Quantitative PCR

Molecular Research in Aquaculture

Volumn , Issue , 2009, Pages 39-61

  Overturf, Ken ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Aquaculture and molecular biology convergence; Aquatic products for food production; DNA detailing position of chemical components; Fish farming and aquaculture research and molecular technology; Fugu or pufferfish (Tetraodon nigroviridis) and medaka (Oryzias latipes); Identification and study of zebrafish mutations; Molecular biology and genetics; Molecular biology, genetics and biochemistry linkage; Product marketing, economics of production and aquaculture intensification; Vitamin free purified diet supporting growth

Indexed keywords

EID: 84861731820     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780813807379.ch3     Document Type: Chapter

References (102)

1. Allawi, H., Dahlberb, J., Olson, S., Elsebet, L., Olson, M., Wu-Po, M., Takova, T., Neri, B., Lyamichev, V. 2004. Quantitation of microRNAs using a modified Invader assay. RNA. 10:1153-1161.
2. Baric, S., Kerschbamer, C., Dalla Via, J. 2006. TaqMan real-time PCR versus four conventional PCR assay for detection of apple proliferation phytoplasma. Plant Molecular Biology Reporter. 24:169-184.
3. Bashiardes, S., Lovett, M. 2001. cDNA detection and analysis. Current Opinions in Chemical Biology. 5:15-20.
4. Bernard, P., Aijoka, R., Kushner, J., Wittwer, C. 1998. Homogeneous multiplex genotyping of hemochromatosis mutations with fluorescent hybridization probes. American Journal of Pathology. 153:1055-1061.
5. Biga, P., Schelling, G., Hardy, R., Cain, K., Overturf, K., Ott, T. 2004. The effects of recombinant bovine somatotropin (rbST) on tissue IGF-I, IGF-I receptor, and GH mRNA levels in rainbow trout, Oncorhynchus mykiss.General and Comparative Endocrinology. 135:324-333.
6. Bilodeau, A.L., Peterson, B.C., Bosworth, B.G. 2006. Response of toll-like receptors, lysozyme, and IGF-1 in back-cross hybrid (F1 male (blue × channel) × female channel) catfish challenged with virulent Edwardsiella ictaluri. Fish and Shellfish Immunology. 20:29-39.
7. Bogaert, L., Van Poucke, M., De Baere, C., Peelman, L., Gasthuys, F., Martens, A. 2006. Selection of a set of reliable reference genes for quantitative real-time PCR in normal equine skin and in equine sarcoids. BMC Biotechnology. 6:24.
8. Burgos,C., Carrodeguas, J., Moreno, C., Sanchez, A., Tarrafeta, L., Barcelona, J., Lopez-Buesa, P. 2005. A real time PCR (RT-PCR) alternative assay to detect the T/C mutation in position 1843 of the ryanodine receptor gene. Meat Science. 70:395-398.
9. Burke, J.,Wang, H., Hide,W., Davison, D. 1998. Alternative gene form discovery and candidate gene selection from gene indexing projects. Genome Research. 8:276-290.
10. Bustin, S. 2000. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. Journal of Molecular Endocrinology. 25:169-193.
11. Bustin, S. 2002. Quantification ofmRNAusing real-time reverse transcription PCR (RT-PCR): Trends and problems. Journal of Molecular Endocrinology. 29:23-39.
12. Bustin, S. 2005. Real-Time Reverse Transcription PCR. In: Fuchs, J., Podda, M. (eds), Encyclopedia of Diagnostic Genomics and Proteomics. Marcel Dekker, New York, pp. 718-726.
13. Cavender, W., Wood, J., Powell, M., Overturf, K., Cain, K. 2004. Real-time quantitative polymerase chain reaction (QPCR) to identify Myxobolus cerebralis in rainbow trout Oncorhynchus mykiss. Diseases of Aquatic Organisms. 60:205-213.
14. Chandler, D., Wagnon, C., Bolton, H. 1998. Reverse transcriptase (RT) inhibition of PCR at low concentrations of template and its implications for quantitative RT-PCR. Applied Environmental Microbiology. 64:669-677.
