Martin et al. BMC Genomics 2010, 11:418 http://www.biomedcentral.com/1471-2164/11/418 their hepatic mRNAs: The role of dietary protein content and tumor necrosis factor in malnourished rats. Metab-Clin Exp 1996, 45(10):1273-1278. 54. Rehulka J, Minarik B: Blood parameters in brook trout Salvelinus fontinalis (Mitchill, 1815), affected by columnaris disease. Aquaculture Research 2007, 38(11):1182-1197. 55. Anstead GM, Chandrasekar B, Zhao WG, Yang J, Perez LE, Melby PC: Malnutrition alters the innate immune response and increases early visceralization following Leishmania donovani infection. Infection and Immunity 2001, 69(8):4709-4718. 56. Raida MK, Buchmann K: Innate immune response in rainbow trout (Oncorhynchus mykiss) against primary and secondary infections with Yersinia ruckeri O1. Developmental and Comparative Immunology 2009, 33(1):35-45. 57. Douglas SE, Gallant JW, Liebscher RS, Dacanay A, Tsoi SCM: Identification and expression analysis of hepcidin-like antimicrobial peptides in bony fish. Developmental and Comparative Immunology 2003, 27(6-7):589-601. 58. Gerwick L, Corley-Smith GE, Nakao M, Watson J, Bayne CJ: Intracranial injections induce local transcription of a gene encoding precerebellin- like protein. Fish Physiology and Biochemistry 2005, 31(4):363-372. 59. Kishimoto T: Interleukin-6: From basic science to medicine - 40 years in immunology. Annual Review of Immunology 2005, 23:1-21. 60. Ren YS, Liao WSL: Transcription factor AP-2 functions as a repressor that contributes to the liver-specific expression of serum amyloid A1 gene. Journal of Biological Chemistry 2001, 276(21):17770-17778. 61. Rasmussen SB, Reinert LS, Paludan SR: Innate recognition of intracellular pathogens: detection and activation of the first line of defense. Apmis 2009, 117(5-6):323-337. 62. Wang T, Secombes CJ: Rainbow trout suppressor of cytokine signalling (SOCS)-1, 2 and 3: Molecular identification, expression and modulation. Molecular Immunology 2008, 45(5):1449-1457. 63. Ling PR, Smith RJ, Kie S, Boyce P, Bistrian BR: Effects of protein malnutrition on IL-6-mediated signaling in the liver and the systemic acute-phase response in rats. American Journal of Physiology-Regulatory Integrative and Comparative Physiology 2004, 287(4):R801-R808. 64. Lin E, Kotani JG, Lowry SF: Nutritional modulation of immunity and the inflammatory response. Nutrition 1998, 14(6):545-550. 65. Jurkovic S, Osredkar J, Marc J: Molecular impact of glutathione peroxidases in antioxidant processes. Biochem Medica 2008, 18(2):162-174. 66. Gourley ME, Kennedy CJ: Energy allocations to xenobiotic transport and biotransformation reactions in rainbow trout (Oncorhynchus mykiss) during energy intake restriction. Comp Biochem Physiol C-Toxicol Pharmacol 2009, 150(2):270-278. 67. Fujita T, Matsushita M, Endo Y: The lectin-complement pathway - its role in innate immunity and evolution. Immunological Reviews 2004, 198:185-202. 68. Harboe M, Mollnes TE: The alternative complement pathway revisited. J Cell Mol Med 2008, 12(4):1074-1084. 69. Boshra H, Gelman AE, Sunyer JO: Structural and functional characterization of complement C4 and C1s-like molecules in teleost fish: Insights into the evolution of classical and alternative pathways. Journal of Immunology 2004, 173(1):349-359. 70. Gerwick L, Corley-Smith G, Bayne CJ: Gene transcript changes in individual rainbow trout livers following an inflammatory stimulus. Fish & Shellfish Immunology 2007, 22(3):157-171. 71. Kjaer MA, Vegusdal A, Berge GM, Galloway TF, Hillestad M, Krogdahl A, Holm H, Ruyter B: Characterisation of lipid transport in Atlantic cod (Gadus morhua) when fasted and fed high or low fat diets. Aquaculture 2009, 288(3-4):325-336. 72. Hihi AK, Michalik L, Wahli W: PPARs: transcriptional effectors of fatty acids and their derivatives. Cellular and Molecular Life Sciences 2002, 59(5):790-798. 73. Leaver MJ, Boukouvala E, Antonopoulou E, Diez A, Favre-Krey L, Ezaz MT, Bautista JM, Tocher DR, Krey G: Three peroxisome proliferator-activated receptor isotypes from each of two species of marine fish. Endocrinology 2005, 146(7):3150-3162. 74. Jorgensen SM, Afanasyev S, Krasnov A: Gene expression analyses in Atlantic salmon challenged with infectious salmon anemia virus reveal differences between individuals with early, intermediate and late mortality. BMC Genomics 2008, 9. Page 20 of 20 75. Olsen RE, Sundell K, Hansen T, Hemre GI, Myklebust R, Mayhew TM, Ringo E: Acute stress alters the intestinal lining of Atlantic salmon, Salmo salar L.: An electron microscopical study. Fish Physiology and Biochemistry 2002, 26(3):211-221. 76. Harris J, Bird DJ: Modulation of the fish immune system by hormones. Veterinary Immunology and Immunopathology 2000, 77(3-4):163-176. 77. Marsden MJ, Devoy A, Vaughan LM, Foster TJ, Secombes CJ: Use of a genetically attenuated strain of Aeromonas salmonicida to vaccinate salmonid fish. Aquac Int 1996, 4(1):55-66. 78. R Development Core Team: R: A language and environment for statistical computing. R foundation for statistical computing. Vienna, Austria 2009. 79. Smyth GK, Michaud J, Scott HS: Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005, 21(9):2067-2075. 80. Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth GK: A comparison of background correction methods for two- colour microarrays. Bioinformatics 2007, 23(20):2700-2707. 81. Smyth GK, Speed T: Normalization of cDNA microarray data. Methods 2003, 31(4):265-273. 82. Smyth GK: Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 2004, 3(1):1-26. 83. Benjamini Y, Hochberg Y: Controlling the False Discovery Rate - a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B-Methodological 1995, 57(1):289-300. 84. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, et al: Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nature Genetics 2001, 29(4):365-371. 85. Zheng Q, Wang XJ: GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Research 2008, 36:W358-W363. 86. Olsvik PA, Lie KK, Jordal AEO, Nilsen TO, Hordvik I: Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon. BMC Molecular Biology 2005, 6. 87. Pfaffl MW: A new mathematical model for relative quantification in real- time RT-PCR. Nucleic Acids Research 2001, 29(9). doi:10.1186/1471-2164-11-418 Cite this article as: Martin et al.: Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar). BMC Genomics 2010 11:418. Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color ﬁgure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit