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Sequence, organization, and genes characteristics of ORFs identified in a metagenomic DNA fragment from microbial community of the deep brine environment of Atlantis II in the Red Sea.
Microbial communities that reside in different natural habitats, particularly those of extreme environments, constitute a rich source for novel industrial enzymes and bioactive compounds. Until the advent of metagenomics technique, extreme environments represented a locked area with huge genetic rep...
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2015
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| _version_ | 1867613416340848640 |
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| access_status_str | Open Access |
| author | Assal, Dina Hassan |
| author_browse | Assal, Dina Hassan |
| author_facet | Assal, Dina Hassan |
| author_sort | Assal, Dina Hassan |
| collection | Thesis |
| dc_rights_str_mv | The author retains all rights with regard to copyright. The author certifies that written permission from the owner(s) of third-party copyrighted matter included in the thesis, dissertation, paper, or record of study has been obtained. The author further certifies that IRB approval has been obtained for this thesis, or that IRB approval is not necessary for this thesis. Insofar as this thesis, dissertation, paper, or record of study is an educational record as defined in the Family Educational Rights and Privacy Act (FERPA) (20 USC 1232g), the author has granted consent to disclosure of it to anyone who requests a copy. |
| description | Microbial communities that reside in different natural habitats, particularly those of extreme environments, constitute a rich source for novel industrial enzymes and bioactive compounds. Until the advent of metagenomics technique, extreme environments represented a locked area with huge genetic repertoire that remained unexplored. The Atlantis II brine pool of the Red Sea (ATII) is one of such unexplored extreme environment. The lower part of this pool, the lower convective layer (LCL), has a pH of 5.3, high temperature (68C), elevated concentration of toxic heavy metals, and extreme salinity (26% salt). To understand the metabolic and the physiological properties of proteins and enzymes that contribute to the survival of microorganisms in this extreme and hostile environment, the structure and characteristics of their genes should be determined. Metagenomics approach helped in this task through two different techniques: 1) mass sequencing of environmental DNA by high throughput sequencing technique such as pyrosequencing technique; 2) sequencing of environmental DNA fragments from metagenomic fosmid library. The advantage of the first approach is that it produces massive number of reads that can be assembled into long contigs. Its disadvantage is that the majority of the contigs are chimeric i.e. assembled from reads belong to genomes of different microbial species. The second technique has an advantage of establishing the sequence of a contiguous piece of genomic DNA of around 30 to 40 kb‚ that most probably is not a chimeric. The major disadvantages however are the high cost of the sequencing process, it involves elaborate steps, and it has a limited output of nucleotide sequences. In this work we sequenced a contiguous fragment of DNA from the microbial community of the ATII-LCL environment and presenting the structural and potential function of its annotated genes. Interestingly, out of the 39 identified ORFs, 10 ORFs (25%) have no matches in the database. The structure and the function of the potential annotated genes are presented and discussed. In addition, we were able to assembled 28.378 kb out of 33.819 kb of the insert in the recombinant fosmid. The unassembled 5.441 kb is most probably due to the detection of characteristic patterns of low complexity regions, simple repeats as well as gene duplication exists at the end of the assembled sequence. |
| format | Thesis |
| id | oai:fount.aucegypt.edu:etds-2175 |
| institution | American University in Cairo (Egypt) |
| last_indexed | 2026-06-10T12:35:47.730Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from AUC Knowledge Fountain — bepress |
| publishDate | 2015 |
| publishDateRange | 2015 |
| publishDateSort | 2015 |
| publisher | AUC Knowledge Fountain |
| publisherStr | AUC Knowledge Fountain |
| record_format | dspace |
| source_str | AUC Knowledge Fountain — bepress |
