Martin et al. BMC Genomics 2010, 11:418 http://www.biomedcentral.com/1471-2164/11/418 Page 11 of 20 Table 4 Genes responding differently to infection between fed and starved fish (Continued) spl_sts_17H08_sti_sal_std_5p_11C ova_opk_10D15_osl_sgp_std_5p_11C int_oss_T6A03_osl_sal_std_5p_11C AJ425625 -3.60 CK891273 -5.23 CK884084 -9.32 -1.07 -1.14 -1.27 -3.37 -4.60 -7.36 (P63326) 40S ribosomal protein S10 (Q18268) Phosphodiesterase delta-like protein rRNA promoter binding protein List of mRNAs found to respond to the bacterial infection in a differential manner depending on prior feeding regime. The genes were differentially expressed with P < 0.001 following correction for multiple tests. Only those with a two fold difference in response are shown. 1Indicates the unique identifier for the microarray clone on the microarray, 2Accession number of the sequence deposited to GenBank, when “No Acc” the sequence can be obtained from the TRAITS web page as described in materials. 3Fold change in gene expression between diseased fed and uninfected fed (numbers in italics indicate they are non significant at P < 0.001). 4Fold change in gene expression between diseased starved and uninfected starved (numbers in italics indicate they are non significant at P < 0.001). 5The fold difference in the response to the disease challenge as result of the prior feeding regime. 6Identity of the cDNAs following BlastX or BlastN. Full list shown in Additional file 2 Table S3. sexual maturation status [37] can alter the profile of the response and are impacted by husbandry, developmental and environmental parameters. Our results showed that both starvation and infection lead to large transcriptional responses. We used 12 microarray slides per experimental group which allowed robust statistical analysis to be performed [38]. All data presented was highly significant at P < 0.001 following correction for multiple tests. Additionally we only con- sidered genes that had a greater than 2 fold difference in expression to help interpret the results. Following starvation, GO analysis showed a number of biological processes to be significantly altered. On examination, genes encoding proteins involved in protein and amino acid metabolism, fatty acid and steroid metabolism, immune function and general energy metabolism were both increased and decreased, whereas genes relating to blood and ion transport, lipid metabolism and energy metabolism were down regulated following starvation. The liver is a tissue with very high and variable rates of protein synthesis and degradation [39,40]. During starvation the liver receives reduced levels of free amino acids from digestion, and a multitude of hormonal sig- nals mainly from growth hormone and insulin like growth factor [41] which when reduced result in decreased protein synthesis rates. The decrease in pro- tein synthesis rates begins with reduced transcription as seen by the reduction in transcriptional machinery including ribosomal RNA binding proteins and tran- scription initiation factors. In mammals [19,20] and fish [30] protein synthesis is depressed following reduction in protein intake which appears to be a conserved response. Although both synthesis and degradation are decreased during starvation, the balance between synth- esis and degradation shifts towards greater relative degradation [25,42,43], and in turn the reduced protein synthesis levels are reflected in the lower quantities of serum proteins synthesised and secreted [44]. Protein degradation, similar to protein synthesis is a tightly con- trolled process [45], with two key pathways of protein degradation down regulated in the starved fish, namely genes relating to the ubiquitin proteasome pathway of degradation [46] and lysosomal pathway enzymes including cathepsin D. Although the ubiquitin protea- some pathway in mammals is most often viewed as important in muscle tissue [47] clearly the general decreased transcription of genes in liver in the present study show it is an important pathway in liver tissue in fish. A gene encoding the calcium dependant cysteine protease, calpain-1 was found increased in the starved fish, which demonstrates proteolytic pathways are inde- pendently regulated with each pathway targeting differ- ent proteins for destruction. Both protein synthesis and degradation are energy demanding processes and it is highly likely reduced pro- tein turnover acts as an energy conserving mechanism. Following infection there was a rise in genes relating to protein turnover, with those genes relating to both pro- tein synthesis and degradation being up regulated in both the AFL and ASL groups. This would lead to increased demand for ATP production and also in the case of starved animals an increased supply of free amino acids as substrates for protein synthesis. It would be expected that this would have a greater energetic impact on the starved animals which already have reduced energy reserves. Catabolism of amino acids was found increased in starved fish which could suggest further oxidation of amino acids leading to gluconeo- genesis and subsequent oxidation [48]. In the diseased fish there was a marked decrease in genes related to amino acid catabolism which could be explained by amino acids being used for increased protein synthesis, however amino acid modification is increased by amino acid transferases and amino acid methylases which may be involved in amino acid biosynthesis. Control of amino acid biosynthesis and oxidation can be dramati- cally altered by food deprivation [49] and infection [50] in mammals, with redistribution of amino acids, particu- larly those required for synthesis of inflammatory response proteins (such as APR proteins) which have a different amino acid composition to proteins synthesized during normal growth and metabolism. During normal growth the liver is a major producer of plasma proteins including serum albumin [51], apolipo- proteins [52] and other blood associated proteins which represent a considerable part of the transcription and