Aquaculture-Related Applications of DNA Microarray Technology

Molecular Research in Aquaculture

Volumn , Issue , 2009, Pages 63-101

  Rise, Matthew L ^a   Liu, Zhanjiang ^b   Douglas, Susan E ^c   Brown, Laura L ^d   Nash, John H E ^e   McFall Ngai, Margaret J ^f  

^a MEMORIAL UNIVERSITY OF NEWFOUNDLAND   (Canada)

^b AUBURN UNIVERSITY   (United States)

^c NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^d PACIFIC BIOLOGICAL STATION   (Canada)

^e PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^f UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Aquaculture related applications of DNA microarray technology; Aquaculture relevant microarray research on zebrafish; Bastard halibut, Japanese flounder (Paralichthys olivaceus); Beneficial bacteria in health; DNA microarrays tools for aquaculture related research; Microarray research on catfish; Microarray technology in squid vibrio symbiosis; Microarray based research for current aquaculture industry concerns; Salmonid DNA microarrays and salmonid immune responses; Salmonid nutrigenomics

Indexed keywords

EID: 84889282778     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780813807379.ch4     Document Type: Chapter

References (125)

1. Bakke-McKellep, A.M., Koppang, E.O., Gunnes, G., Sanden, M., Hemre, G.I., Landsverk, T., Krogdahl, A. 2007. Histological, digestive, metabolic, hormonal and some immune factor responses in Atlantic salmon, Salmo salar L., fed genetically modified soybeans. Journal of Fish Diseases. 30:65-79.
2. Bonnet, E., Fostier, A., Bobe, J. 2007. Microarray-based analysis of fish egg quality after natural or controlled ovulation. BMC Genomics. 8:55.
3. Broderick, N.A., Raffa, K.F., Goodman, R.M., Handelsman, J. 2004. Census of the bacterial community of the gypsy moth larval midgut by using culturing and culture-independent methods. Applied and Environmental Microbiology. 70:293-300.
4. Byon, J.Y., Ohira, T., Hirono, I., Aoki, T. 2005. Use of a cDNA microarray to study immunity against viral hemorrhagic septicemia (VHS) in Japanese flounder (Paralichthys olivaceus) following DNA vaccination. Fish and Shellfish Immunology. 18:135-147.
5. Byon, J.Y., Ohira, T., Hirono, I., Aoki, T. 2006. Comparative immune responses in Japanese flounder, Paralichthys olivaceus after vaccination with viral hemorrhagic septicemia virus (VHSV) recombinant glycoprotein and DNA vaccine using a microarray analysis. Vaccine. 24:921-930.
6. Cahu, C.L., Zambonin-Infante, J.L. 2001. Substitution of live food by formulated diets marine fish larvae. Aquaculture. 200:161-180.
7. Cao, D., Kocabas, A., Ju, Z., Karsi, A., Li, P., Patterson, A., Liu, Z. 2001. Transcriptome of channel catfish (Ictalurus punctatus): Initial analysis of genes and expression profiles of the head kidney. Animal Genetics. 32(4:169-188.
8. Carrillo, C.D., Taboada, E., Nash, J.H.E., Lanthier, P., Kelly, J., Lau, P.C., Verhulp, R., Mykytczuk, O., Sy, J., Findlay, W.A., Amoako, K., Gomis, S., Willson, P., Austin, J.W., Potter, A., Babiuk, L., Allan, B., Szymanski, C.M. 2004. Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. Journal of Biological Chemistry. 279:20327-20338.
9. Cheesman, S.E., Guillemin, K. 2007. We know you are in there: Conversing with the indigenous gut microbiota. Research in Microbiology. 158:2-9.
10. Chen, L.M., Wang, F., Song, W., Hew, C.L. 2006. Temporal and differential gene expression of Singapore grouper iridovirus. Journal of General Virology. 87:2907-2915.
11. Chen, Y.A., McKillen, D.J., Wu, S., Jenny, M.J., Chapman, R., Gross, P.S., Warr, G.W., Almeida, J.S. 2004. Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. BMC Bioinformatics. 5:191.
12. Chun, C.K., Scheetz, T.E., Bonaldo, M.F., Brown, B., Clemens, A., Crookes-Goodson, W.J.,Crouch, K., Demartini, T., Eyestone, M., Goodson, M.S., Janssens, B., Kimbell, J.L., Koropatnick, T.A., Kucaba, T., Smith, C., Stewart, J.J., Tong, D., Troll, J.V., Webster, S., Winhall-Rice, J., Yap, C., Casavant, T.L., McFall-Ngai, M.J., Soares, M.B. 2006. An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeri. BMC Genomics. 7:154-163.
