Aswini Leela Loganathan (2014) Phylogenetic and bioinformatic analysis of genes related to immunity and retroviral elements in Nasalis larvatus genome. Masters thesis, Universiti Malaysia Sabah.
![[img]](https://eprints.ums.edu.my/style/images/fileicons/text.png) |
Text
24 PAGES.pdf Download (997kB) |
|
Text
FULLTEXT.pdf Restricted to Registered users only Download (22MB) |
Abstract
The Proboscis monkey (Nasalis laNatus) also known locally as Monyet Belanda I Bayau are endemic to the island of Borneo. Unfortunately the N. laNatus habitat loss has resulted in severe decline in endemic population and listed in Appendix I by the Convention on International Trade in Endangered Species (CITES). This research is divided into two parts. The first part of this research focused on the Mitochondrial DNA (mtDNA) of the N. laNatus. At present, there are only 2 data available for N. laNatus mtDNA and this research served as a benchmark for validating those data. Furthermore the importance of this study is to amplify the mitochondrial genome of the species Nasalis laNatus from two regions which is Sabah and Sarawak, which is then utilized for sequencing and ultimately comparative mitochondrial genomics with other Primates. Second part of this research focused on characterizing the genes linked to immunity and host defence which are the Major histocompatibility complex (MHC), Defensins and Retroviral elements present in the N. laNatus genome. In order to achieve this, the polymerase chain reaction (PCR) primers were designed from a total of 31 immune genes which were MHC, Defensins and Retroviruses of Non human primate genes obtained from EST. Cloning was carried out using CloneJET PCR cloning kit (Thermo Scientific). The plasmid was purified using Gene Jet Plasmid Mini Prep Kit (Thermo Scientific). The plasmid was then sequenced using BigDye Terminator v3.1 cycle sequencing kit chemistry. All novel immunology and retrovirus sequences have been deposited in GenBank (accession no: KF279631-KF279640, KP064501- KP064501 and KM889667). From the study, the mitochondrial genome of N. laNatus from Sabah and Sarawak is 16,574 bp and 16,573 bp long, respectively. Selection at the amino acid level was measured as the rates of nonsynonymous ( dn) and synonymous ( ds) substitutions per codon site. From the data, mtDNA genes underwent neutral selection. For the MHC data, there were no positive selection detected while for defensin and retrovirus data, it shows that some primates underwent neutral selection and some underwent positive selection. The phylogenetic tree was created using the Neighbor-Joining and maximum likelihood method. The MHC data shows that the tree topology is orthologous with the primates. As for the defensins, phylogenetic tree results show it is highly paralogous with Macaca mulatta while as for the Retroviruses the phylogenetic tree shows orthologous divergent. Because the two different methods used, give trees with the same topology, the phylogenetic relationships derived from these sequence comparisons appear reliable. In this study, the aim is not to get the complete coverage of the retroviral and immunology genes but to compare the sequences to N. laNatusto see if they are homologous.
| Item Type: | Thesis (Masters) |
|---|---|
| Keyword: | Nasalis larvatus, Monyet Proboscis, Genom mitokondria, Gen imuniti, MHC |
| Subjects: | Q Science > QL Zoology > QL1-991 Zoology > QL605-739.8 Chordates. Vertebrates > QL700-739.8 Mammals |
| Department: | INSTITUTE > Biotechnology Research Institute (BRI) |
| Depositing User: | DG MASNIAH AHMAD - |
| Date Deposited: | 18 Jun 2025 10:10 |
| Last Modified: | 18 Jun 2025 10:10 |
| URI: | https://eprints.ums.edu.my/id/eprint/44188 |
Actions (login required)
 |
View Item |