15. Chang, J., Wooten, E., Tsimelzon, A., Hisenbeck, S., Guierrez, M., Elledge, R., Mohsin, S., Osborne, C., Chamness, G., Allred, D., O'Connell, P. 2003. Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer. The Lancet. 362:362-369.
16. Chen, M., Raymond, R.F. 2007. Time course of increased heme oxygenase activity and expression after experimental intracerebral hemorrhage: Correlation with oxidative injury. Journal of Neurochemistry. 103:2015-2021.
17. Chen, X., Zehnbauer, B., Gnirke, A., Kwok, P. 1997. Fluorescence energy transfer detection as a homogeneous DNA diagnostic method. Proceedings of the National Academy of Sciences. 94:10756-10761.
18. Clementi, M., Menzo, S., Manzin, A., Bagnarelli, P. 1995. Quantitative molecular methods in virology. Archives of Virology. 140:1523-1539.
19. Diffenbach, C., Lowe, T., Dveksler, G. 1995. General concepts for PCR primer design. In: Dieffenbach, C., Dveksler, G. (eds), PCR Primer-A Laboratory Manual. Cold Springs Harbor Laboratory Press, Plainview, New York, pp. 133-142.
20. Donia, D., Divizia, M., Pana, A. 2005. Use of armored RNA as a standard to construct a calibration curve for real-time RT-PCR. Journal of Virological Methods. 126:157-163.
21. Edmonds, J., Wyckoff, Y.G., Wang, Y., Stanley, E.R., Jones, J., Segall, J., Condeelis, J. 1996. Elongation factor-1 alpha is an overexpressed actin binding protein in metastatic rat mammary adenocarcinoma. Journal of Cell Science. 109:2705-2714.
22. Fiandaca, M., Hyldig-Nielsen, J., Gildea, B., Coull, J. 2001. Self-reporting PNA/DNA primers for PCR analysis. Genome Research. 11:609-613.
23. Foltz, J., Plant, K., Overturf, K., Clemens, K., Powell, M. 2009. Detection of Nucleospora salmonis in steelhead, Oncorhynchus mykiss (Walbaum), using quantitative polymerase chain reaction (qPCR). Journal of Fish Diseases. DOI: 10.1111/j.1365-2761.2009.0095.
24. Forster, T. 1948. Zwischenmolekulare Energiewanderung und Fluoreszenz. Annals of Physik. 437:55.
25. Foss, D., Baarsch, M., Murtaugh, M. 1998. Regulation of hypoxanthine phosphoribosyltransferase, glyceraldehey-3-phosphate dehydrogenase and beta-actin mRNA expression in porcine immune cells and tissues. Animal Biotechnology. 9:67-78.
26. Freeman,W., Walker, S., Vrana, K. 1999. QuantitativeRT-PCR: Pitfalls and potential. Biotechniques. 26:112-125.
27. Gao, L., Mejias, R., Echevarria, M., Lopez-Barneo, J. 2004. Induction of the glucose-6-phosphate dehydrogenase gene expression by chronic hypoxia in PC12 cells. FEBS Letters. 569:256-260.
28. Gaylord, T.,Barrows, F., Teague, A., Johansen,K., Overturf,K., Shepherd,B. 2007. Supplementation of taurine and methionine to all-plant protein diets for rainbow trout (Oncorhynchus mykiss). Aquaculture. 269:514-524.
29. Ginzinger, D. 2002. Gene quantification using real-time quantitative PCR: An emerging technology hits the mainstream. Experimental Hematology. 30:503-512.
30. Giulietti, A., Overbergh, L., Valckx, D., Decallonne, B., Bouillon, R., Mathieu, C. 2001. An overview of real-time quantitative PCR: Applications to quantify cytokine gene expression. Methods. 25:386-401.
31. Goldsworthy, S., Goldsworthy, T., Sprankle, C., Butterworth, B. 1993. Variation in expression of genes used for normalization of Northern blots after induction of cell proliferation. Cellular Profiles. 26:511-518.
32. Halford, W., Falco, V., Gebhardt, B., Carr, D. 1999. The inherent quantitative capacity of the reverse transcription-polymerase chain reaction. Analytical Biochemistry. 266:181-191.