13. Cossins, A.R., Crawford, D.L. 2005. Fish as models for environmental genomics. Nature Reviews Genetics. 6:324-340.
14. Cox, C.R., Gilmore, M.S. 2007. Native microbial colonization of Drosophila melanogaster and its use as a model of Enterococcus faecalis pathogenesis. Infection and Immunity. 75:1565-1576.
15. Cruden, D.L., Markovetz, A.J. 1987. Microbial ecology of the cockroach gut. Annual Reviews of Microbiology. 41:617-643.
16. de la Vega, E., Hall, M.R., Wilson, K.J., Reverter, A., Woods, R.G., Degnan, B.M. 2007. Stressinduced gene expression profiling in the black tiger shrimp Penaeus monodon. Physiological Genomics. 31:126-138.
17. Denslow, N.D., Garcia-Reyero, N., Barber, D.S. 2007. Fish 'n' chips: The use of microarrays for aquatic toxicology. Molecular BioSystems. 3:172-177.
18. Dethlefsen, L., Eckburg, P.B., Bik, E.M., Relman, D.A. 2006. Assembly of the human intestinal microbiota. Trends in Ecology and Evolution. 21:517-523.
19. Dethlefsen, L., McFall-Ngai, M., Relman, D.A. 2007. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 449:811-818.
20. Douglas, A.E., Raven, J.A. 2003. Genomes at the interface between bacteria and organelles. Philosophical Transactions of the Royal Society of London B: Biological Science. 358:5-17.
21. Douglas, S.E. 2006. Microarray studies of gene expression in fish. OMICS. 10:474-489.
22. Douglas, S.E., Knickle, L.C., Kimball, J., Reith, M.E. 2007. Comprehensive EST analysis of Atlantic halibut (Hippoglossus hippoglossus), a commercially relevant aquaculture species. BMC Genomics. 8:144-155.
23. Douglas, S.E., Knickle, L.C., Williams, J., Flight, R.M., Reith, M.E. 2008. A first generation Atlantic halibut Hippoglossus hippoglossus (L.) microarray: Application to developmental studies. Journal of Fish Biology. 72:2391-2406.
24. Eckburg, P.B., Bik, E.M., Bernstein, C.N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S.R., Nelson, K.E., Relman, D.A. 2005. Diversity of the human intestinal microbial flora. Science. 308:1635-1638.
25. Eriksson, S., Lucchini, S., Thompson, A., Rhen, M., Hinton, J.C.D. 2003. Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica. Molecular Microbiology. 47:103-118.
26. Ewart, K.V., Belanger, J.C., Williams, J., Karakach, T., Penny, S., Tsoi, S.C.M., Richards, R.C., Douglas, S.E. 2005. Identification of genes differentially expressed in Atlantic salmon (Salmo salar) in response to infection by Aeromonas salmonicida using cDNA microarray technology. Developmental and Comparative Immunology. 29:333-347.
27. Ewart, K.V., Williams, J., Richards, R.C., Gallant, J.W., Melville, K., Douglas, S.E. 2008. The early response of Atlantic salmon (Salmo salar) macrophages exposed in vitro to Aeromonas salmonicida cultured in broth and in fish. Developmental and Comparative Immunology. 32:380-390.
28. Finne, E.F., Cooper, G.A., Koop, B.F., Hylland, K., Tollefsen, K.E. 2007. Toxicogenomic responses in rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to model chemicals and a synthetic mixture. Aquatic Toxicology. 81:293-303.
29. Fraune, I., Bosch, T.C. 2007. Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra. Proceedings of the National Academy of Sciences of the United States of America. 104:13146-13151.
30. Gerwick, L., Corley-Smith, G., Bayne, C.J. 2007. Gene transcript changes in individual rainbow trout livers following an inflammatory stimulus. Fish and Shellfish Immunology. 22:157-171.
31. Gonzalez, S.F., Krug,M.J., Nielsen, M.E., Santos, Y., Call, D.R. 2004. Simultaneous detection of marine fish pathogens by using multiplex PCR and a DNA microarray. Journal of Clinical Microbiology. 42:1414-1419.
32. Gracey, A.Y., Fraser, E.J., Li, W., Fang, Y., Taylor, R.R., Rogers, J., Brass, A., Cossins, A.R. 2004. Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proceedings of the National Academy of Sciences of the United States of America. 101:16970-16975.
