Quantifying RNA and DNA in planktonic organisms with SYBR Green II and nucleases. Part A. Optimisation of the esssay

Scientia Marina

Volumn 69, Issue 1, 2005, Pages 1-16

  Berdalet, Elisa ^a   Roldán, Cristina ^a   Olivar, M Pilar ^a   Lysnes, Kristine ^b  

^a INSTITUT DE CIÈNCIES DEL MAR   (Spain)

^b UNIVERSITY OF BERGEN   (Norway)

Author keywords

DNase; Plankton; RNA DNA ratios; RNase; SYBR Green II

Indexed keywords

DNA; PLANKTON; QUANTITATIVE ANALYSIS; RNA;

EID: 16344395553     PISSN: 02148358     EISSN: None     Source Type: Journal    
DOI: 10.3989/scimar.2005.69n11     Document Type: Article

References (49)

1. Bashford, C.L. - 1987. An introduction to spectrophotometry and fluorescence spectrometry. In: C.L. Brashford and D.A.: Harris (eds.), Spectrophotometry and spectrofluorimetry: a practical approach, Ch. 1, pp. 1-22. IRL Press, Oxford, Washington DC.
2. Bentle. L.A., D. Seshachalam and J. Metcoff. - 1981. The sequential enzymatic determination of RNA and DNA. Anal. Biochem., 116: 5-16.
3. Berdalet, E. and Q. Dortch. - 1991. New double-staining technique for RNA and DNA measurement in marine phytoplankton. Mar. Ecol.Progr. Ser., 73: 295-305.
4. Berdalet, E. and M. Estrada. - 1993. Effects of turbulence on several phytoplankton species. In: T. Smayda and Y. Shimizu (eds.), Toxic phytoplankton blooms in the Sea. Developments in Marine Biology, 3. pp. 737-743. 5th International Conference on Toxic Marine Phytoplankton, Rhode Island. USA.
5. Berdalet, E, C. Marrasé, M. Estrada, L. Arin and M.L. Mac Lean. - 1996a. Microbial community responses to nitrogen and phosphorus-deficient nutrient inputs: microplankton dynamics and biochemical characterization. J. Plankton Res., 18: 1627-1641.
6. Berdalet, E., Arin, L., Marrasé, C., Cruzado, A. and M. Estrada. - 1996b. Limiting nutrients and biochemical composition of natural microbial communities in the NW Mediterranean. 2nd Workshop of the Mediterranean Targeted Project. 5EMMS. Creta.
7. Berdalet, E. - 2002. Quantization of nucleic acids in marine microplankton samples. In: D.V. Subba Rao (ed.), Pelagic Ecology Methodology, pp. 269-289. A.A. Balkema Publishers, Lisse, Abingdon, Exton PA), Tokyo.
8. Berdalet, E., C. Roldán, and M.P. Olivar. - 2005. Quantifying RNA and DNA in planktonic organisms with SG-II and nucleases. Part B. Quantification in natural samples. Sci. Mar., 69:.
9. Bergeron, J.P. - 1997. Nucleic acids in ichthyoplankton ecology: a review, with emphasis on recent advances for new perspectives. J. Fish Biol., 51: 284-302.
10. Buckley, L.J. 1984. RNA - DNA ratios an index of larval growth in the sea.Mar. Biol., 80: 291-298.
11. Bulow, F.J. - 1970. RNA-DNA ratios as indicators of recent growth rates of a fish. J. Fish. Res. Bd. Can., 27: 2343-2349.
12. Bulow, F.J. - 1987. RNA-DNA ratios indicators of growth in fish: A review. In: R.C. and G.E. Hall (eds.), The age and growth of fish, pp. 45-64. The Iowa State University Press, Ames, Iowa.
13. Caldarone, E.M. and L.J. Buckley. - 1991. Quantification of DNA and RNA in crude tissue extracts by flow injection. Anal. Biochem., 199: 137-141.
14. Caldarone, E.M., M. Wagner, J. St. Onge-Burns and L.J. Buckley. - 2001. Protocol and guide for estimating nucleic acids in larval fish using a fluorescence microplate reader. Northeast Fish. Sci. Cent. Ref. Doc. 01-11: 1-22. http://www.nefse.nefsc.gov/nefsc/publications/.