33. Heid, C.A., Stevens, J., Livak, K.J., Williams, P.M. 1996. Real time quantitative PCR. Genome Research. 6:986-994.
34. Hibbeler, S., Scharsack, J., Becker, S. 2008. Housekeeping genes for quantitative expression studies in the three-spined stickleback Gasterosteus aculeatus. BMC Molecular Biology. 9:18.
35. Huang, X., Pan, W., 2007. Linear regression and two-class classification with gene expression data. Bioinformatics. 19:2072-2078.
36. Huising,M., van Schijndel, J.E., Kruiswijk, C., Nabuurs, S., Savelkoul, H., Flik, G., Verburg-van Kemenade, B. 2006. The presence of multiple and differentially regulated interleukin-12p40 genes in bony fishes signifies an expansion of the vertebrate heterodimeric cytokine family. Molecular Immunology. 43:1519-1530.
37. Illmer, T., Schaich, M., Oelschlagel, U., Nowak, R., Renner, U. Ziegs, B., Subat, S., Neubauer, A., Ehninger, G. 1999. A new PCR MIMIC strategy to quantify low mdr1 mRNA levels in drug resistant cell lines and AML blast samples. Leukemia Research. 23:653-663.
38. Johansen, K., Overturf, K. 2005. Quantitative expression analysis of genes affecting muscle growth during development of rainbow trout (Oncorhynchus mykiss). Marine Biotechnology. 7:576-587.
39. Johansen, K., Overturf, K. 2006. Alterations in expression of genes associated with muscle metabolism and growth during nutritional restriction and refeeding in rainbow trout. Comparative Biochemistry and Physiology, Part B. 144:119-127.
40. Johansen, K., Sealey, W., Overturf, K. 2006. The effects of chronic immune stimulation on muscle growth in rainbow trout. Comparative Biochemistry and Physiology, Part B. 144:520-531.
41. Jorgensen, S., Kleveland, E., Grimholt, U., Gjoen, T. 2006. Validation of reference genes for real-time polymerase chain reaction studies in Atlantic salmon. Marine Biotechnology. 8:398-408.
42. Ke, L., Chen, Z., Yung, L., Wung, W. 2000. A reliability test of standard-based quantitative PCR: Exogenous vs. endogenous standards. Molecular and Cellular Probes. 14:127-135.
43. Kreuzer, K., Lass, U., Landt, O., Nitsche, A., Laser, J., Ellerbrok, H., Pauli, G., Dieter, H., Schmidt, C. 1999. Highly sensitive and specific fluorescence reverse transcription-PCR assay for the pseudogene-free detection of β-actin transcripts as quantitative reference. Clinical Chemistry. 45:297-300.
44. Kutyavin, I.,Afonina, I., Mill, A., Gorn, V., Lukhtanov, E., Belousov, E., Singer,M., Walburger, D.,Lokhov, S., Gall, A., Dempcy, R., Reed,M., Meyer, R., Hedqpeth, J. 2000. 3'-minor groove binder-DNA proves increase sequence specificity at PCR extension temperatures. Nucleic Acids Research. 15:655-661.
45. LaPatra, S., Batts,W., Overturf, K., Jones, G., Shewmaker,W., Winton, J. 2001. Negligible risk associated with the movement of processed rainbow trout, Oncorhynchus mykiss (Walbaum), from an infectious haematopoietic necrosis virus (IHNV) endemic area. Journal of Fish Diseases. 24:390-408.
46. Lee, L., Connell, C., Bloch, W. 1993. Allelic discrimination by nick-translation PCR with fluorgenic probes. Nucleic Acids Research. 21:3761-3766.
47. -ΔΔCT method. Methods. 25:402-408.
48. Low, C., Wadsworth, S., Burrellsand, C., Secombes, C. 2003. Expression of immune genes in turbot (Scopthalmus maximus) fed a nucleotide-supplemented diet. Aquaculture. 221:23-40.
49. Malina, A., Tassakka, R., Masahiro, S. 2004. Expression of immune-related genes in the common carp (Cyprinus carpio L.) after stimulation by CpG oligodeoxynucleotides. Aquaculture. 242:1-12.