33. Grozdanov, L., Hentschel, U. 2007. An environmental genomics perspective on the diversity and function of marine sponge-associated microbiota. Current Opinion in Microbiology. 10:215-220.
34. Gunnarsson, L., Kristiansson, E., Förlin, L., Nerman, O., Larsson, D.G.J. 2007. Sensitive and robust gene expression changes in fish exposed to estrogen-A microarray approach. BMC Genomics. 8:149.
35. Hamre, K., Moren, M., Solbakken, J., Opstad, I., Pittman, K. 2005. The impact of nutrition on metamorphosis in Atlantic halibut (Hippoglossus hippoglossus L.). Aquaculture. 250:555-565.
36. Harden, M.V., Newton, L.A., Lloyd, R.C., Whitlock, K.E. 2006. Olfactory imprinting is correlated with changes in gene expression in the olfactory epithelia of the zebrafish. Journal of Neurobiology. 66:1452-1466.
37. Haygood, M.G. 1993. Light organ symbioses in fishes. Critical Reviews in Microbiology. 19:191-216.
38. Jenny, M.J., Chapman, R.W., Mancia, A., Chen, Y.A., McKillen, D.J., Trent, H., Lang, P., Escoubas, J.M., Bachere, E., Boulo, V., Liu, Z.J., Gross, P.S., Cunningham, C., Cupit, P.M., Tanguy, A., Guo, X., Moraga, D., Boutet, I., Huvet, A., De Guise, S., Almeida, J.S., Warr, G.W. 2007. A cDNA microarray for Crassostrea virginica and C. gigas.Marine Biotechnology (New York). 9:577-591.
39. Johansen, K.A., Sealey, W.M., Overturf, K. 2006. The effects of chronic immune stimulation on muscle growth in rainbow trout. Comparative Biochemistry and Physiology, Part B. 144:520-531.
40. Jordal, A.E., Torstensen, B.E., Tsoi, S., Tocher, D.R., Lall, S.P., Douglas, S.E. 2005. Dietary rapeseed oil affects the expression of genes involved in hepatic lipid metabolism in Atlantic salmon (Salmo salar L.). Journal of Nutrition. 135:2355-2361.
41. Jørgensen, S.M., Afanasyev, S., Krasnov, A. 2008. Gene expression analyses in Atlantic salmon challenged with infectious salmon anemia virus reveal differences between individuals with early, intermediate and late mortality. BMC Genomics. 9:179.
42. Ju, Z., Dunham, R.A., Liu, Z. 2002. Differential gene expression in the brain of channel catfish (Ictalurus punctatus) in response to cold acclimation. Molecular Genetics and Genomics. 268:87-95.
43. Ju, Z., Karsi, A., Kocabas, A., Patterson, A., Li, P., Cao, D., Dunham, R., Liu, Z. 2000. Transcriptome analysis of channel catfish (Ictalurus punctatus): Genes and expression profile from the brain. Gene. 261:373-382.
44. Ju, Z., Wells, M.C., Heater, S.J., Walter, R.B. 2007. Multiple tissue gene expression analyses in Japanese medaka (Oryzias latipes) exposed to hypoxia. Comparative Biochemistry and Physiology, Part C. 145:134-144.
45. Karsi, A., Cao, D., Li, P., Patterson, A., Kocabas, A., Feng, J., Ju, Z., Mickett, K.D., Liu, Z. 2002. Transcriptome analysis of channel catfish (Ictalurus punctatus): Initial analysis of gene expression and microsatellite-containing cDNAs in the skin. Gene. 285:157-168.
46. Kirchner, S.,McDaniel, N.K., Sugiura, S.H., Soteropoulos, P., Tian, B., Fletcher, J.W., Ferraris, R.P. 2007. Salmonid microarrays identify intestinal genes that reliably monitor P deficiency in rainbow trout aquaculture. Animal Genetics. 38:319-331.
47. Kocabas, A.M., Li, P., Cao, D., Karsi, A., He, C., Patterson, A., Ju, Z., Dunham, R.A., Liu, Z. 2002. Expression profile of the channel catfish spleen: Analysis of genes involved in immune functions. Marine Biotechnology. 4:526-536.
48. Koskinen, H., Krasnov, A., Rexroad, C., Gorodilov, Y., Afanasyev, S.,Mölsä, H. 2004a. The 14-3-3 proteins in the teleost fish rainbow trout (Oncorhynchus mykiss). Journal of Experimental Biology. 207:3361-3368.