15. Canino, M.F., K.M. Bailey and L.S. Incze. - 1991. Temporal and geographical differences in feeding and nutritional condition of walleye Pollock larvae Theragra chalcogramma in Shelikof Strait, Gulf of Alaska. Mar. Ecol. Progr. Ser., 79: 27-35.
16. Ceasarone, C.F., C. Bolognesi and L. Santi. - 1979. Improved microfluorimetric DNA determination in biological material using 33258 Hoeschst. Anal. Biochem., 100: 188-197.
17. Clemmesen, C. - 1994. The effect of food availability, age or size on the RNA/DNA ratio of individually measured herring larvae: laboratory calibration. Mar. Biol., 118: 377-382.
18. Dagg, M.J. and J.L. Littlepage. - 1972. Relationships between growth rate and RNA, DNA, protein and dry weight in Artemia salina and Euchaeta elongata. Mar. Biol., 17: 162-170.
19. Dortch, Q., T.L. Roberts, J.R. Clayton, Jr. and S.I. Ahmed. - 1983. RNA/ DNA ratios and DNA concentrations as indicators of growth rate and biomass in planktonic marine organisms. Mar. Ecol. Prog. Ser., 13: 61-71
20. Fara, A., E. Berdalet, and L. Arin. - 1996. Determination of RNA and DNA concentrations in natural plankton samples using thiazole orange in combination with DNase and RNase digestions. J. Phycol., 32: 1074-1083.
21. Folkvord, A., L. Ystanes and E. Moksness. - 1996. RNA:DNA ratios and growth of herring (Clupea harengus) larvae reared in mesocosms. Mar. Biol., 126: 591-602.
22. Gorokhova, E. and M. Kyle. - 2002. Analysis of nucleic acids in Daphnia: development of methods and ontogenic variations in RNA-DNA content. J. Plankton Res., 24: 511-522.
23. Haugland, R.P. - 2002. Nucleic Acid Detection and Genomics Technology. In: J. Gregory (ed.), Handbook of Fluorescent Probes and Research Products, pp. 265-352. Molecular Probes, Inc. USA.
24. Holm-Hansen, 0., W.H. Sutcliffe, Jr. and J. Sharp. - 1968. Measurement of the deoxyribonucleic acid in the ocean and its ecological significance. Limnol. Oceanogr., 13: 507-514.
25. Kemp, P.F., Lee, S. and J. La Roche. - 1993. Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl. Environm. Microbiol., 59: 2594-2601.
26. Klinger, T.S., S.A. Watts and D. Forcucci. - 1988. Effect of short-term feeding and starvation on storage and synthettic capacities of gut tissues of Lytechinus variegatus (Lamarck) (Echinodermata:Echinoidea). J. Exp. Mar. Biol. Ecol., 117: 187-195.
27. Kuropat, C., R. Mercaldo-Allen, E.M. Caldarone, R. Goldberg, B. Phelan and F. Thurberg. - 2002. Evaluation of RNA concentration as an indicator of growth in young-of-the-year winter flounder Pseudopleuronectes americanus and tautog Tautoga onitis. Mar. Ecol. Progr. Ser., 230: 265-274.
28. Le Pecq, J.B. and C. Paoletti. - 1966. A new fluorimetric method for RNA and DNA determination. Anal. Biochem., 17: 100-107.
29. Lysnes, K. - 1998. Determination of DNA and RNA in marine plankton samples. Master thesis, Univ. Bergen, Norway.
30. Marie, D., D. Vaulot and F. Partensky. - 1996. Application of the novel nucleic acid dyes YOYO1 YO-PRO-1 and Pico-Green for flow cytometric analysis of marine prokaryotes. Appl. Environ. Microbiol., 62: 1649-1655.