50. Mao, L., Raine, J., Leatherland, J. 2007. Expression profiles of growth-related genes during the very early development of rainbow trout embryos reared at two incubation temperatures. General and Comparative Endocrinology. 153:302-310.
51. Marten, N., Burke, E., Hayden, J., Strauss, D. 1994. Effect of amino acid limitation on the expression of 19 genes in rat hepatoma cells. FASEB Journal. 8:538-544.
52. Matsuyama, T., Fujiwara, A., Nakayasu, C., Kamaishi, T., Oseko, N., Hirono, I., Aoiki, T. 2006. Gene expression of leucocytes in vaccinated Japanese flounder (Paralichthys olivaceus) during the course of experimental infection with Edwardsiella tarda. Fish and Shellfish Immunology. 22:598-607.
53. Morales, R., Herrera, M., Arenal, A., Cruz, A., Hernandez, O., Pimentel, R., Guillen, I., Martinez, R., Estrada, M. 2001. Tilapia chromosomal growth hormone gene expression accelerates growth in transgenic zebrafish (Danio rerio) [online]. Journal of Biotechnology. 42. (http://www.ejb.org/content/vol4/issue2/full/3).
54. Mori, T., Devlin, B. 1999. Transgene and host growth hormone gene expression in pituitary and nonpituitary tissues of normal and growth hormone transgenic salmon. Molecular and Cellular Endocrinology. 149:129-139.
55. Mullis, K. 1990. Target amplification for DNA analysis by the polymerase chain reaction. Annales de Biologie Clinique. 48:579-582.
56. Nazarenko, I.A., Bhatnagar, S.K., Hohman, R.J. 1997. A closed tube assay format for amplification and detection of DNA based on energy transfer. Nucleic Acids Research. 25:2516-2521.
57. Nielsen, P.E., Egholm, M., Berg, R.H., Buchardt, O. 1991. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science. 6:1497-1500.
58. Ninfali, P., Baronciani, L., Bardoni, A., Bresolin, N. 1995. Muscle expression of glucose-6-phosphate dehydrogenase deficiency in different variants. Clinical Genetics. 48:232-237.
59. Olsvik, P., Lie, K., Jordal, A., Nilsen, T., Hordvik, I. 2005. Evaluation of potential reference genes in real-time RT-CPR studies of Atlantic salmon. BMC Molecular Biology. 6. (http://www.biomedcentral.com/147).
60. Ostbye, T., Galloway, T., Nielsen, C., Gaabestad, I., Bardal, T., Andersen, O. 2001. The two myostatin genes of Atlantic salmon (Salmo salar) are expressed in a variety of tissues. European Journal of Biochemistry. 268:5249-5257.
61. Overturf, K., LaPatra, S. 2006. Quantitative expression of immunological factors in rainbow trout, Oncorhynchus mykiss (Walbaum) after infection with either Flavobacterium psychrophilum, Aeromonas salmonicida, or infectious haematopoietic necrosis virus. Journal of Fish Diseases. 29:215-224.
62. Overturf, K., LaPatra, S., Powell, M. 2001. Real-time PCR for the detection and quantitative analysis of IHNV in salmonids. Journal of Fish Diseases. 24:325-333.
63. Panserat, S., Plagnes-Juan, E., Kaushik, S. 2001. Nutritional regulation and tissue specificity of gene expression for key proteins involved in hepatic glucose metabolism in rainbow trout (Oncorhynchus mykiss). Journal of Experimental Biology. 204:2351-2360.
64. Panserat, S., Plagnes-Juan, E., Kaushik, S. 2002. Gluconeogenic enzyme gene expression is decreased by dietary carbohydrates in common carp (Cyprinus carpio) and gilthead seabream (Sparus aurata). Biochemica et Biophysica Acta. 1579:35-42.
65. Peirson, S. Butler, J., Foster, R. 2003. Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis. Nucleic Acids Research. 31:e73.
66. Peterson, B., Bosworth, B., Bilodeau, L. 2005. Differential gene expression of IGF-I, IGF-II, and toll-like receptors 3 and 5 during embryogenesis in hybrid (channelxblue) and channel catfish. Comparative Biochemistry and Physiology, Part A. 141:42-47.