49. Koskinen, H., Pehkonen, P., Vehniäinen, E.,Krasnov, A., Rexroad, C., Afanasyev, S.,Mölsä, H., Oikari, A. 2004b. Response of rainbow trout transcriptome to model chemical contaminants. Biochemical and Biophysical Research Communications. 320:745-753.
50. Krasnov, A., Koskinen, H., Pehkonen, P., Rexroad, C.E., Afanasyev, S.,Mölsä, H. 2005a. Gene expression in the brain and kidney of rainbow trout in response to handling stress. BMC Genomics. 6:3.
51. Krasnov, A., Koskinen, H., Rexroad, C., Afanasyev, S.,Mölsä, H., Oikari, A. 2005b. Transcriptome responses to carbon tetrachloride and pyrene in the kidney and liver of juvenile rainbow trout (Oncorhynchus mykiss). Aquatic Toxicology. 74:70-81.
52. Kurobe, T., Yasuike, M., Kimura, T., Hirono, I., Aoki, T. 2005. Expression profiling of immunerelated genes from Japanese flounder Paralichthys olivaceus kidney cells usingcDNAmicroarrays. Developmental and Comparative Immunology. 29:515-523.
53. Lam, S.H.,Wu, Y.L., Vega, V.B.,Miller, L.D., Spitsbergen, J., Tong, Y., Zhan, H., Govindarajan, K.R., Lee, S., Mathavan, S., Murthy, K.R.K., Buhler, D.R., Liu, E.T., Gong, Z. 2006. Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression. Nature Biotechnology. 24:73-75.
54. Lan, Y.,Xu, X., Yang, F.,Zhang,X. 2006. Transcriptional profile of shrimp white spot syndrome virus (WSSV) genes with DNA microarray. Archives of Virology. 151:1723-1733.
55. Lewis, L.M., Lall, S.P. 2006. Development of the axial skeleton and skeletal abnormalities of Atlantic halibut (Hippoglossus hippoglossus) from first feeding through metamorphosis. Aquaculture. 257:124-135.
56. Ley, R.E., Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Bircher, J.S., Schlegel, M.L., Tucker, T.A., Schrenzel, M.D., Knight, R., Gordon, J.I. 2008. Evolution of mammals and their gut microbes. Science. 320:1647-1651.
57. Li, P., Peatman, E., Wang, S., Feng, J., He, C., Baoprasertkul, P., Xu, P., Kucuktas, H., Nandi, S., Somridhivej, B., Serapion, J., Simmons, M., Turan, C., Liu, L., Muir, W., Dunham, R., Brady, Y., Grizzle, J., Liu, Z. 2007. Towards the ictalurid catfish transcriptome: Generation and analysis of 31,215 catfish ESTs. BMC Genomics. 8:177.
58. Li, R.W., Waldbieser, G.C. 2006. Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus. BMC Genomics. 7:134.
59. Lua, D.T., Yasuike, M., Hirono, I., Aoki, T. 2005. Transcription program of red sea bream iridovirus as revealed by DNA microarrays. Journal of Virology. 79:15151-15164.
60. MacKenzie, S., Iliev, D., Liarte, C., Koskinen, H., Planas, J.V., Goetz, F.W., Mölsä, H., Krasnov, A., Tort, L. 2006a. Transcriptional analysis of LPS-stimulated activation of trout (Oncorhynchus mykiss) monocyte/macrophage cells in primary culture treated with cortisol. Molecular Immunology. 43:1340-1348.
61. MacKenzie, S.,Montserrat, N., Mas, M.,Acerete, L., Tort, L., Krasnov, A., Goetz, F.W., Planas, J.V. 2006b. Bacterial lipopolysaccharide induces apoptosis in the trout ovary. Reproductive Biology and Endocrinology. 4:46.
62. Malek, R.L., Sajadi, H., Abraham, J., Grundy, M.A., Gerhard, G.S. 2004. The effects of temperature reduction on gene expression and oxidative stress in skeletal muscle from adult zebrafish. Comparative Biochemistry and Physiology, Part C: Comparative Toxicology Pharmacology. 138:363-373.
63. Manganelli, R., Voskuil, M.I., Schoolnik, G.K., Smith, I. 2001. The Mycobacterium tuberculosis ECF sigma factor σE: Role in global gene expression and survival inmacrophages. Molecular Microbiology. 41:423-437.
64. Marks, H., Vorst, O., van Houwelingen, A.M.M.L., van Hulten, M.C.W., Vlak, J.M. 2005. Gene-expression profiling of White spot syndrome virus in vivo. Journal of General Virology. 86:2081-2100.
