Thesis |
| dc_rights_str_mv | © 2013 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. |
| description | Thesis (PhD)--University of Pretoria, 2013. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/40248 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:37:06.816Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2014 |
| publishDateRange | 2014 |
| publishDateSort | 2014 |
| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/40248 Development of novel computational tools to infer the distribution patterns of bacterial accessory genomic elements and the implications of microevolution towards pathogenicity Reva, Oleg N. Tuemmler, Burkhard Bezuidt, Keoagile Ignatius Oliver Horizontal gene transfer (HGT) DNA mutations Bacteria DNA patterns Pseudomonas aeruginosa UCTD Thesis (PhD)--University of Pretoria, 2013. Bacterial diversity has always been associated with micro-evolutionary events such as horizontal gene transfer and DNA mutations. Such events influence the rapid evolution of bacteria as a result of the environmental conditions which they encounter. They further establish beneficial phenotypic effects that allow bacteria to specialize in new habitats. Due to the increase in number of bacterial genomic sequences, studying microbial evolution has been made possible, and the impact of micro-evolution on bacterial diversity is becoming more apparent. To gain biological information from this ever increasing genomic data, a variety of computational tools are required. This thesis therefore, focuses on the development and application of computational approaches to identify genomic regions of divergence which have resulted from horizontal gene transfer or small mutational changes. The first and major part of the thesis describes the application of DNA patterns, termed oligonucleotide signatures to identify horizontally acquired genomic regions in prokaryotes. These DNA patterns are demonstrated to differentiate between signatures of the core genome and those which have been acquired through horizontal transfer events. DNA patterns are further demonstrated to: reveal the distribution patterns of horizontally acquired genomic elements, determine their acquisition periods, and predict their putative donor organisms. The second part of the thesis focuses on the evaluation of modern short read sequence data of geographically unrelated Pseudomonas aeruginosa to study their intraclonal genomic diversity. The work described in the thesis was purely in silico driven and performed at Hannover Medical School and the Bioinformatics and Computation Biology Unit at the University of Pretoria. gm2014 Biochemistry unrestricted 2014-06-17T13:06:07Z 2014-06-17T13:06:07Z 2014-04-09 2013 Thesis Bezuidt, KIO 2013, Development of novel computational tools to infer the distribution patterns of bacterial accessory genomic elements and the implications of microevolution towards pathogenicity, PhD thesis, University of Pretoria, Pretoria, viewed yymmdd <http://hdl.handle.net/2263/40248> D14/4/113/gm http://hdl.handle.net/2263/40248 en © 2013 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. application/pdf University of Pretoria |
| spellingShingle | Horizontal gene transfer (HGT) DNA mutations Bacteria DNA patterns Pseudomonas aeruginosa UCTD Development of novel computational tools to infer the distribution patterns of bacterial accessory genomic elements and the implications of microevolution towards pathogenicity |
| title | Development of novel computational tools to infer the distribution patterns of bacterial accessory genomic elements and the implications of microevolution towards pathogenicity |
| title_full | Development of novel computational tools to infer the distribution patterns of bacterial accessory genomic elements and the implications of microevolution towards pathogenicity |
| title_fullStr | Development of novel computational tools to infer the distribution patterns of bacterial accessory genomic elements and the implications of microevolution towards pathogenicity |
| title_full_unstemmed | Development of novel computational tools to infer the distribution patterns of bacterial accessory genomic elements and the implications of microevolution towards pathogenicity |
| title_short | Development of novel computational tools to infer the distribution patterns of bacterial accessory genomic elements and the implications of microevolution towards pathogenicity |
| title_sort | development of novel computational tools to infer the distribution patterns of bacterial accessory genomic elements and the implications of microevolution towards pathogenicity |
| topic | Horizontal gene transfer (HGT) DNA mutations Bacteria DNA patterns Pseudomonas aeruginosa UCTD |
| url | http://hdl.handle.net/2263/40248 |