Total RNA Extraction for the Red Seaweed Gracilaria changii (Gracilariales, Rhodophyta)

Chan, Cheong Xin, Ho, Chai-Ling, Othman, Rofina Yasmin and Phang, Siew-Moi (2002). Total RNA Extraction for the Red Seaweed Gracilaria changii (Gracilariales, Rhodophyta). In: Asia-Pacific Conference in Marine Science and Technology, Kuala Lumpur, Malaysia, (). 12-16 May, 2002.

Attached Files (Some files may be inaccessible until you login with your UQ eSpace credentials)
Name Description MIMEType Size Downloads
Chan_APCMST.pdf Chan_APCMST.pdf application/pdf 86.30KB 0
Author Chan, Cheong Xin
Ho, Chai-Ling
Othman, Rofina Yasmin
Phang, Siew-Moi
Title of paper Total RNA Extraction for the Red Seaweed Gracilaria changii (Gracilariales, Rhodophyta)
Conference name Asia-Pacific Conference in Marine Science and Technology
Conference location Kuala Lumpur, Malaysia
Conference dates 12-16 May, 2002
Publication Year 2002
Sub-type Fully published paper
Abstract/Summary Five different RNA extraction methods have been tried out on the red seaweed, Gracilaria changii collected from the mangrove area at Morib, Selangor, Malaysia. Two methods, one utilising guanidinium thiocyanate, and another using cetyltrimethyl ammonium bromide (CTAB), were found to be potential alternatives to obtain pure RNA. By incorporating sand while grinding the tissue, the method using CTAB was found most suitable to obtain pure RNA (high A260:280nm ratio) with high yield (0.16ug RNA per gram of fresh tissue).
Subjects 270804 Genetic Technologies - Transformation, Site-directed Mutagenesis, etc.
270404 Phycology
270199 Biochemistry and Cell Biology not elsewhere classified
Keyword RNA extraction
seaweed
marine macroalgae
Gracilaria changii
References Ainsworth C (1994). Isolation of RNA from floral tissue of Rumex acetosa (Sorrel). Plant Mol. Biol. Reptr. 12: 198-203. Ambion (2002). The Use of LiCl Precipitation for RNA Purification. Ambion Technical Bulletin #160 [online]. Accessed 01/02/2002. Available: http://www.ambion.com/techlib/tb/tb_160.html Apt KE, Clendennen SK, Powers DA and Grossman AR (1995). The gene family encoding the fucoxanthin chlorophyll proteins from the brown alga Macrocystis pyrifera. Mol. Gen. Genet. 246: 455-464. Asamizu E, Nakamura Y, Sato S and Tabata S (2000). A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries. DNA Res. 7: 175-180. Bang DD, Timmermans V, Verhage R, Zeeman AM, van de Putte P and Brouwer J (1995). Regulation of the Saccharomyces cerevisiae DNA repair gene RAD16. Nucleic Acids Res. 23: 1679-1685. Barlow JJ, Mathias AP, Williamson R and Gammack DB (1963). A Simple Method for the Quantitative Isolation of Undegraded High Molecular Weight Ribonucleic Acid. Biochem. Biophys. Res. Comm. 13: 61-66. Bekesiova I, Nap JP and Mlynarova L (1999). Isolation of high quality DNA and RNA from leaves of the carnivorous plant Drosera rotundifolia. Plant Mol. Biol. Reptr. 17: 269-277. Cato SA, Gardner RC, Kent J and Richardson TE (2001). A rapid PCR-based method for genetically mapping ESTs. Theor. Appl. Genet. 102: 296-306. Chirgwin JM, Przybyla AE, MacDonald RJ and Rutter WJ (1979). Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry 18: 5294-5299. Chomczynski P and Mackey (1995). Modification of the TRI ReagentTM procedure for isolation of RNA from polysaccharide- and proteoglycan-rich sources. Biotechniques 19: 942-945. Chomczynski P and Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thocyanate-phenol-chloroform extraction. Anal. Biochem. 