65. Martin, S.A.M., Blaney, S.C., Houlihan, D.F., Secombes, C.J. 2006. Transcriptome response following administration of a live bacterial vaccine in Atlantic salmon (Salmo salar). Molecular Immunology. 43:1900-1911.
66. Martin, S.A.M., Zou, J., Houlihan, D.F., Secombes, C.J. 2007. Directional responses following recombinant cytokine stimulation of rainbow trout (Oncorhynchus mykiss) RTS-11 macrophage cells as revealed by transcriptome profiling. BMC Genomics. 8:150.
67. Matsuyama, T., Fujiwara, A., Nakayasu, C., Kamaishi, T., Oseko, N., Hirono, I., Aoki, T. 2007. 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.
68. McFall-Ngai, M.J. 2005. The interface of microbiology and immunology:Acomparative analysis of the animal kingdom. In: McFall-Ngai,M.J., Henderson, B.,Ruby,E.G. (eds), The Influence of Cooperative Bacteria on Animal Host Biology. Cambridge University Press, Cambridge, pp. 35-56.
69. Meijer, A.H., Verbeek, F.J., Salas-Vidal, E., Corredor-Adámez,M., Bussman, J., Van Der Sar, A.M., Otto, G.W., Geisler, R., Spaink, H.P. 2005. Transcriptome profiling of adult zebrafish at the late stage of chronic tuberculosis due to Mycobacterium marinum infection. Molecular Immunology. 42:1185-1203.
70. Mori, T., Hiraka, I., Kurata, Y., Kawachi, H., Mano, N., Devlin, R.H., Nagoya, H., Araki, K. 2007. Changes in hepatic gene expression related to innate immunity, growth and iron metabolism in GH-transgenic amago salmon (Oncorhynchus masou) by cDNA subtraction and microarray analysis, and serum lysozyme activity. General and Comparative Endocrinology. 151:42-54.
71. Morrison, R.N., Cooper, G.A., Koop, B.F., Rise, M.L., Bridle, A.R., Adams, M.B., Nowak, B.F. 2006. Transcriptome profiling of the gills of amoebic gill disease (AGD)-affected Atlantic salmon (Salmo salar L.): A role for the tumor suppressor protein p52 in AGD-pathogenesis? Physiological Genomics. 26:15-34.
72. Naess, T., Lie, O. 1998. A sensitive period during first feeding for the determination of pigmentation pattern in Atlantic halibut, Hippoglossus hippoglossus L., juveniles: The role of diet. Aquaculture Research. 29:925-934.
73. Nash, J.H.E., Findlay, W.A., Luebbert, C.C., Mykytczuk, O.L., Foote, S.J., Taboada, E.N., Carrillo, C.D., Boyd, J.M., Colquhoun, D.J., Reith, M.E., Brown, L.L. 2006. Comparative genomics profiling of clinical isolates of Aeromonas salmonicida using DNA microarrays. BMC Genomics. 7:43.
74. Nuwaysir, E.F., Huang,W., Albert, T.J., Singh, J.,Nuwaysir, K., Pitas, A., Richmond, T., Gorski, T., Berg, J.P., Ballin, J., McCormick, M., Norton, J., Pollock, T., Sumwalt, T., Butcher, L., Porter, D., Molla, M., Hall, C., Blattner, F., Sussman, M.R., Wallace, R.L., Cerrina, F., Green, R.D. 2002. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Research. 12:1749-1755.
75. Nyholm, S.V., McFall-Ngai,M.J. 2004. The winnowing: Establishing the squid-vibrio symbiosis. Nature Reviews Microbiology. 2:632-642.
76. Olohan, L.A., Li, W., Wulff, T., Jarmer, H., Gracey, A.Y., Cossins, A.R. 2008. Detection of anoxia-responsive genes in cultured cells of the rainbow trout Oncorhynchus mykiss (Walbaum), using an optimized, genome-wide oligoarray. Journal of Fish Biology. 72:2170-2186.
77. Ong, C., Ooi, C.H., Wang, D., Chong, H., Ng, K.C., Rodrigues, F., Lee, M.A., Tan, P. 2004. Patterns of large-scale genomic variation in virulent and avirulent Burkholderia species. Genome Research. 14:2295-2307.
78. Palmer, C., Bik, E.M., Digiulio, D.B., Relman, D.A., Brown, P.O. 2007. Development of the human infant intestinal microbiota. PLoS Biology. 5:e177.
79. Paster, B.J., Olsen, I., Aas, J.A., Dewhirst, F.E. 2006. The breadth of bacterial diversity in the human periodontal pocket and other oral sites. Periodontology 2000. 42:80-87.
