Optimization Of RNA Extraction And Generation Of Expressed Sequence Tags From Sargassum Binderi (Sonder) J. Agardh

Brown seaweeds are macroalgae in the marine habitat. They are widely used as food, sources for cosmetics, pharmaceuticals, soap, agar, textile, and alginate. Sargassum binderi is one of the most abundant brown seaweeds in Malaysia. Previous studies have shown that S. binderi contains high qualit...

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Main Author:	Wong, Tony Kok Min
Format:	Thesis
Language:	English
Published:	2005
Subjects:	Sargassum - RNA
Online Access:	http://psasir.upm.edu.my/id/eprint/5926/1/FBSB_2005_15%20IR.pdf
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id	my-upm-ir.5926
record_format	uketd_dc
spelling	my-upm-ir.59262022-02-07T07:48:46Z Optimization Of RNA Extraction And Generation Of Expressed Sequence Tags From Sargassum Binderi (Sonder) J. Agardh 2005-07 Wong, Tony Kok Min Brown seaweeds are macroalgae in the marine habitat. They are widely used as food, sources for cosmetics, pharmaceuticals, soap, agar, textile, and alginate. Sargassum binderi is one of the most abundant brown seaweeds in Malaysia. Previous studies have shown that S. binderi contains high quality of alginate compared to commercially used seaweeds such as Laminaria hyberborea, Macrocystis pyrifera and Ascophyllum nodosum. Expressed sequence tag (EST) approach is a powerful tool in providing genetic information of an organism, especially for S. benderi in which little genetic information is available. This study presents the first attempt in generating ESTs from S. binden. RNA extraction from seaweeds was the main challenge in this study, as the RNA yield was low and the polysaccharide contamination was difficult to be eliminated. A total of ten different RNA extraction methods (including five modifications) have been carried out to obtain sufficient RNA of high quality to construct a representative cDNA library for ESTs generation. The optimized S. binderispecific CTAB RNA extraction method developed in this study was able to produce high yield of RNA with minimum polysaccharide contamination. Sufficient amount of mRNA was obtained to construct a primary cDNA library with a titer of 9.2 x lo5 pfulml. A total of 2051 ESTs were generated and analyzed from the amplified cDNA library of S. binden (with a titer of 1.31 x lo9 pfulml). The ESTs were putatively identified by comparison to the nonredundant peptide database in NCBI. Approximately 82% of the ESTs were assigned as unknown and novel sequences that are potentially important for new gene discovery, whereas the 18% ESTs with significant matches to the database were classified into various putative functional groups, including protein synthesis, energy, protein destination and storage, metabolism, cell structurel division, diseasel defense, signal transduction, transcription, and miscellaneous. The EST information generated from this study may contribute towards better understanding of the biochemistry and molecular biology of S. binder; and other brown seaweeds in the future. Sargassum - RNA 2005-07 Thesis http://psasir.upm.edu.my/id/eprint/5926/ http://psasir.upm.edu.my/id/eprint/5926/1/FBSB_2005_15%20IR.pdf text en public masters Universiti Putra Malaysia Sargassum - RNA Faculty of Biotechnology and Biomocular Sciences Ho, Chai Ling
institution	Universiti Putra Malaysia
collection	PSAS Institutional Repository
language	English
advisor	Ho, Chai Ling
topic	Sargassum - RNA
spellingShingle	Sargassum - RNA Wong, Tony Kok Min Optimization Of RNA Extraction And Generation Of Expressed Sequence Tags From Sargassum Binderi (Sonder) J. Agardh
description	Brown seaweeds are macroalgae in the marine habitat. They are widely used as food, sources for cosmetics, pharmaceuticals, soap, agar, textile, and alginate. Sargassum binderi is one of the most abundant brown seaweeds in Malaysia. Previous studies have shown that S. binderi contains high quality of alginate compared to commercially used seaweeds such as Laminaria hyberborea, Macrocystis pyrifera and Ascophyllum nodosum. Expressed sequence tag (EST) approach is a powerful tool in providing genetic information of an organism, especially for S. benderi in which little genetic information is available. This study presents the first attempt in generating ESTs from S. binden. RNA extraction from seaweeds was the main challenge in this study, as the RNA yield was low and the polysaccharide contamination was difficult to be eliminated. A total of ten different RNA extraction methods (including five modifications) have been carried out to obtain sufficient RNA of high quality to construct a representative cDNA library for ESTs generation. The optimized S. binderispecific CTAB RNA extraction method developed in this study was able to produce high yield of RNA with minimum polysaccharide contamination. Sufficient amount of mRNA was obtained to construct a primary cDNA library with a titer of 9.2 x lo5 pfulml. A total of 2051 ESTs were generated and analyzed from the amplified cDNA library of S. binden (with a titer of 1.31 x lo9 pfulml). The ESTs were putatively identified by comparison to the nonredundant peptide database in NCBI. Approximately 82% of the ESTs were assigned as unknown and novel sequences that are potentially important for new gene discovery, whereas the 18% ESTs with significant matches to the database were classified into various putative functional groups, including protein synthesis, energy, protein destination and storage, metabolism, cell structurel division, diseasel defense, signal transduction, transcription, and miscellaneous. The EST information generated from this study may contribute towards better understanding of the biochemistry and molecular biology of S. binder; and other brown seaweeds in the future.
format	Thesis
qualification_level	Master's degree
author	Wong, Tony Kok Min
author_facet	Wong, Tony Kok Min
author_sort	Wong, Tony Kok Min
title	Optimization Of RNA Extraction And Generation Of Expressed Sequence Tags From Sargassum Binderi (Sonder) J. Agardh
title_short	Optimization Of RNA Extraction And Generation Of Expressed Sequence Tags From Sargassum Binderi (Sonder) J. Agardh
title_full	Optimization Of RNA Extraction And Generation Of Expressed Sequence Tags From Sargassum Binderi (Sonder) J. Agardh
title_fullStr	Optimization Of RNA Extraction And Generation Of Expressed Sequence Tags From Sargassum Binderi (Sonder) J. Agardh
title_full_unstemmed	Optimization Of RNA Extraction And Generation Of Expressed Sequence Tags From Sargassum Binderi (Sonder) J. Agardh
title_sort	optimization of rna extraction and generation of expressed sequence tags from sargassum binderi (sonder) j. agardh
granting_institution	Universiti Putra Malaysia
granting_department	Faculty of Biotechnology and Biomocular Sciences
publishDate	2005
url	http://psasir.upm.edu.my/id/eprint/5926/1/FBSB_2005_15%20IR.pdf
_version_	1747810510878801920

Optimization Of RNA Extraction And Generation Of Expressed Sequence Tags From Sargassum Binderi (Sonder) J. Agardh

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