162: 156-159. Crepineau F, Roscoe T, Kaass R, Kloareg B and Boyen C (2000). Characterization of complementary DNAs from the expressed sequence tag analysis of life cycle stages of Laminaria digitata (Phaeophyceae). Plant Mol. Biol. 43: 503-513. Delseny M, Cooke R, Raynal M and Grellet F (1997). The Arabidopsis thaliana cDNA sequencing projects. FEBS Lett. 403: 221-224. Dolferus R (1991). Isolation of DNA and RNA from Arabidopsis thaliana. In: Negrutiu I and Gharti-Chhetri GB (Eds.) A laboratory guide for cellular and molecular plant biology. Switzerland: Birkhauser Verlag Basel. p133-156. Doty MS, Santos GA and Ong KS (1983). Agar from Gracilaria cylindrica. Aquat. Bot. 15: 299-306. Dring MJ (1982). The biology of marine plants. London: Edward Arnold. p199. Eggermaont K and Goderis IJ (1996). High-throughput RNA extraction from plant samples based on homogenisation by reciprocal shaking in the presence of a mixture of sand and glass beads. Plant Mol. Biol. Reptr. 14: 273-279. Emmett M and Petrack B (1988). Rapid isolation of total RNA from mammalian tissues. Anal. Biochem. 174: 658-661. Evans LV (1963). The use of lithium chloride as a pretreatment to an acetocarmine technique on Fucus. Phycologia 2: 187-195. Gehrig HH, Winter K, Cuishman J Borland A and Taybi T (2000). An improved RNA isolation method for succulent plant species rich in polyphenols and polysaccharides. Plant Mol. Biol. Reptr. 18: 369-376. Geuna F, Hartings H and Scienza A (1998). A new method for rapid extraction of high quality RNA from recalcitrant tissues of grapevine. Plant Mol. Biol. Reptr. 16: 61-67. Glisin V, Crkvenjakov R and Byus C (1974). Ribonucleic acid isolated by cesium chloride centrifugation. Biochemistry 13: 2633-2637. Hillier LD, Lennon G, Becker M, Bonaldo MF, Chiapelli B, Chissoe S, Dietrich N, DuBuque T, Favello A, Gish W, Hawkins M, Hultman M, Kucaba T, Lacy M, Le M, Le N, Mardis E, Moore B, Morris M, Parsons J, Prange C, Rifkin L, Rohlfing T, Schellenberg K, Marra M et al. (1996). Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6: 807-828. Ho CL, Phang SM, Sinnappah ND and Pang T (1996). Molecular approaches in the taxonomy of the red and brown seaweeds. In: Chaudhary BR and Agrawal SB (Eds.) Cytolology, Genetics and Molecular Biology of Algae. Amsterdam: SPB Academic Publishing. p351-362. Hong YK, Coury DA, Polne-Fuller M and Gibor A (1992). Lithium chloride extraction of DNA from the seaweed Porphyra perforata (Rhodophyta). J. Phycol. 28: 717-720. Hong YK, Kim SD, Polne-Fuller M and Gibor A (1995a). DNA extraction conditions from Porphyra perforata using LiCl. J. Appl. Phycol. 7: 101-107. Hong YK, Sohn CH, Lee KW and Kim HG (1997). Nucleic acid extraction from seaweed tissues for polymerase chain reaction. J. Mar. Biotechnol. 5: 95-99. Hong YK, Sohn CH, Polne-Fuller M and Gibor A (1995b). Differential display of tissue-specific messenger RNAs in Porphyra perforata (Rhodophyta) thallus. J. Phycol. 31: 640-643. Hoppe HA and Schmid OJ (1969). Commercial Products. In: Levring T, Hoppe HA and Schmid OJ (Eds.) Marine Algae: a Survery of Research and Utilization. Hamburg: Cram, de Gruyter & Co., p288-300. Hughes DW and Galau G (1988). Preparation of RNA from cotton leaves and pollen. Plant Mol. Biol. Reptr. 