80. Peatman, E., Baoprasertkul, P., Terhune, J., Xu, P., Nandi, S., Kucuktas, H., Li, P., Wang, S., Somridhivej, B., Dunham, R., Liu, Z. 2007. Expression analysis of the acute phase response in channel catfish (Ictalurus punctatus) after infection with a Gram-negative bacterium. Developmental and Comparative Immunology. 31:1183-1196.
81. Peatman, E., Terhune, J., Baoprasertkul, P., Xu, P., Nandi, S., Wang, S., Somridhivej, B., Kucuktas, H., Li, P., Dunham, R., Liu, Z. 2008. Microarray analysis of gene expression in the blue catfish liver reveals early activation of the MHC class I pathway after infection with Edwardsiella ictaluri. Molecular Immunology. 45:553-566.
82. Peatman, E.J., Wei, X., Feng, J., Liu, L., Kucuktas, H., Li, P., He, C., Rouse, D., Wallace, R., Dunham, R., Liu, Z. 2004. Development of expressed sequence tags from Eastern oyster (Crassostrea virginica): Lessons learned from previous efforts. Proceedings in Marine Biotechnology. 6:S491-S496.
83. Purcell, M.K., Nichols, K.M., Winton, J.R., Kurath, G., Thorgaard, G.H.,Wheeler, P., Hansen, J.D., Herwig, R.P., Park, L.K. 2006. Comprehensive gene expression profiling following DNA vaccination of rainbow trout against infectious hematopoietic necrosis virus.Molecular Immunology. 43:2089-2106.
84. Rawls, J.F., Samuel, B.S., Gordon, J.I. 2004. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proceedings of the National Academy of Sciences of the United States of America. 101:4596-4601.
85. Rise, M.L., Douglas, S.E., Sakhrani, D., Williams, J., Ewart, K.V., Rise, M., Davidson, W.S., Koop, B.F., Devlin, R.H. 2006. Multiple microarray platforms utilized for hepatic gene expression profiling of growth hormone transgenic coho salmon with and without ration restriction. Journal of Molecular Endocrinology. 37:259-282.
86. Rise,M.L., Hall, J.,Rise, M., Hori, T., Gamperl, A.K., Kimball, J., Hubert, S., Bowman, S., Johnson, S.C. 2008. Functional genomic analysis of the response of Atlantic cod (Gadus morhua) spleen to the viral mimic polyriboinosinic polyribocytidylic acid (pIC). Developmental and Comparative Immunology. 32:916-931.
87. Rise, M.L., Jones, S.R.M., Brown, G.D., von Schalburg, K.R., Davidson, W.S., Koop, B.F. 2004a. Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection. Physiological Genomics. 20:21-35.
88. Rise,M.L., von Schalburg, K.R., Brown, G.D.,Mawer,M.A., Devlin, R.H., Kuipers, N., Busby, M., Beetz-Sargent, M., Alberto, R., Gibbs, A.R., Hunt, P., Shukin, R., Zeznik, J.A., Nelson, C., Jones, S.R.M., Smailus,D.E., Jones, S.J.M., Schein, J.E.,Marra,M.A., Butterfield, Y.S.N., Stott, J.M., Ng, S.H.S., Davidson, W.S., Koop, B.F. 2004b. Development and application of a salmonid EST database and cDNA microarray: Data mining and interspecific hybridization characteristics. Genome Research. 14:478-490.
89. Rise, M.L., von Schalburg, K.R., Cooper, G.A., Koop, B.F. 2007. Salmonid DNA microarrays and other tools for functional genomics research. In: Liu, Z. (ed.), Aquaculture Genome Technologies. Blackwell Publishing, Ames, IA, pp. 369-411.
90. Robalino, J., Almeida, J.S., McKillen, D., Colglazier, J., Trent, H.F., Chen, Y.A., Peck,M.E.T., Browdy, C.L., Chapman, R.W., Warr, G.W., Gross, P.S. 2007. Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: Tissue-specific expression profiles and transcriptomic responses to immune challenge. Physiological Genomics. 29:44-56.
91. Roberge, C., Páez,D.J., Rossignol, O., Guderley,H., Dodson, J., Bernatchez, L. 2007. Genomewide survey of the gene expression response to saprolegniasis in Atlantic salmon. Molecular Immunology. 44:1374-1383.
