Development and optimization of quantitative PCR assays to aid Ostrea lurida carpenter 1864 restoration efforts

Journal of Shellfish Research

Volumn 28, Issue 1, 2009, Pages 33-41

  Wight, Nathan A ^a   Suzuki, Jason ^a   Vadopalas, Brent ^a   Friedman, Carolyn S ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Burrowing shrimp; Larvae; Neotrypea; Olympia oyster; Ostrea; Quantitative PCR; Upogebia

Indexed keywords

DECAPODA (CRUSTACEA); NEOTRYPAEA CALIFORNIENSIS; OSTREA; OSTREA CONCHAPHILA; OSTREA LURIDA; OSTREIDAE; UPOGEBIA; UPOGEBIA PUGETTENSIS;

EID: 77649262490     PISSN: 07308000     EISSN: None     Source Type: Journal    
DOI: 10.2983/035.028.0108     Document Type: Article

References (34)

1. Baker, P. & R. Mann. 2003. Late stage bivalve larvae in a well-mixed estuary are not inert particles. Estuaries 26:837-845.
2. Baker, P. 1995. Review of the ecology and fishery of the Olympia oyster, Ostrea lurida with annotated bibliography. J. Shellfish Res. 14:501-518.
3. Countway, P. D. & D. A. Caron. 2006. Abundance and Distribution of Ostreococcus sp. in the San Pedro Channel, California, as Revealed by Quantitative PCR. Appl. Environ. Microbiol. 72:2496-2506.
4. Feldman, K. L., D. A. Armstrong, B. R. Dumbauld, H. Dewitt & D. C. Doty. 2000. Oysters, crabs, and burrowing shrimp: review of an environmental conflict over aquatic resources and pesticide use in Washington state's (USA) coastal estuaries. Estuaries 23:141-176.
5. Folmer, O., M. Black, W. Hoeh, R. Lutz & R. Vrijenhoek. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3:294-299.
6. Gilg, M. R. & T. J. Hilbish. 2003. The geography of marine larval dispersal: coupling genetics with fine-scale physical oceanography. Ecology 84:2989-2998.
7. Giglio, S., P. T. Monis & C. P. Saint. 2003. Demonstration of preferential binding of SYBR Green I to specific DNA fragments in real-time multiplex PCR. Nucleic Acids Res. 31:136.
8. Hare, M., S. Palumbi & C. Butman. 2000. Single-step species identification of bivalve larvae using multiplex polymerase chain reaction. Mar. Biol. 137:953-961.
9. Hartman, L., S. Coyne & D. Norwood. 2005. Development of a novel internal positive control for Taqman based assays. Mol. Cell. Probes 19:51-59.
10. Hebert, P., A. Cywinska, S. Ball & J. deWaard. 2003. Biological identifications through DNA barcodes. Proc. Roy. Soc. Lond. 270:313-322.
11. Hubert, S. & D. Hedgecock. 2004. Linkage maps of microsatellite DNA markers for the Pacific Oyster Crassostrea gigas. Genetics 168:351-362.
12. Ignatov, K. B., A. I. Miroshnikov & V. M. Kramarov. 2003. A New Approach to Enhanced PCR Specificity. Russ. J. Bioorganic Chem. 29:368-371.
13. Kirby, M. X. 2004. Fishing down the coast: Historical expansion and collapse of oyster fisheries along continental margins. Proc. Natl. Acad. Sci. USA 101:13096-13099.
14. Larionov, A., A. Krause & W. Miller. 2005. A standard curve based method for relative real time PCR data processing. BMC Bioinfor-matics 6:62.
15. Lin, L. I. K. 1989. A concordance correlation coefficient to evaluate reproducibility. Biometrics 45:255-268.
16. Locke, A. & S. Corey. 1989. Amphipods, isopods and surface currents: a case for passive dispersal in the Bay of Fundy, Canada. J. Plankton Res. 11:419-430.
17. Loosanoff, V. L., H. C. Davis & P. E. Chanley. 1953a. Behavior of clam larvae in different concentrations of food organisms. Anat. Rec. 117:586-587.
18. Loosanoff, V. L., H. C. Davis & P. E. Chanley. 1953b. Effect of overcrowding on rate of growth of clam larvae. Anat. Rec. 117:645-664.
19. McBeath, A. J. A., M. J. Penston, M. Snow, P. F. Cook, I. R. Bricknell & C. O. Cunningham. 2006. Development and application of realtime PCR for specific detection of Lepeophtheirus salmonis and Caligus elongatus larvae in Scottish plankton samples. Dis. Aquat. Organ. 73:141-150.
20. Newell, R. 2004. Ecosystem influences of natural and cultivated populations of suspension-feeding bivalve molluscs: a review. J. Shellfish Res. 23:51-61.
21. Nagai, M., A. Yoshida & N. Sato. 1998. Additive effects of bovine serum albumin, dithiothreitol, and glycerol on PCR. Biochem. Mol. Biol. Int. 44:157-163.
22. Nunan, L. M., B. T. Poulos & D. V. Lightner. 2000. Use of polymerase chain reaction for the detection of infectious hypodermal and hematopoietic necrosis virus in penaeid shrimp. Mar. Biotechnol. 2:319-328.
23. Queiroga, H. & J. Blanton. 2005. Interactions between behaviour and physical forcing in the control of horizontal transport of decapod crustacean larvae. Adv. Mar. Biol. 47:107-214.
24. Robin, E. D. & R. Wong. 2005. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J. Cell. Physiol. 136:507-513.
25. Rozen, S. & H. J. Skaletsky. 2000. Primer 3 on the WWW for general users and for biologist programmers. In: S. Krawetz & S. Misener, editors. Bioinformatics Methods and Protocols: Methods in Molecular Biology. Totowa, NJ: Humana Press. 365-386.
26. Reyns, N. B., D. B. Eggleston & R. A. Luettich. 2007. Dispersal dynamics of post-larval blue crabs, Callinectes sapidus, within a wind-driven estuary. Fish. Oceanogr. 16:257-272.
27. Scheltema, R. S. 1995. The relevance of passive dispersal for the biogeography of Caribbean mollusks. Am. Malacol. Bull. 11:99-115.
28. Shanks, A. L. 2001. An identification guide to the larval marine invertebrates of the Pacific Northwest. Corvallis, OR: OSU Press. 320 pp.
29. Simpson, R. J., C. S. Wilding & J. Grahame. 1999. Simple protocol for extracting nuclear DNA from single embryos of a marine snail. Biotechniques 26:1050-1052.
30. Thompson, J. D., D. G. Higgins & T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
31. Vadopalas, B., J. Bouma, C. Jackels & C. S. Friedman. 2006. Application of quantitative PCR for simultaneous identification and quantification of larval abalone. J. Exp. Mar. Biol. Ecol. 334: 219-228.
32. Wang, Q., L. M. Nunan & D. V. Lightner. 2000. Identification of genomic variations among geographic isolates of white spot syndrome virus using restriction analysis and southern blot hybridization. Dis. Aquat. Organ. 43:175-181.
33. Wong, M. L. & J. F. Medrano. 2005. Real-time PCR for mRNA quantification. Biotechniques 39:75-85.
34. Zhu, F., R. Massana, F. Not, D. Marie & D. Vaulot. 2005. Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol. Ecol. 52:79-92.