67. Pfaffl, M. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Research. 29:2002-2007.
68. Powell, M.,Overturf, K., Hogge, C., Johnson, K. 2005. Detection of Renibacterium salmoninarun in Chinook salmon, Oncorhynchus tshawytscha (Walbaum), using quantitative PCR. Journal of Fish Diseases. 28:615-622.
69. Purcell, M., Kurath, G., Garver, K., Herwig, R., Winton, J. 2004. Quantitative expression profiling of immune response genes in rainbow trout following infectious haematopoietic necrosis virus (IHNV) infection or DNA vaccination. Fish and Shellfish Immunology. 17:447-462.
70. Radoni, A., Thulke, S.,Mackay, I., Landt, O., Siegert, W., Nitsche, A. 2003. Guideline to reference gene selection for quantitative real-time PCR. Biochemical and Biophysical Research Communications. 313:856-862.
71. Raeymaekers, L. 2000. Basic principles of quantitative PCR. Molecular Biotechnology. 15:115-122.
72. Rahman, M., Mak, R., Ayad, H., Smith, A., Maclean, N. 2004. Expression of a novel piscine growth hormone gene results in growth enhancement in transgenic tilapia (Oreochromis niloticus). Transgenic Research. 7:357-370.
73. Reid, S., Ferris, N., Hutching, G., Zhang, Z., Belsham, J., Alexandersen, S. 2002. Detection of all seven serotypes of foot-and-mouth disease virus by real-time, fluorogenic reverse transcription polymerase chain reaction assay. Journal of Virological Methods. 105:67-80.
74. Rescan, P., Jutel, I., Ralliere, C. 2001. Two myostatin genes are differentially expressed in myotomal muscles of the trout (Oncorhynchus mykiss). Journal of Experimental Biology. 204:3523-3529.
75. Robinson, N., Goddard,M., Hayes, B. 2008. Use of gene expression data for predicting continuous phenotypes for animal production and breeding. Animal. 2:1413-1420.
76. Rodrigues, P.N., Vazquez-Dorado, S., Neves, J., Wilson, J.M. 2006. Dual function of fish hepcidin: Response to experimental iron overload and bacterial infection in sea bass (Dicentrarchus labrax). Developmental and Comparative Immunology. 30:1156-1167.
77. Rutledge, R., Cote, C. 2003. Mathematics of quantitative kinetic PCR and the application of standard curves. Nucleic Acids Research. 31:e93.
78. Saint-Jean, S., Perez-Prieto, S. 2007. Effects of salmonid fish viruses on Mx gene expression and resistance to single or dual viral infections. Fish and Shellfish Immunology. 23:390-400.
79. Salem, M., Kenney, P., Rexroad, C., Yao, J. 2006. Molecular characterization of muscle atrophy and proteolysis associated with spawning in rainbow trout. Comparative Biochemistry and Physiology, Part B. 141:227-237.
80. Salem, M., Yao, J., Rexroad, C., Kenney, P., Semmens, K., Killefer, J., Nath, J. 2005. Characterization of calpastatin gene in fish: Its potential role in muscle growth and fillet quality. Comparative Biochemistry and Physiology, Part B. 141:488-497.
81. Sarraf, P., Mueller, E., Jones, D., King, F., DeAngelo, D., Partridge, J., Holden, S., Chen, L.B., Singer, L., Fletcher, S., Spiegelman, B. 1998. Differentiation and reversal of malignant changes in colon cancer through PPARγ. Nature Medicine. 4:1046-1052.
82. Saunders, N. 2004. Quantitative real-time PCR. In: Edwards, K., Logan, J., Saunders, N. (eds), Real-Time PCR-An Essential Guide. Horizon Bioscience, Norfalk, UK, pp. 103-123.
83. Sealey, W., Barrows, F., Hang, A., Johansen, K., Overturf, K., LaPatra, S., Hardy, R. 2007a. Evaluation of the ability of barely genotypes containing different amounts of β-glucan to alter growth and disease resistance of rainbow trout Oncorhynchus mykiss. Animal Feed Science and Technology. 141:115-126.
84. Sealy, W.M., Barrows, F., Johansen, K.A., Overturf, K.E., Lapatra, S.E., Hardy, R.W. 2007b. Evaluation of the ability of partially autolyzed yeast and Grobiotic-A to improve disease resistance in rainbow trout. North American Journal of Aquaculture. 69:400-406.