31. Mathers, E.M., D.F. Houlihan and L.J. Burren. - 1994. RNA, DNA and protein concentrations in fed and starved herring Clupea harengus larvae. Mar. Ecol. Progr. Ser., 107: 223-231.
32. Mordy, C.W. and D.J. Carlson. - 1991. An evaluation of fluorescence techniques for measuring DNA and RNA in marine microorganisms. Mar. Ecol. Prog. Ser., 73: 283-293.
33. Munro, H. N. and A. Fleck. - 1966. The determination of nucleic acids. In: D. Glick (ed.), Methods of Biochemical Analysis, pp. 113-176. Interscience Publishers, New York.
34. Nakata, K., H. Nakano and H. Kikuchi. - 1994. Relationship between egg productivity and RNA/DNA ratio in Paracalanus sp. In the frontal waters of the Kurshio. Mar. Biol., 119: 591-596.
35. Nobel, R.T. and J.A. Furhman. - 1997. Use of SYBR Green I for use of rapid epifluorescence counts of marine viruses and bacteria. Aquat.Microb. Ecol. 14: 113-118.
36. Regnault, M. and P. Luquet. - 1974. Study by evolution of nucelic acid content of prepuberal growth in the shrimp Crangon vulgaris. Mar. Biol., 25: 291-298.
37. Saiz, E., A. Calbet, A. Fara. and E. Berdalet. - 1998. RNA content of copepods as a tool for determining adult growth rates in the field. Limnol. Occeanogr., 43: 465-470.
38. Sambrook, J., E.F. Fritsch and T. Maniatis. - 1989. Molecular cloning: A laboratory manual, C. Nolan (ed.). Cold Spring Harbor Laboratory Press, USA.
39. Schmidt, G. and S.J. Tannhauser. - 1945. A method for the determination of deoxyribonucleic acid, ribonucleic acid, and phosproteins in animal tissues. J. Biol. Chem., 161: 83-89.
40. Schmidt, D.M. and J.D. Ernst. - 1995. A Fluorometric assay for the quantification of RNA in solution with nanogram sensitivity. Anal. Biochem., 232: 144-146.
41. Sutcliffe, W.H.J. - 1970. Relationship between growth rate and ribonucleic acid concentration in some invertebrates. J. Fish. Res. Bd. Can., 27: 606-609.
42. Suthers, I.M., J.J. Cleary, S.C. Battaglene and R. Evans. - 1996. Relative RNA content as a measure of condition in larval and juvenile fish. Mar. Freshwater Res., 47: 301-307.
43. Tabor, S. and K. Struhl. - 1998. Endonucleases. In: F.M. Ausubel, R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith and K. Struhl (eds.), Current protocols in molecular biology. Vol. I. pp. 3.12.1-3.12.6. John Wiley and Sons, Inc. USA.
44. Thoresen, S.S., J.R. Clayton, Q. Dortch and S.I. Ahmed. - 1983. A rapid technique for the determination of RNA and DNA in marine phytoplankton. J. Plankton Res., 5: 253-261.
45. Veldhuis, M.J.W., T.L. Cucci and M.E. Sieracki. - 1997. Cellular DNA content of marine phytoplankton using two new fluorochromes: taxonomic and ecological implications.J. Phycol., 33: 527-541.
46. Vrede, T., J. Persson and G. Aronsen. - 2002. The influence of food quality (P:C) ratio and somatic growth rate of Daphnia. Linmol. Oceanogr., 47: 487-494.
47. Walser, R. and H. Güde. - 1994. DNA and RNA contents of bacteria-sized particles from Lake Constance. Arch. Hydrobiol., 131: 257-276.
48. Wagner, M., E. Durbin. and L. Buckley. - 1998. RNA:DNA ratios as indicators of nutritional condition in the copepod Calanus finmarchicus. Mar. Ecol. Prog. Ser., 162: 173-181.
49. Westerman, M. and G. Holt. - 1994. RNA:DNA ratio during the critical period and early larval growth of the red drum Sciaenops ocellatus. Mar. Biol., 121: 1-9.