| spelling | oai:fount.aucegypt.edu:etds-2175 Sequence, organization, and genes characteristics of ORFs identified in a metagenomic DNA fragment from microbial community of the deep brine environment of Atlantis II in the Red Sea. Assal, Dina Hassan Microbial communities that reside in different natural habitats, particularly those of extreme environments, constitute a rich source for novel industrial enzymes and bioactive compounds. Until the advent of metagenomics technique, extreme environments represented a locked area with huge genetic repertoire that remained unexplored. The Atlantis II brine pool of the Red Sea (ATII) is one of such unexplored extreme environment. The lower part of this pool, the lower convective layer (LCL), has a pH of 5.3, high temperature (68C), elevated concentration of toxic heavy metals, and extreme salinity (26% salt). To understand the metabolic and the physiological properties of proteins and enzymes that contribute to the survival of microorganisms in this extreme and hostile environment, the structure and characteristics of their genes should be determined. Metagenomics approach helped in this task through two different techniques: 1) mass sequencing of environmental DNA by high throughput sequencing technique such as pyrosequencing technique; 2) sequencing of environmental DNA fragments from metagenomic fosmid library. The advantage of the first approach is that it produces massive number of reads that can be assembled into long contigs. Its disadvantage is that the majority of the contigs are chimeric i.e. assembled from reads belong to genomes of different microbial species. The second technique has an advantage of establishing the sequence of a contiguous piece of genomic DNA of around 30 to 40 kb‚ that most probably is not a chimeric. The major disadvantages however are the high cost of the sequencing process, it involves elaborate steps, and it has a limited output of nucleotide sequences. In this work we sequenced a contiguous fragment of DNA from the microbial community of the ATII-LCL environment and presenting the structural and potential function of its annotated genes. Interestingly, out of the 39 identified ORFs, 10 ORFs (25%) have no matches in the database. The structure and the function of the potential annotated genes are presented and discussed. In addition, we were able to assembled 28.378 kb out of 33.819 kb of the insert in the recombinant fosmid. The unassembled 5.441 kb is most probably due to the detection of characteristic patterns of low complexity regions, simple repeats as well as gene duplication exists at the end of the assembled sequence. 2015-02-01T08:00:00Z thesis application/pdf https://fount.aucegypt.edu/etds/1176 https://fount.aucegypt.edu/context/etds/article/2175/viewcontent/Dina_20Hassan_20Final_20thesis.pdf The author retains all rights with regard to copyright. The author certifies that written permission from the owner(s) of third-party copyrighted matter included in the thesis, dissertation, paper, or record of study has been obtained. The author further certifies that IRB approval has been obtained for this thesis, or that IRB approval is not necessary for this thesis. Insofar as this thesis, dissertation, paper, or record of study is an educational record as defined in the Family Educational Rights and Privacy Act (FERPA) (20 USC 1232g), the author has granted consent to disclosure of it to anyone who requests a copy. Theses and Dissertations AUC Knowledge Fountain metagenomics sequencing |
| spellingShingle | metagenomics sequencing Assal, Dina Hassan Sequence, organization, and genes characteristics of ORFs identified in a metagenomic DNA fragment from microbial community of the deep brine environment of Atlantis II in the Red Sea. |
| title | Sequence, organization, and genes characteristics of ORFs identified in a metagenomic DNA fragment from microbial community of the deep brine environment of Atlantis II in the Red Sea. |
| title_full | Sequence, organization, and genes characteristics of ORFs identified in a metagenomic DNA fragment from microbial community of the deep brine environment of Atlantis II in the Red Sea. |
| title_fullStr | Sequence, organization, and genes characteristics of ORFs identified in a metagenomic DNA fragment from microbial community of the deep brine environment of Atlantis II in the Red Sea. |
| title_full_unstemmed | Sequence, organization, and genes characteristics of ORFs identified in a metagenomic DNA fragment from microbial community of the deep brine environment of Atlantis II in the Red Sea. |
| title_short | Sequence, organization, and genes characteristics of ORFs identified in a metagenomic DNA fragment from microbial community of the deep brine environment of Atlantis II in the Red Sea. |
| title_sort | sequence organization and genes characteristics of orfs identified in a metagenomic dna fragment from microbial community of the deep brine environment of atlantis ii in the red sea |
| topic | metagenomics sequencing |
| url | https://fount.aucegypt.edu/etds/1176 https://fount.aucegypt.edu/context/etds/article/2175/viewcontent/Dina_20Hassan_20Final_20thesis.pdf |
| work_keys_str_mv | AT assaldinahassan sequenceorganizationandgenescharacteristicsoforfsidentifiedinametagenomicdnafragmentfrommicrobialcommunityofthedeepbrineenvironmentofatlantisiiintheredsea |