6: 253-257. IHGSC International Human Genome Sequencing Consortium (2001). Initial sequencing and analysis of the human genome. Nature 409: 860-921. Jahara Y and Phang SM (1990). Seaweed Marketing and Agar Utilizing Industries in Malaysia. In: Gracilaria Production and Utilization in the Bay of Bengal. BOBP/REP 45: 75-86. Jensen A (1993). Present and future needs for algae and algal products. Hydrobiologia 260/261: 15-23. Karlinsey J, Stamatoyannopoulos G and Enver T (1989). Simultaneous purificaiton of DNA and RNA from small numbers of eukaryotic cells. Anal. Biochem. 180: 303-306. Kiefer E, Heller W and Ernst D (2000). A simple and efficient protocol for isolation of functional RNA from plant tissues rich in secondary metabolites. Plant Mol. Biol. Reptr. 18: 33-39. Lim PE, Thong KL and Phang SM (2001). Molecular differentiation of two morphological variants of Gracilaria salicornia. J. Appl. Phycol. 13: 335-342. Liu JJ, Goh CJ, Loh CS, Liu P and Pua EC (1998). A method for isolation of total RNA from fruit tissues of banana. Plant Mol. Biol. Reptr. 16: 1-6. Lluisma AO and Ragan MA (1997). ESTs from the marine red alga Gracilaria gracilis. J. Appl. Phycol. 9: 287-293. Lluisma AO and Ragan MA (1998a). Cloning and characterization of a nuclear gene encoding a starch-branching enzyme from the marine red alga Gracilaria gracilis. Curr. Genet. 34: 105-111. Lluisma AO and Ragan MA (1998b). Characterization of a galactose-1-phosphate uridylyltransferase gene from the marine red alga Gracilaria gracilis. Curr. Genet. 34: 112-119. Matthews CK, van Holde KE and Ahern KG (2000). Biochemistry, 3rd Ed. New York: Addison Wesley Publishing Co., p48-50, 209. Mayes C, Saunders GW, Tan IH and Druehl LD (1992). DNA extraction methods for kelp (Laminariales) tissue. J. Phycol. 28: 712-716. Meneses I, Santelices B and Sanchez P (1999). Growth-related intraclonal genetic changes in Gracilaria chilensisi (Gracilariales: Rhodophyta). Mar. Biol. 135: 391-397. Nikaido I, Asamizu E, Nakajima M, Nakamura Y, Saga N and Tabata S (2000). Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis. DNA Res. 7: 223-227. Norziah MH and Chio YC (2000). Nutritional composition of edible seaweed Gracilaria changii. Food Chem. 68: 69-76. Pawlowski K, Kunze R, de Vries S and Bisseling T (1994). Isolation of total, poly(A) and polysomal RAN from plant tissues. Plant Mol. Biol. Manual. Belgium: Kluwer Academic Publishers. D5: 1-13. Phang SM (1994b). Some species of Gracilaria from Peninsular Malaysia and Singapore. In: Abbott IA (Ed.) Taxonomy of Economic Seaweeds Vol. IV. California: California Sea Grant Programme, University of California. p125-134. Phang SM and Maheswary (1989). Phycocolloid content of some Malaysian seaweeds. Proc. 12th Ann. Seminar Mal. Soc. Mar. Sci. Kuala Lumpur. p65-77. Phang SM, Shaharuddin S, Noraishah H and Sasekumar A (1996). Studies on Gracilaria changii (Gracilariales, Rhodophyta) from Malaysian mangroves. Hydrobiologia 326/327: 347-352. Renn D (1997). Biotechnology and the red seaweed polysaccharide industry: status, need and prospects. Trends Biotechnol. 15: 9-14. Salzman RA, Fujita T, Zhu-Salzman K, Hasegawa PM and Bressan RA (1999). An improved RNA isolation method for plant tissues containing high levels of phenolic compounds or carbohydrates. Plant Mol. Biol. Reptr. 