85. Siebert, P., Larrick, J. 1993. PCR MIMICS: Competitive DNA fragments for use as internal standards in quantitative PCR. BioTechniques. 14:244-249.
86. Small, B., Murdock, C., Bilodeau-Bourgeois, L., Peterson, B.,Waldbieser, G. 2008. Stability of reference genes for real-time PCR analyses in channel catfish (Ictulurus punctatus) tissues under varying physiological conditions. Comparative Biochemistry and Physiology, Part B. 151:296-304.
87. Small, B., Peterson, B. 2005. Establishment of a time-resolved fluoroimmunoassay for measuring plasma insulin-like growth factor I (IGF-I) in fish: Effect of fasting on plasma concentrations and tissue mRNA expression of IGF-I and growth hormone (GH) in catfish. Domestic Animal Endocrinology. 28:202-215.
88. +-ATPase. Analytical Biochemistry. 217:91-97.
89. Suslov, O., Steindler, D. 2005.PCR inhibition by reverse transcriptase leads to an overestimation of amplification efficiency. Nucleic Acids Research. 33:e181.
90. Takara, K., Takagi, M., Tsujimoto, M., Ohnishi, N., Yokoyama, T. 2003. Digoxin up-regulates multidrug resistance transporter (MDR1)mRNAand simultaneously down-regulates steroid xenobiotic receptor mRNA. Biochemical and Biophysical Research Communications. 306:116-120.
91. Tang,W., Qi, M., Van, G., Wariner, G., Samal, B. 1996. Leukemia inhibitory factor ameliorates experimental anti-GBM Ab glomerulonephritis. Kidney International. 50:1922-1927.
92. Thellin, O., Zorzi,W., Lakaye, B., De Borman, B., Coumans, B., Hennen, G., Grisar, T., Igout, A., Heinen, E. 1999. Housekeeping genes as internal standards: Use and limits. Journal of Biotechnology. 75:291-295.
93. Todd, A., Fuery, C., Impey, H., Applegate, T., Haughton, M. 2000. DzyNA-PCR: Use of DNAzymes to detect and quantify nucleic acid sequences in a real-time fluorescent format. Clinical Chemistry. 46:625-630.
94. Tyagi, S., Kramer, F.R. 1996. Molecular beacons: Probes that fluoresce upon hybridization. Nature Biotechnology. 14:303-308.
95. Valasek,M., Repa, J. 2005. The power of real-time PCR. Advances in Physiological Education. 29:151-159.
96. Van Rheenen, J., Langeslag, M., Jalink, K. 2004. Correcting confocal acquisition to optimize imaging of fluorescence resonance energy transfer by sensitized emission. Journal of Biophysics. 86:2517-2519.
97. Walker,N. 2001. Real-time and quantitative PCR:Applications to mechanism-based toxicology. Journal of Biochemical and Molecular Toxicology. 15:121-127.
98. Weiss, J., Albermann, N. 2003. Quantification of mRNA levels with reverse transcriptionpolymerase chain reaction. Biochemical and Biophysical Research Communications. 311:561-562.
99. Welle, S., Thornton, C. 1997. Insulin-like growth factor-1, actin, and myosin heavy chain messenger RNAs in skeletal muscle after an injection of growth hormone in subjects over 60 years old. Journal of Endocrinology. 155:93-97.
100. Whitcombe, D., Theaker, J., Guy, S.P., Brown, T., Little, S. 1999. Detection of PCR products using self-probing amplicons and fluorescence. Nature Biotechnology. 17:804-807.
101. Yaron, A., Carmel, A., Katchalski-Katzir, E. 1979. Intramolecularly quenched fluorogenic substrates for hydrolytic enzymes. Analytical Biochemistry. 95:228-235.
102. Yasuike, M.,Kondo, H., Hirono, I.,Aoki, T. 2006. Difference in Japanese flounder, Paralichthys olivaceus gene expression profile following hirame rhabdovirus (HIRRV) G and N protein DNA vaccination. Fish and Shellfish Immunology. 23:531-541.