Staff View: In Silico Development of Species Specific Oligonucleotide Probes Of Harmful/Toxic Unarmored Dinoflagellates for Whole-cell In Situ Hybridization (FISH)

In Silico Development of Species Specific Oligonucleotide Probes Of Harmful/Toxic Unarmored Dinoflagellates for Whole-cell In Situ Hybridization (FISH)

Unarmored dinoflagellates consist of species in the division Pyrrhophyta and class Dinophyceae. They are found in all types of aquatic system including freshwater and marine. Some of the marine species are best known to cause harmful algal brooms (HABs) that often kill fish and/or shellfish by clog...

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Main Author:	Chai, Hui Chin
Format:	Final Year Project Report
Language:	English
Published:	Universiti Malaysia Sarawak, (UNIMAS) 2011
Subjects:	QL Zoology
Online Access:	http://ir.unimas.my/id/eprint/5323/7/Chai%2C%20Hui%20Chin.pdf http://ir.unimas.my/id/eprint/5323/
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spelling	my.unimas.ir.53232023-02-02T09:53:17Z http://ir.unimas.my/id/eprint/5323/ In Silico Development of Species Specific Oligonucleotide Probes Of Harmful/Toxic Unarmored Dinoflagellates for Whole-cell In Situ Hybridization (FISH) Chai, Hui Chin QL Zoology Unarmored dinoflagellates consist of species in the division Pyrrhophyta and class Dinophyceae. They are found in all types of aquatic system including freshwater and marine. Some of the marine species are best known to cause harmful algal brooms (HABs) that often kill fish and/or shellfish by clogging the animal gills and deplete oxygen in the water column when the algae proliferated. Some of the species produce neurotoxins that cause human intoxication by consumption of contaminated shellfish. In this study, species specific oligonucleotide probes of harmful and/or toxic unarmored dinoflagellates were designed in silico for rapid detection by using whole-cell Flourescence in situ hybridization (FISH). Species-specific rRNAtargeted oligonucleotide probes were designed toward the known sequences of the large subunit (LSU) ribosomal DNA region based on the sequence signatures of each target species. A total of 44 sequence signatures were defined for 32 of unarmore inoflagellates, of which 6 species are harmful and/or toxic. The probe information in this study will be useful in future application of FISH in the natural environment. In parallel with the study, dinoflagellates from Borneo were isolated and established into clonal cultures. A total of 14 clonal cultures of dinoflagellates were successfully established and the morphology of each species was documented. Among the strains isolated, a few are potentially harmful and some are toxic. The major outcome in this study is the finding of a toxic dinoflagellate, Alexandrium tamiyavanichii from Samariang estuary. This is the first report of the occurrence of this species in Sarawak waters. Universiti Malaysia Sarawak, (UNIMAS) 2011 Final Year Project Report NonPeerReviewed text en http://ir.unimas.my/id/eprint/5323/7/Chai%2C%20Hui%20Chin.pdf Chai, Hui Chin (2011) In Silico Development of Species Specific Oligonucleotide Probes Of Harmful/Toxic Unarmored Dinoflagellates for Whole-cell In Situ Hybridization (FISH). [Final Year Project Report]
institution	Universiti Malaysia Sarawak
building	Centre for Academic Information Services (CAIS)
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaysia Sarawak
content_source	UNIMAS Institutional Repository
url_provider	http://ir.unimas.my/
language	English
topic	QL Zoology
spellingShingle	QL Zoology Chai, Hui Chin In Silico Development of Species Specific Oligonucleotide Probes Of Harmful/Toxic Unarmored Dinoflagellates for Whole-cell In Situ Hybridization (FISH)
description	Unarmored dinoflagellates consist of species in the division Pyrrhophyta and class Dinophyceae. They are found in all types of aquatic system including freshwater and marine. Some of the marine species are best known to cause harmful algal brooms (HABs) that often kill fish and/or shellfish by clogging the animal gills and deplete oxygen in the water column when the algae proliferated. Some of the species produce neurotoxins that cause human intoxication by consumption of contaminated shellfish. In this study, species specific oligonucleotide probes of harmful and/or toxic unarmored dinoflagellates were designed in silico for rapid detection by using whole-cell Flourescence in situ hybridization (FISH). Species-specific rRNAtargeted oligonucleotide probes were designed toward the known sequences of the large subunit (LSU) ribosomal DNA region based on the sequence signatures of each target species. A total of 44 sequence signatures were defined for 32 of unarmore inoflagellates, of which 6 species are harmful and/or toxic. The probe information in this study will be useful in future application of FISH in the natural environment. In parallel with the study, dinoflagellates from Borneo were isolated and established into clonal cultures. A total of 14 clonal cultures of dinoflagellates were successfully established and the morphology of each species was documented. Among the strains isolated, a few are potentially harmful and some are toxic. The major outcome in this study is the finding of a toxic dinoflagellate, Alexandrium tamiyavanichii from Samariang estuary. This is the first report of the occurrence of this species in Sarawak waters.
format	Final Year Project Report
author	Chai, Hui Chin
author_facet	Chai, Hui Chin
author_sort	Chai, Hui Chin
title	In Silico Development of Species Specific Oligonucleotide Probes Of Harmful/Toxic Unarmored Dinoflagellates for Whole-cell In Situ Hybridization (FISH)
title_short	In Silico Development of Species Specific Oligonucleotide Probes Of Harmful/Toxic Unarmored Dinoflagellates for Whole-cell In Situ Hybridization (FISH)
title_full	In Silico Development of Species Specific Oligonucleotide Probes Of Harmful/Toxic Unarmored Dinoflagellates for Whole-cell In Situ Hybridization (FISH)
title_fullStr	In Silico Development of Species Specific Oligonucleotide Probes Of Harmful/Toxic Unarmored Dinoflagellates for Whole-cell In Situ Hybridization (FISH)
title_full_unstemmed	In Silico Development of Species Specific Oligonucleotide Probes Of Harmful/Toxic Unarmored Dinoflagellates for Whole-cell In Situ Hybridization (FISH)
title_sort	in silico development of species specific oligonucleotide probes of harmful/toxic unarmored dinoflagellates for whole-cell in situ hybridization (fish)
publisher	Universiti Malaysia Sarawak, (UNIMAS)
publishDate	2011
url	http://ir.unimas.my/id/eprint/5323/7/Chai%2C%20Hui%20Chin.pdf http://ir.unimas.my/id/eprint/5323/
_version_	1758582465704755200
score	13.211869

In Silico Development of Species Specific Oligonucleotide Probes Of Harmful/Toxic Unarmored Dinoflagellates for Whole-cell In Situ Hybridization (FISH)

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