92. Rozen, S., Skaletsky, H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology. 132:365-386.
93. Ruby,E.G., Urbanowski, M.,Campbell, J., Dunn, A., Faini, M., Gunsalus, R., Lostroh, P., Lupp, C., McCann, J., Millikan, D., Schaefer, A., Stabb, E., Stevens, A., Visick, K., Whistler, C., Greenberg, E.P. 2005. Complete genome sequence of Vibrio fischeri: A symbiotic bacterium with pathogenic congeners. Proceedings of the National Academy of Sciences of the United States of America. 102:3004-3009.
94. Saele, O., Solbakken, J., Watanabe, K., Hamre, K., Power, D., Pittman, K. 2004. Staging of Atlantic halibut (Hippoglossus hippoglossus L.) from first feeding through metamorphosis, including cranial ossification independent of eye migration. Aquaculture. 239:445-465.
95. Saele, O., Solbakken, J.S., Watanabe, K., Hamre, K., Pittman, K. 2003. The effect of diet on ossification and eye migration in Atlantic halibut larvae (Hippoglossus hippoglossus L.). Aquaculture. 220:683-696.
96. Salem, M., Kenney, P.B., Rexroad, C.E., Yao, J. 2006. Microarray gene expression analysis in atrophying rainbow trout muscle: A unique nonmammalian muscle degradation model. Physiological Genomics. 28:33-45.
97. Salem, M., Kenney, P.B., Rexroad, C.E., Yao, J. 2008. Development of a 37K high-density oligonucleotide microarray: A new tool for functional genome research in rainbow trout. Journal of Fish Biology. 72:2187-2206.
98. Salem, M., Silverstein, J., Rexroad, C.E., Jianbo, Y. 2007. Effect of starvation on global gene expression and proteolysis in rainbow trout (Oncorhynchus mykiss). BMC Genomics. 8:328.
99. Salyers, A.A., Whitt, D.D. 2001. Bacterial Pathogenesis:AMolecularApproach, 2nd edn. ASM Press, Washington, DC, 560 pp.
100. Santos, E.M., Workman, V.L., Paull, G.C., Filby, A.L., Van Look, K.J.W., Kille, P., Tyler, C.R. 2007. Molecular basis of sex and reproductive status in breeding zebrafish. Physiological Genomics. 30:111-122.
101. Sarropoulou, E., Kotoulas, G., Power, D.M., Geisler, R. 2005. Gene expression profiling of gilthead sea bream during early development and detection of stress-related genes by the application of cDNA microarray technology. Physiological Genomics. 23:182-191.
102. Schmitt-Wagner, D., Friedrich, M.W., Wagner, B., Brune, A. 2003. Phylogenetic diversity, abundance, and axial distribution of bacteria in the intestinal tract of two soil-feeding termites (Cubitermes spp.). Applied Environmental Microbiology. 69:6007-6017.
103. Singh-Gasson, S., Green, R.D., Yue, Y., Nelson, C., Blattner, F., Sussman, M.R., Cerrina, F. 1999. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nature Biotechnology. 17:974-978.
104. Sneddon, L.U., Margareto, J., Cossins, A.R. 2005. The use of transcriptomics to address questions in behaviour: Production of a suppression subtractive hybridization library from dominance hierarchies of rainbow trout. Physiological and Biochemical Zoology. 78:695-705.
105. Stappenbeck, T.S., Hooper, L.V., Gordon, J.I. 2002. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proceedings of the National Academy of Sciences of the United States of America. 99:15451-15455.
106. Taboada, E.N., Acedillo, R.R., Carrillo, C.D., Findlay, W.A., Medeiros,D.T., Mykytczuk, O.L., Roberts, M.J., Valencia, C.A., Farber, J.M., Nash, J. 2004. Large-scale comparative genomics meta-analysis of Campylobacter jejuni isolates reveals low level of genome plasticity. Journal of Clinical Microbiology. 42:4566-4576.
107. Taggart, J.B., Bron, J.E., Martin, S.A.M., Seear, P.J., Høyheim, B., Talbot, R., Carmichael, S.N., Villeneuve, L., Sweeney, G.E., Houlihan, D.F., Secombes, C.J., Tocher, D.R., Teale, A.J. 2008. A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray. Journal of Fish Biology. 72:2071-2094.
108. Talaat, A.M., Hunter, P., Johnston, S.A. 2000. Genome-directed primers for selective labeling of bacterial transcripts for DNA microarray analysis. Nature Biotechnology. 18:679-682.
109. Thi, L.D., Yasuike, M., Hirono, I., Kondo, H., Aoki, T. 2007. Transcriptional profile of red seabream iridovirus in a fish model as revealed by viral DNA microarrays. Virus Genes. 35:449-461.