17: 11-17. Santos GA and Doty MS (1983). Agarose from Gracilaria cylindrica. Bot. Mar. 26: 31-34. Saunders GW (1993). Gel purification of red algal genomic DNA: an inexpensive and rapid method for the isolation of polymerase chain reaction-friendly DNA. J. Phycol. 29: 251-254. Schmitt ME, Brown TA and Trumpower BL (1990). A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 18: 3091-3092. Schramm W (1991). Cultivation of unattached seaweeds. In: Guiry MD and Blunden G (Eds.) Seaweed Resources in Europe: Uses and Potential. New York: John Wiley & Sons, Inc. p379-408. Shoop E, Carlis J. and Retzel EF (1994). Automating and streamlining inference of function of ESTs within a data analysis system. In: The Regents of the University of Minnesota. Minnesota: University of Minnesota. [online]. Accessed 01/02/2002. Available: http://www.cbc.med.umn.edu/VirtLibrary/Shoop/paper/est_paper.ss.html Soares MB and Bonaldo MF (1997). Constructing and screening normalized cDNA libraries. In: Birren B, Green ED, Klapholz S, Myers RM and Roskams J (Eds.) Genome Analysis: a Laboratory Manual Volume 2 - Detecting Genes. New York: Cold Spring Harbor Laboratory Press. p49-157. Sterky F and Lundeberg J (2000). Sequence analysis of genes and genomes. J. Biotechnol. 76: 1-31. Tseng CK and Xia BM (1999). On the Gracilaria in the Western Pacific and the Southeastern Asia Region. Bot. Mar. 42: 209-217. Verwoerd TC, Dekker BMM and Hoekema A (1989). A small-scale procedure for the rapid isolation of plant RNAs. Nucleic Acids Res. 17: 2362. Villemur R (1990). Circular plasmid DNAs from the red alga Gracilaria chilensis. Curr. Genet. 18: 251-257. Wilkinson M (2000). Purification of RNA. In: Brown TA (Ed.) Essential Molecular Biology Volume One: A Practical Approach, 2nd Ed., Oxford: Oxford University Press. p69-88. Wu W, Welsh MJ, Kaufman PB and Zhang HH (1997). Methods in Gene Biotechnology. New York: CRC Press. p30-32. Zhou YH and Ragan MA (1993). cDNA cloning and characterization of the nuclear gene encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa. Curr. Genet. 23: 483-489. Zhou YH and Ragan MA (1995a). Characterization of the polyubiquitin gene in the marine red alga Gracilaria verrucosa. Biochim. Biophys. Acta 1261: 215-222. Zhou YH and Ragan MA (1995b). Cloning and characterization of the nuclear gene and cDNAs for triosephosphate isomerase of the marine red alga Gracilaria verrucosa. Curr. Genet. 28: 317-323. Zhou YH and Ragan MA (1995c). The nuclear gene and cDNAs encoding cytosolic glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa: cloning, characterization and phylogenetic analysis. Curr. Genet. 28: 324-332.
Q-Index Code E1
Q-Index Status Provisional Code
Institutional Status Unknown
Additional Notes This paper is later published as: Chan CX, Ho CL, Othman RY and Phang SM (2004). Optimisation of RNA extraction for Gracilaria changii (Gracilariales, Rhodophyta). In: Phang SM, Chong VC, Ho SC, Mokhtar N and Ooi JLS (eds.) Marine Science into the New Millenium: New Perspectives & Challenges. Kuala Lumpur: University of Malaya Maritime Research Centre. pp. 477-487.

 
Versions
Version Filter Type
Citation counts: Google Scholar Search Google Scholar
Created: Mon, 04 Sep 2006, 10:00:00 EST by Cheong Xin Chan