110. Tilton, S.C., Gerwick, L.G., Hendricks, J.D., Rosato, C.S., Corley-Smith, G., Givan, S.A., Bailey, G.S., Bayne, C.J., Williams, D.E. 2005. Use of a rainbow trout oligonucleotide microarray to determine transcriptional patterns in aflatoxin B1-induced hepatocellular carcinoma compared to adjacent liver. Toxicological Sciences. 88:319-330.
111. Ton, C., Stamatiou, D., Liew, C. 2003. Gene expression profile of zebrafish exposed to hypoxia during development. Physiological Genomics. 13:97-106.
112. van der Meer, D.L.M., van den Thillart, G., Witte, F., de Bakker, M., Besser, J., Richardson, M.K., Spaink, H.P., Leito, J.T.D., Bagowski, C.P. 2005. Gene expression profiling of the long-term adaptive response to hypoxia in the gills of adult zebrafish. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology. 289:R1512-R1519.
113. Visick, K.L., Ruby, E.G. 2006. Vibrio fischeri and its host: It takes two to tango. Current Opinion in Microbiology. 9:632-638.
114. von Schalburg, K.R., Cooper, G.A., Leong, J., Robb, A., Lieph, R., Rise,M.L., Davidson, W.S., Koop, B.F. 2008a. Expansion of the genomics research on Atlantic salmon Salmo salar L. project (GRASP) microarray tools. Journal of Fish Biology. 72:2051-2070.
115. von Schalburg, K.R., Cooper, G.A., Yazawa, R., Davidson, W.S., Koop, B.F. 2008b.Microarray analysis reveals differences in expression of cell surface and extracellular matrix components during development of the trout ovary and testis. Comparative Biochemistry and Physiology, Part D. 3:78-90.
116. von Schalburg, K.R., Rise, M.L., Brown, G.D., Davidson, W.S., Koop, B.F. 2005a. A comprehensive survey of the genes involved in maturation and development of the rainbow trout ovary. Biology of Reproduction. 72:687-699.
117. von Schalburg, K.R., Rise,M.L., Cooper, G.A., Brown, G.D., Gibbs, A.R., Nelson, C.C.,Davidson, W.S., Koop, B.F. 2005b. Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics. 15:126.
118. Vornanen, M., Hassinen, M., Koskinen, H., Krasnov, A. 2005. Steady-state effects of temperature acclimation on the transcriptome of the rainbow trout heart. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology. 289:R1177-R1184.
119. Williams,D.R., Li,W., Hughes, M.A., Gonzalez, S.F., Vernon, C.,Vidal, M.C., Jeney, Z., Jeney, G., Dixon, P., McAndrew, B., Bartfai, R., Orban, L., Trudeau, V., Rogers, J., Matthews, L., Fraser, E.J., Gracey, A.Y., Cossins, A.R. 2008. Genomic resources and microarrays for the common carp Cyprinus carpio L. Journal of Fish Biology. 72:2095-2117.
120. Wilson, A.C., Dunbar, H.E., Davis, G.K., Hunter, W.B., Stern, D.L., Moran, N.A. 2006. A dual-genome microarray for the pea aphid, Acyrthosiphon pisum, and its obligate bacterial symbiont, Buchnera aphidicola. BMC Genomics. 7:50.
121. Wiseman, S., Osachoff, H., Bassett, E., Malhotra, J., Bruno, J., VanAggelen, G., Mommsen, T.P., Vijayan, M.M. 2007. Gene expression pattern in the liver during recovery from an acute stressor in rainbow trout. Comparative Biochemistry and Physiology, Part D: Genomics and Proteomics. 2:234-244.
122. Wynne, J.W., O'Sullivan,M.G., Cook,M.T., Stone, G., Nowak, B.F., Lovell, D.R., Elliott, N.G. 2008. Transcriptome analyses of amoebic gill disease-affected Atlantic salmon (Salmo salar) tissues reveal localized host gene suppression. Marine Biotechnology. 10:388-403.
123. Yang, H., Schmitt-Wagner, D., Stingl, U., Brune, A. 2005. Niche heterogeneity determines bacterial community structure in the termite gut (Reticulitermes santonensis). Environmental Microbiology. 7:916-932.
124. Yasuike, M.,Kondo, H., Hirono, I.,Aoki, T. 2007. 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.
125. Young, N.D., Cooper, G.A., Nowak, B.F.,Koop, B.F.,Morrison, R.N. 2008. Coordinated downregulation of the antigen processing machinery in the gills of amoebic gill disease-affected Atlantic salmon (Salmo salar L.). Molecular Immunology. 45:2581-2597.